5A12 - JenaLib

Title :   CRYSTAL STRUCTURE OF CHLORITE DISMUTASE FROM MAGNETOSPIRILLUM SP. IN COMPLEX WITH AZIDE

Authors :   H. D. Correia, T. Santos-Silva

Date :   27 Apr 15 (Deposition) - 02 Sep 15 (Release) - 22 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Oxidoreductase, Chlorite, Chloride, Detoxification, Heme, Iron (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. De Schutter, H. Correia, D. M. Freire, M. G. Rivas, A. C. Rizzi, T. Santos-Silva, P. J. Gonzalez, S. Van Doorslaer
Ligand Binding To Chlorite Dismutase From Magnetospirillum Sp.
J. Phys. Chem. B V. 119 13859 2015
PubMed-ID: 26287794 | Reference-DOI: 10.1021/ACS.JPCB.5B04141

Compounds

Molecule 1 - CHLORITE DISMUTASE
	Chains	:	A, B, C, D, E
	EC Number	:	1.13.11.49
	Organism Scientific	:	MAGNETOSPIRILLUM SP.
	Organism Taxid	:	31872

Structural Features

Chains, Units

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 18)

Asymmetric/Biological Unit (3, 18)

No.	Name	Count	Type	Full Name
1	AZI	5	Ligand/Ion	AZIDE ION
2	GOL	8	Ligand/Ion	GLYCEROL
3	HEM	5	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:116 , ASN A:117 , TYR A:118 , ILE A:119 , ILE A:147 , LYS A:151 , TRP A:155 , HIS A:170 , THR A:171 , THR A:174 , ARG A:183 , PHE A:196 , THR A:198 , PHE A:200 , LEU A:211 , LEU A:212 , LEU A:215 , AZI A:251 , HOH A:2231 , HOH A:2242 , HOH A:2243 , HOH A:2409	BINDING SITE FOR RESIDUE HEM A 250
02	AC2	SOFTWARE	ARG A:183 , THR A:198 , HEM A:250	BINDING SITE FOR RESIDUE AZI A 251
03	AC3	SOFTWARE	THR A:16 , THR A:17 , THR A:113 , LYS A:114 , LYS A:184 , HOH A:2232 , HOH A:2238 , HOH A:2347 , HOH A:2410	BINDING SITE FOR RESIDUE GOL A 252
04	AC4	SOFTWARE	LEU B:116 , ASN B:117 , TYR B:118 , ILE B:119 , LYS B:151 , TRP B:155 , HIS B:170 , THR B:171 , THR B:174 , ARG B:183 , PHE B:196 , PHE B:200 , LEU B:211 , LEU B:212 , LEU B:215 , AZI B:251 , HOH B:2195 , HOH B:2206 , HOH B:2207 , HOH B:2362	BINDING SITE FOR RESIDUE HEM B 250
05	AC5	SOFTWARE	ARG B:183 , THR B:198 , HEM B:250	BINDING SITE FOR RESIDUE AZI B 251
06	AC6	SOFTWARE	THR B:16 , THR B:113 , LYS B:114 , HOH B:2019 , HOH B:2194 , HOH B:2299 , HOH B:2364	BINDING SITE FOR RESIDUE GOL B 252
07	AC7	SOFTWARE	LEU C:116 , ASN C:117 , TYR C:118 , ILE C:119 , ILE C:147 , LYS C:151 , TRP C:155 , HIS C:170 , THR C:171 , THR C:174 , ARG C:183 , PHE C:196 , THR C:198 , PHE C:200 , LEU C:211 , LEU C:212 , LEU C:215 , AZI C:251 , HOH C:2190 , HOH C:2201 , HOH C:2203 , HOH C:2353	BINDING SITE FOR RESIDUE HEM C 250
08	AC8	SOFTWARE	ARG C:183 , THR C:198 , HEM C:250	BINDING SITE FOR RESIDUE AZI C 251
09	AC9	SOFTWARE	THR C:16 , THR C:17 , THR C:113 , LYS C:114 , LYS C:184 , HOH C:2191 , HOH C:2297	BINDING SITE FOR RESIDUE GOL C 252
10	BC1	SOFTWARE	MET B:34 , ARG B:67 , THR B:245 , GLY B:248 , HOH B:2128 , VAL C:92 , ARG C:95 , HOH C:2173 , HOH C:2354	BINDING SITE FOR RESIDUE GOL C 253
11	BC2	SOFTWARE	LEU D:116 , ASN D:117 , TYR D:118 , ILE D:119 , LYS D:151 , TRP D:155 , HIS D:170 , THR D:171 , THR D:174 , ARG D:183 , PHE D:196 , PHE D:200 , LEU D:211 , LEU D:212 , LEU D:215 , AZI D:251 , HOH D:2151 , HOH D:2157 , HOH D:2159 , HOH D:2299	BINDING SITE FOR RESIDUE HEM D 250
12	BC3	SOFTWARE	ARG D:183 , THR D:198 , HEM D:250	BINDING SITE FOR RESIDUE AZI D 251
13	BC4	SOFTWARE	VAL B:92 , ARG B:95 , HOH B:2171 , MET D:34 , ARG D:67 , THR D:245 , GLY D:248 , HOH D:2115 , HOH D:2300	BINDING SITE FOR RESIDUE GOL D 252
14	BC5	SOFTWARE	THR D:16 , THR D:17 , PRO D:18 , THR D:113 , LYS D:114 , LYS D:184 , HOH D:2021 , HOH D:2150 , HOH D:2250	BINDING SITE FOR RESIDUE GOL D 253
15	BC6	SOFTWARE	LEU E:116 , ASN E:117 , TYR E:118 , ILE E:119 , LYS E:151 , TRP E:155 , HIS E:170 , THR E:171 , THR E:174 , ARG E:183 , PHE E:196 , THR E:198 , PHE E:200 , LEU E:211 , LEU E:212 , LEU E:215 , AZI E:251 , HOH E:2164 , HOH E:2175 , HOH E:2176 , HOH E:2316	BINDING SITE FOR RESIDUE HEM E 250
16	BC7	SOFTWARE	ARG E:183 , THR E:198 , HEM E:250	BINDING SITE FOR RESIDUE AZI E 251
17	BC8	SOFTWARE	THR E:16 , THR E:17 , THR E:113 , LYS E:114 , LYS E:184 , HOH E:2021 , HOH E:2165 , HOH E:2266	BINDING SITE FOR RESIDUE GOL E 252
18	BC9	SOFTWARE	VAL A:92 , ARG A:95 , HOH A:2211 , MET E:34 , ARG E:67 , THR E:245 , HOH E:2317	BINDING SITE FOR RESIDUE GOL E 253

