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3OWM
Biol. Unit 1
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Asym.Unit (227 KB)
Biol.Unit 1 (622 KB)
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(1)
Title
:
STRUCTURE OF THE THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE IN A COMPLEX WITH HYDROXYLAMINE
Authors
:
A. A. Trofimov, K. M. Polyakov, K. M. Boyko, T. V. Tikhonova, V. S. Lamzin G. P. Bourenkov, V. O. Popov
Date
:
20 Sep 10 (Deposition) - 26 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Alpha Protein, Eight Hemes C, Tyr-Cys Bond, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, V. O. Popov
Binding Of Sulfite By The Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase
To Be Published
[
close entry info
]
Hetero Components
(5, 117)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: HEME C (HECa)
2b: HEME C (HECb)
2c: HEME C (HECc)
2d: HEME C (HECd)
2e: HEME C (HECe)
2f: HEME C (HECf)
2g: HEME C (HECg)
2h: HEME C (HECh)
2i: HEME C (HECi)
2j: HEME C (HECj)
2k: HEME C (HECk)
2l: HEME C (HECl)
2m: HEME C (HECm)
2n: HEME C (HECn)
2o: HEME C (HECo)
2p: HEME C (HECp)
3a: SODIUM ION (NAa)
4a: NITRITE ION (NO2a)
4b: NITRITE ION (NO2b)
5a: TETRAETHYLENE GLYCOL (PG4a)
5b: TETRAETHYLENE GLYCOL (PG4b)
5c: TETRAETHYLENE GLYCOL (PG4c)
5d: TETRAETHYLENE GLYCOL (PG4d)
5e: TETRAETHYLENE GLYCOL (PG4e)
5f: TETRAETHYLENE GLYCOL (PG4f)
5g: TETRAETHYLENE GLYCOL (PG4g)
5h: TETRAETHYLENE GLYCOL (PG4h)
5i: TETRAETHYLENE GLYCOL (PG4i)
5j: TETRAETHYLENE GLYCOL (PG4j)
5k: TETRAETHYLENE GLYCOL (PG4k)
5l: TETRAETHYLENE GLYCOL (PG4l)
6a: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6a)
6b: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6b)
6c: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6c)
6d: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6d)
6e: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6e)
6f: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6f)
6g: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6g)
7a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
7b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
HEC
48
Ligand/Ion
HEME C
3
NA
-1
Ligand/Ion
SODIUM ION
4
NO2
6
Ligand/Ion
NITRITE ION
5
PG4
36
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PG6
21
Ligand/Ion
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
7
TRS
6
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(45, 45)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NO2 A:1 , HIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , 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:630 , HOH A:775 , HOH A:776 , HOH A:783 , HOH A:794 , HEC A:1006 , HOH A:1128
BINDING SITE FOR RESIDUE HEC A 1004
02
AC2
SOFTWARE
CYS A:66 , HIS A:70 , GLN A:73 , PHE A:74 , LEU A:225 , ASN A:226 , CYS A:227 , CYS A:230 , HIS A:231 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HOH A:746 , HOH A:878 , HOH A:901 , HOH A:991 , HEC A:1003 , HEC A:1006 , HOH A:1049
BINDING SITE FOR RESIDUE HEC A 1005
03
AC3
SOFTWARE
CA A:3 , SER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , LYS A:188 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , HOH A:620 , HOH A:638 , HOH A:769 , HEC A:1004 , HEC A:1005 , HEC A:1007
BINDING SITE FOR RESIDUE HEC A 1006
04
AC4
SOFTWARE
CA A:3 , 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:769 , HOH A:770 , HOH A:771 , HOH A:784 , HEC A:1006 , HOH A:1077
BINDING SITE FOR RESIDUE HEC A 1007
05
AC5
SOFTWARE
ASN A:141 , TRP A:142 , GLN A:143 , VAL A:371 , HIS A:372 , ASN A:375 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , PHE A:490 , PG4 A:533 , HOH A:714 , HOH A:804 , HOH A:1050 , HOH A:1066 , HOH A:1102
BINDING SITE FOR RESIDUE HEC A 1008
06
AC6
SOFTWARE
CYS A:14 , PHE A:15 , HIS A:18 , ILE A:21 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , THR A:59 , 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:550 , HOH A:705 , HOH A:739 , HEC A:1001 , HEC A:1003
BINDING SITE FOR RESIDUE HEC A 1002
07
AC7
SOFTWARE
LYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , CYS A:69 , HIS A:70 , CYS A:227 , HIS A:231 , ALA A:236 , HOH A:960 , HOH A:962 , HEC A:1002 , HEC A:1005 , HOH A:1021 , HOH A:1055 , HOH A:1141
BINDING SITE FOR RESIDUE HEC A 1003
08
AC8
SOFTWARE
GLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , VAL A:45 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HOH A:545 , HOH A:548 , HOH A:707 , HOH A:744 , HEC A:1002
