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2OT4
Biol. Unit 1
Info
Asym.Unit (741 KB)
Biol.Unit 1, α-C (2.1 MB)
Biol.Unit 1 (2.1 MB)
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(1)
Title
:
STRUCTURE OF A HEXAMERIC MULTIHEME C NITRITE REDUCTASE FROM THE EXTREMOPHILE BACTERIUM THIOLKALIVIBRIO NITRATIREDUCENS
Authors
:
K. M. Polyakov, K. M. Boyko, A. Slutsky, T. V. Tikhonova, A. N. Antipov, R. A. Zvyagilskaya, A. N. Popov, V. S. Lamzin, G. P. Bourenkov, V. O. Pop
Date
:
07 Feb 07 (Deposition) - 08 Apr 08 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Cytochrome C Nitrite Reductase, Nrfa, Sulfite Reductase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. M. Polyakov, K. M. Boyko, T. V. Tikhonova, A. Slutsky, A. N. Antipov, R. A. Zvyagilskaya, A. N. Popov, G. P. Bourenkov, V. S. Lamzin, V. O. Popov
High-Resolution Structural Analysis Of A Novel Octaheme Cytochrome C Nitrite Reductase From The Haloalkaliphilic Bacterium Thioalkalivibrio Nitratireducens.
J. Mol. Biol. V. 389 846 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 72)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CITRIC ACID (CITa)
3a: HEME C (HECa)
3b: HEME C (HECb)
3c: HEME C (HECc)
3d: HEME C (HECd)
3e: HEME C (HECe)
3f: HEME C (HECf)
3g: HEME C (HECg)
3h: HEME C (HECh)
3i: HEME C (HECi)
3j: HEME C (HECj)
3k: HEME C (HECk)
3l: HEME C (HECl)
3m: HEME C (HECm)
3n: HEME C (HECn)
3o: HEME C (HECo)
3p: HEME C (HECp)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
4c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
5a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
5b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
5c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
5d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CIT
3
Ligand/Ion
CITRIC ACID
3
HEC
48
Ligand/Ion
HEME C
4
MPD
9
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
MRD
12
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
[
close Hetero Component info
]
Sites
(26, 26)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:3068 , HOH A:3069
BINDING SITE FOR RESIDUE CA A 2744
02
AC2
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:2478 , HOH B:2479
BINDING SITE FOR RESIDUE CA B 2333
03
AC3
SOFTWARE
HIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , ARG A:131 , CYS A:184 , CYS A:187 , LYS A:188 , ARG A:242 , CYS A:299 , HIS A:300 , TYR A:303 , CYS A:305 , HIS A:361 , ASN A:486 , HOH A:2759 , HOH A:2950 , HOH A:2951 , HOH A:2958 , HOH A:2972
BINDING SITE FOR RESIDUE HEC A 1004
04
AC4
SOFTWARE
CYS A:66 , HIS A:70 , GLN A:73 , PHE A:74 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HOH A:3065 , HOH A:3094 , HOH A:3326
BINDING SITE FOR RESIDUE HEC A 1005
05
AC5
SOFTWARE
SER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , LEU A:225 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , GLN A:400 , HOH A:2748 , HOH A:2767 , HOH A:2769 , HOH A:2944
BINDING SITE FOR RESIDUE HEC A 1006
06
AC6
SOFTWARE
HIS A:300 , PHE A:367 , HIS A:372 , ALA A:378 , CYS A:379 , CYS A:382 , HIS A:383 , THR A:402 , ARG A:404 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , HOH A:2767 , HOH A:2944 , HOH A:2945 , HOH A:2946 , HOH A:2954 , HOH A:2959
BINDING SITE FOR RESIDUE HEC A 1007
07
AC7
SOFTWARE
ASN A:141 , TRP A:142 , GLN A:143 , HIS A:372 , ASN A:375 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ALA A:423 , ILE A:427 , PHE A:490 , HOH A:2866 , HOH A:2982
BINDING SITE FOR RESIDUE HEC A 1008
08
AC8
SOFTWARE
CYS A:14 , PHE A:15 , HIS A:18 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HOH A:2853 , HOH A:2900 , HOH A:2922
BINDING SITE FOR RESIDUE HEC A 1002
09
AC9
SOFTWARE
LYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , THR A:68 , CYS A:69 , HIS A:70 , CYS A:227 , HIS A:231 , ALA A:236 , HOH A:2906 , HOH A:3189 , HOH A:3193 , THR B:68
