2NYB - JenaLib

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Title :   CRYSTAL STRUCTURE OF E.COLI IRON SUPEROXIDE DISMUTASE Q69E AT 1.1 ANGSTROM RESOLUTION

Authors :   J. C. Porta, A. Vahedi-Faridi, G. E. O. Borgstahl

Date :   20 Nov 06 (Deposition) - 05 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

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

Keywords :   Iron Superoxide Dismutase Q69E, Fesod, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Yikilmaz, J. Porta, L. E. Grove, A. Vahedi-Faridi, Y. Bronshteyn, T. C. Brunold, G. E. Borgstahl, A. F. Miller
How Can A Single Second Sphere Amino Acid Substitution Cause Reduction Midpoint Potential Changes Of Hundreds Of Millivolts?
J. Am. Chem. Soc. V. 129 9927 2007
PubMed-ID: 17628062 | Reference-DOI: 10.1021/JA069224T
(for further references see the PDB file header)

Molecule 1 - SUPEROXIDE DISMUTASE [FE]
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SODB, B1656, JW1648
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	IRON SUPEROXIDE DISMUTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	FE2	4	Ligand/Ion	FE (II) ION
2	O	4	Ligand/Ion	OXYGEN ATOM

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	FE2	2	Ligand/Ion	FE (II) ION
2	O	-1	Ligand/Ion	OXYGEN ATOM

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	FE2	2	Ligand/Ion	FE (II) ION
2	O	-1	Ligand/Ion	OXYGEN ATOM

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:73 , ASP A:156 , HIS A:160 , O A:194	BINDING SITE FOR RESIDUE FE2 A 193
2	AC2	SOFTWARE	HIS B:26 , HIS B:73 , ASP B:156 , HIS B:160 , O B:194	BINDING SITE FOR RESIDUE FE2 B 193
3	AC3	SOFTWARE	HIS C:26 , HIS C:73 , ASP C:156 , HIS C:160 , O C:194	BINDING SITE FOR RESIDUE FE2 C 193
4	AC4	SOFTWARE	HIS D:26 , HIS D:73 , ASP D:156 , HIS D:160 , O D:194	BINDING SITE FOR RESIDUE FE2 D 193
5	AC5	SOFTWARE	GLU A:69 , HIS A:73 , TRP A:122 , ASP A:156 , TRP A:158 , HIS A:160 , FE2 A:193	BINDING SITE FOR RESIDUE O A 194
6	AC6	SOFTWARE	GLU B:69 , HIS B:73 , TRP B:122 , ASP B:156 , TRP B:158 , HIS B:160 , FE2 B:193	BINDING SITE FOR RESIDUE O B 194
7	AC7	SOFTWARE	GLU C:69 , HIS C:73 , TRP C:122 , ASP C:156 , TRP C:158 , HIS C:160 , FE2 C:193	BINDING SITE FOR RESIDUE O C 194
8	AC8	SOFTWARE	GLU D:69 , HIS D:73 , TRP D:122 , ASP D:156 , TRP D:158 , HIS D:160 , FE2 D:193	BINDING SITE FOR RESIDUE O D 194

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

Asymmetric Unit

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

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

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.	SODF_ECOLI	157-164	4	A:156-163 B:156-163 C:156-163 D:156-163

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_ECOLI	157-164	2	A:156-163 B:156-163 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_ECOLI	157-164	2	- - C:156-163 D:156-163

(no "Exon" information available for 2NYB)

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:192
 aligned with SODF_ECOLI | P0AGD3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_ECOLI     2 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 193
               SCOP domains d2nyba1 A:1-82 Fe superoxide dismutase (FeSOD)                                    d2nyba2 A:83-192 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nyb A   1 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAEVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:192
 aligned with SODF_ECOLI | P0AGD3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_ECOLI     2 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 193
               SCOP domains d2nybb1 B:1-82 Fe superoxide dismutase (FeSOD)                                    d2nybb2 B:83-192 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nyb B   1 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAEVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:192
 aligned with SODF_ECOLI | P0AGD3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_ECOLI     2 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 193
               SCOP domains d2nybc1 C:1-82 Fe superoxide dismutase (FeSOD)                                    d2nybc2 C:83-192 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nyb C   1 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAEVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain D from PDB  Type:PROTEIN  Length:192
 aligned with SODF_ECOLI | P0AGD3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           SODF_ECOLI     2 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 193
               SCOP domains d2nybd1 D:1-82 Fe superoxide dismutase (FeSOD)                                    d2nybd2 D:83-192 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-2nybD05 D:1-81                                                          ----Sod_Fe_C-2nybD01 D:86-190                                                                                -- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-2nybD06 D:1-81                                                          ----Sod_Fe_C-2nybD02 D:86-190                                                                                -- Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-2nybD07 D:1-81                                                          ----Sod_Fe_C-2nybD03 D:86-190                                                                                -- Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-2nybD08 D:1-81                                                          ----Sod_Fe_C-2nybD04 D:86-190                                                                                -- Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nyb D   1 SFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAEVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 2NYB)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sod_Fe_C] (46)

Family: Sod_Fe_C (46)

Escherichia coli (strain K12) (7)

1a	Sod_Fe_C-2nybD01	D:86-190
1b	Sod_Fe_C-2nybD02	D:86-190
1c	Sod_Fe_C-2nybD03	D:86-190
1d	Sod_Fe_C-2nybD04	D:86-190

Clan: no clan defined [family: Sod_Fe_N] (46)

Family: Sod_Fe_N (46)

Escherichia coli (strain K12) (7)

2a	Sod_Fe_N-2nybD05	D:1-81
2b	Sod_Fe_N-2nybD06	D:1-81
2c	Sod_Fe_N-2nybD07	D:1-81
2d	Sod_Fe_N-2nybD08	D:1-81

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SODF_ECOLI | P0AGD3)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0000303	response to superoxide	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:15 - Pro A:16	[ RasMol ]
		Ala B:15 - Pro B:16	[ RasMol ]
		Ala C:15 - Pro C:16	[ RasMol ]
		Ala D:15 - Pro D:16	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2nyb
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	SODF_ECOLI \| P0AGD3	:	1isa 1isb 1isc 1za5 2bkb

(no "Related Entries Specified in the PDB File" available for 2NYB)

Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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