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:229	-	Pro A:230
2	Asn B:229	-	Pro B:230
3	Asn C:229	-	Pro C:230
4	Asn D:229	-	Pro D:230
5	Asn E:229	-	Pro E:230

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeee...........hhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a12 A   8 MADRAKLLTTPGVFGNFSTYKVRADYMKLPAAERKAAAAEAQMVIDKHKDKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRATKLGMYSDVTENLVGITKALNYISKDKSPDLNAGLSSATYSDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYLVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGNPTVLGTIQSADVLVKTLSGM 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeee...........hhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a12 B   8 MADRAKLLTTPGVFGNFSTYKVRADYMKLPAAERKAAAAEAQMVIDKHKDKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRATKLGMYSDVTENLVGITKALNYISKDKSPDLNAGLSSATYSDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYLVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGNPTVLGTIQSADVLVKTLSGM 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeee...........hhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a12 C   8 MADRAKLLTTPGVFGNFSTYKVRADYMKLPAAERKAAAAEAQMVIDKHKDKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRATKLGMYSDVTENLVGITKALNYISKDKSPDLNAGLSSATYSDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYLVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGNPTVLGTIQSADVLVKTLSGM 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeee...........hhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a12 D   8 MADRAKLLTTPGVFGNFSTYKVRADYMKLPAAERKAAAAEAQMVIDKHKDKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRATKLGMYSDVTENLVGITKALNYISKDKSPDLNAGLSSATYSDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYLVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGNPTVLGTIQSADVLVKTLSGM 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain E from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeee...........hhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a12 E   8 MADRAKLLTTPGVFGNFSTYKVRADYMKLPAAERKAAAAEAQMVIDKHKDKVIVDTYLTRGLGAGSDYLLRVHSTDMAATQAFLVDWRATKLGMYSDVTENLVGITKALNYISKDKSPDLNAGLSSATYSDSAPRYVIVIPVKKDAAWWNMSDEQRLKEIEVHTQPTLQYLVNVKRKLYHSTGLADADFITYFETADLAAFNNLLIALAKVPENTHHVRWGNPTVLGTIQSADVLVKTLSGM 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Legend:		→ Mismatch	(orange background)
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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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	Cis Peptide Bonds
		Asn A:229 - Pro A:230	[ RasMol ]
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		Asn D:229 - Pro D:230	[ RasMol ]
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Description