BINDING SITE FOR RESIDUE HEC A 1003
10
BC1
SOFTWARE
GLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HOH A:2842 , HOH A:2856 , HOH A:2905 , HOH A:2920 , HOH A:3124
BINDING SITE FOR RESIDUE HEC A 1001
11
BC2
SOFTWARE
HIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , ARG B:131 , ALA B:179 , CYS B:184 , CYS B:187 , LYS B:188 , ARG B:242 , CYS B:299 , HIS B:300 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , HOH B:2363 , HOH B:2475 , HOH B:2608 , HOH B:2611 , HOH B:2765
BINDING SITE FOR RESIDUE HEC B 1004
12
BC3
SOFTWARE
CYS B:66 , HIS B:70 , GLN B:73 , PHE B:74 , LEU B:225 , CYS B:227 , CYS B:230 , HIS B:231 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HOH B:2490 , HOH B:2671 , HOH B:2672 , HOH B:2926
BINDING SITE FOR RESIDUE HEC B 1005
13
BC4
SOFTWARE
SER B:84 , PRO B:116 , ARG B:117 , HIS B:119 , PHE B:121 , MET B:122 , ASP B:125 , CYS B:187 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , HOH B:2341 , HOH B:2351 , HOH B:2368 , HOH B:2585
BINDING SITE FOR RESIDUE HEC B 1006
14
BC5
SOFTWARE
HIS B:300 , PHE B:367 , HIS B:372 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , ARG B:404 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , HOH B:2368 , HOH B:2474 , HOH B:2585 , HOH B:2587 , HOH B:2589 , HOH B:2610
BINDING SITE FOR RESIDUE HEC B 1007
15
BC6
SOFTWARE
ASN B:141 , TRP B:142 , GLN B:143 , HIS B:372 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ALA B:423 , ILE B:427 , PHE B:490 , HOH B:2415 , HOH B:2749 , HOH B:2867
BINDING SITE FOR RESIDUE HEC B 1008
16
BC7
SOFTWARE
CYS B:14 , PHE B:15 , HIS B:18 , ILE B:21 , HIS B:25 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HOH B:2563 , HOH B:2564
BINDING SITE FOR RESIDUE HEC B 1002
17
BC8
SOFTWARE
THR A:68 , LYS B:29 , HIS B:30 , HIS B:37 , ALA B:65 , CYS B:66 , THR B:68 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HOH B:2566 , HOH B:2711 , HOH B:2712 , HOH B:2713 , HOH B:2781 , HOH B:2841 , HOH B:2914
BINDING SITE FOR RESIDUE HEC B 1003
18
BC9
SOFTWARE
GLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , HIS B:44 , ALA B:48 , SER B:49 , SER B:50 , ARG B:51 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , GLN B:275 , ARG B:276 , HOH B:2404 , HOH B:2431 , HOH B:2468 , HOH B:2487 , HOH B:2564 , HOH B:2573
BINDING SITE FOR RESIDUE HEC B 1001
19
CC1
SOFTWARE
SER B:49 , SER B:50 , ARG B:51 , HOH B:2877
BINDING SITE FOR RESIDUE CIT B 2010
20
CC2
SOFTWARE
PRO A:8 , HOH A:3269 , ALA B:11 , HIS B:25 , ALA B:31 , ASN B:34 , HOH B:2924
BINDING SITE FOR RESIDUE MRD B 2004
21
CC3
SOFTWARE
ALA A:11 , HIS A:25 , ALA A:31 , THR A:32 , ASN A:34 , HOH A:3269 , HOH A:3321 , HOH A:3345 , PRO B:8
BINDING SITE FOR RESIDUE MRD A 2005
22
CC4
SOFTWARE
THR A:59 , HOH A:3128 , HOH A:3313 , HOH A:3322
BINDING SITE FOR RESIDUE MRD A 2270
23
CC5
SOFTWARE
GLN B:310 , LEU B:311 , ASP B:313 , GLY B:314 , ARG B:348
BINDING SITE FOR RESIDUE MRD B 2288
24
CC6
SOFTWARE
ARG A:87 , GLN A:138 , PHE A:139 , TRP A:142 , ARG A:497 , HOH A:3200
BINDING SITE FOR RESIDUE MPD A 2001
25
CC7
SOFTWARE
ARG B:87 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:2849
BINDING SITE FOR RESIDUE MPD B 2002
26
CC8
SOFTWARE
ASP B:23 , HOH B:2916 , HOH B:2925
BINDING SITE FOR RESIDUE MPD B 2040
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:9-420,B:9-420)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
NIR_THIND
37-448
6
A:9-420
B:9-420
[
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]
Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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Sorry, no Info available
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CATH Domains
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Sorry, no Info available
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Pfam Domains
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