2CDY - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   MANGANESE SUPEROXIDE DISMUTASE (MN-SOD) FROM DEINOCOCCUS RADIODURANS

Authors :   R. Dennis, E. Micossi, J. Mccarthy, E. Moe, E. Gordon, G. Leonard, S. Mcsweeney

Date :   31 Jan 06 (Deposition) - 13 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Manganese Superoxide Dismutase, Deinococcus Radiodurans, Radiation Resistance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Dennis, E. Micossi, J. Mccarthy, E. Moe, E. Gordon, G. Leonard, S. Mcsweeney
Structure Of The Manganese Superoxide Dismutase From Deinococcus Radiodurans In Two Crystal Forms.
Acta Crystallogr. , Sect. F V. 62 325 2006
PubMed-ID: 16582477 | Reference-DOI: 10.1107/S1744309106008402

Molecule 1 - SUPEROXIDE DISMUTASE [MN]
	Atcc	:	13939
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector	:	GATEWAY PDEST17
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	243230
	Strain	:	R1
	Synonym	:	MNSOD

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:80 , ASP A:172 , HIS A:176 , HOH A:2183	BINDING SITE FOR RESIDUE MN A1211
2	AC2	SOFTWARE	HIS B:26 , HIS B:80 , ASP B:172 , HIS B:176 , HOH B:2100	BINDING SITE FOR RESIDUE MN B1211
3	AC3	SOFTWARE	HIS C:26 , HIS C:80 , ASP C:172 , HIS C:176 , HOH C:2120	BINDING SITE FOR RESIDUE MN C1211
4	AC4	SOFTWARE	HIS D:26 , HIS D:80 , ASP D:172 , HIS D:176 , HOH D:2164	BINDING SITE FOR RESIDUE MN D1211

(no "SS Bond" information available for 2CDY)

Asymmetric Unit

No.	Residues
1	Glu A:15	-	Pro A:16
2	Glu B:15	-	Pro B:16
3	Glu C:15	-	Pro C:16
4	Glu D:15	-	Pro D:16

(no "SAP(SNP)/Variant" information available for 2CDY)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_DEIRA	173-180	4	A:172-179 B:172-179 C:172-179 D:172-179

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_DEIRA	173-180	1	A:172-179 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_DEIRA	173-180	1	- B:172-179 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_DEIRA	173-180	1	- - C:172-179 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_DEIRA	173-180	1	- - - D:172-179

(no "Exon" information available for 2CDY)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:208
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:212
                             1                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209  
           SODM_DEIRA     - -MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains d2cdya1 A:-2-87 automated matches                                                        -----------d2cdya2 A:99-210 automated matches                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdy A  -2 ALAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQ----ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 210
                             ||      8        18        28        38        48        58        68        78        88  |    |98       108       118       128       138       148       158       168       178       188       198       208  
                             ||                                                                                        91   96                                                                                                                  
                            -1|                                                                                                                                                                                                                 
                              1

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:212
                             1                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209  
           SODM_DEIRA     - -MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains d2cdyb1 B:-2-87 automated matches                                                        ----     --d2cdyb2 B:99-210 automated matches                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhhhhhhh--.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....-----....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdy B  -2 ALAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALE--EFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQ-----NQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 210
                             ||      8        18        28        38    |  |48        58        68        78        88  |     98       108       118       128       138       148       158       168       178       188       198       208  
                            -1|                                        43 46                                           91    97                                                                                                                 
                              1

Chain C from PDB  Type:PROTEIN  Length:209
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODM_DEIRA     1 MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains d2cdyc1 C:-1-87 automated matches                                                       -----------d2cdyc2 C:99-210 automated matches                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhhhhhhhhhhhhhhhhh.....--......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdy C  -1 LAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQ--NGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 210
                            ||       9        19        29        39        49        59        69        79        89 |  |   99       109       119       129       139       149       159       169       179       189       199       209 
                           -1|                                                                                        91 94                                                                                                                    
                             1

Chain D from PDB  Type:PROTEIN  Length:207
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODM_DEIRA     1 MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains d2cdyd1 D:-1-87 automated matches                                                       -----------d2cdyd2 D:99-210 automated matches                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdy D  -1 LAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQ----ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 210
                            ||       9        19        29        39        49        59        69        79        89 |    | 99       109       119       129       139       149       159       169       179       189       199       209 
                           -1|                                                                                        91   96                                                                                                                  
                             1

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 2CDY)

(no "Pfam Domain" information available for 2CDY)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SODM_DEIRA | Q9RUV2)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu B:15 - Pro B:16	[ RasMol ]
		Glu C:15 - Pro C:16	[ RasMol ]
		Glu D:15 - Pro D:16	[ RasMol ]

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	2cdy
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	1.15.1.1
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UniProtKB/Swiss-Prot
	SODM_DEIRA \| Q9RUV2	:	1y67 2aw9 2ce4 3kky

1y67	CRYSTAL STRUCTURE OF MANGANESE SUPEROXIDE DISMUTASE FROMDEINOCOCCUS RADIODURANS
2ce4	MANGANESE SUPEROXIDE DISMUTASE (MN-SOD) FROM DEINOCOCCUS RADIODURANS

Description

Compounds

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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