BINDING SITE FOR RESIDUE HEC A 1001
09
AC9
SOFTWARE
TYR A:303 , GLN A:360 , HIS A:361 , HOH A:782 , HEC A:1004 , HOH A:1128
BINDING SITE FOR RESIDUE NO2 A 1
10
BC1
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:881 , HOH A:882
BINDING SITE FOR RESIDUE CA A 2
11
BC2
SOFTWARE
PRO A:116 , HOH A:645 , HOH A:652 , HEC A:1006 , HEC A:1007 , HOH A:1077
BINDING SITE FOR RESIDUE CA A 3
12
BC3
SOFTWARE
LYS A:102 , HOH A:665 , HOH A:976 , HOH A:1072 , HOH A:1082 , HOH A:1097
BINDING SITE FOR RESIDUE TRS A 524
13
BC4
SOFTWARE
HOH A:1068 , HOH A:1082
BINDING SITE FOR RESIDUE CA A 525
14
BC5
SOFTWARE
TYR A:309 , LEU A:311 , GLY A:314 , ARG A:348 , ALA A:355 , HOH A:590 , HOH A:1016
BINDING SITE FOR RESIDUE PG6 A 526
15
BC6
SOFTWARE
GLN A:138 , PHE A:139 , TRP A:142 , HOH A:951
BINDING SITE FOR RESIDUE PG4 A 527
16
BC7
SOFTWARE
THR A:94 , LYS A:431 , ASN A:432 , HIS A:435 , HOH A:613 , HOH A:989
BINDING SITE FOR RESIDUE PG6 A 528
17
BC8
SOFTWARE
ALA A:31 , ASN A:34 , HOH A:1075 , HOH B:561
BINDING SITE FOR RESIDUE PG6 A 529
18
BC9
SOFTWARE
ARG A:171 , PHE A:172 , SER A:174
BINDING SITE FOR RESIDUE PG4 A 530
19
CC1
SOFTWARE
ASP A:62 , GLU A:64
BINDING SITE FOR RESIDUE PG4 A 531
20
CC2
SOFTWARE
MET A:53 , GLY A:54 , GLU A:55 , ARG A:56 , HOH A:611
BINDING SITE FOR RESIDUE PG4 A 532
21
CC3
SOFTWARE
ASN A:375 , ASP A:381 , HOH A:539 , HEC A:1008
BINDING SITE FOR RESIDUE PG4 A 533
22
CC4
SOFTWARE
HOH A:728 , HOH A:1098 , HEC B:1003
BINDING SITE FOR RESIDUE NA A 4
23
CC5
SOFTWARE
NO2 B:1 , HIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , 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:583 , HOH B:812 , HOH B:813 , HOH B:820 , HOH B:831 , HEC B:1006 , HOH B:1167
BINDING SITE FOR RESIDUE HEC B 1004
24
CC6
SOFTWARE
CYS B:66 , HIS B:70 , GLN B:73 , PHE B:74 , LEU B:225 , ASN B:226 , CYS B:227 , CYS B:230 , HIS B:231 , ALA B:290 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HOH B:783 , HOH B:915 , HOH B:938 , HEC B:1003 , HEC B:1006 , HOH B:1036 , HOH B:1088
BINDING SITE FOR RESIDUE HEC B 1005
25
CC7
SOFTWARE
CA B:3 , HOH B:4 , 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:591 , HOH B:806 , HEC B:1004 , HEC B:1005 , HEC B:1007
BINDING SITE FOR RESIDUE HEC B 1006
26
CC8
SOFTWARE
CA B:3 , 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:806 , HOH B:807 , HOH B:808 , HOH B:821 , HEC B:1006 , HOH B:1116
BINDING SITE FOR RESIDUE HEC B 1007
27
CC9
SOFTWARE
ASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , ASN B:375 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , PHE B:490 , HOH B:751 , HOH B:841 , HOH B:1089 , HOH B:1105 , HOH B:1141
BINDING SITE FOR RESIDUE HEC B 1008
28
DC1
SOFTWARE
CYS B:14 , PHE B:15 , HIS B:18 , ILE B:21 , HIS B:25 , VAL B:33 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , ILE B:193 , 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:742 , HOH B:776 , HEC B:1001 , HEC B:1003
BINDING SITE FOR RESIDUE HEC B 1002
29
DC2
SOFTWARE
NA A:4 , HIS A:37 , LYS B:29 , HIS B:30 , VAL B:33 , HIS B:37 , ALA B:65 , CYS B:66 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HOH B:551 , HOH B:638 , HOH B:997 , HOH B:999 , HEC B:1002 , HEC B:1005 , HOH B:1060 , HOH B:1094
BINDING SITE FOR RESIDUE HEC B 1003
30
DC3
SOFTWARE
GLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , ALA B:41 , HIS B:44 , VAL B:45 , 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:625 , HOH B:626 , HOH B:628 , HOH B:744 , HOH B:776 , HOH B:781 , HEC B:1002
BINDING SITE FOR RESIDUE HEC B 1001
31
DC4
SOFTWARE
TYR B:303 , HIS B:361 , HOH B:819 , HEC B:1004 , HOH B:1167
BINDING SITE FOR RESIDUE NO2 B 1
32
DC5
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:918 , HOH B:919
BINDING SITE FOR RESIDUE CA B 2
33
DC6
SOFTWARE
PRO B:116 , HOH B:598 , HOH B:605 , HEC B:1006 , HEC B:1007 , HOH B:1116
BINDING SITE FOR RESIDUE CA B 3
34
DC7
SOFTWARE
LYS B:102 , HOH B:608 , HOH B:618 , HOH B:1021 , HOH B:1111 , HOH B:1121 , HOH B:1136 , HOH B:1164
BINDING SITE FOR RESIDUE TRS B 524
35
DC8
SOFTWARE
HOH B:1107 , HOH B:1121
BINDING SITE FOR RESIDUE CA B 525
36
DC9
SOFTWARE
LEU B:311 , GLY B:314 , ARG B:348 , ALA B:355 , PG6 B:527 , HOH B:1055
BINDING SITE FOR RESIDUE PG6 B 526
37
EC1
SOFTWARE
TYR B:309 , ARG B:348 , PG6 B:526 , HOH B:921
BINDING SITE FOR RESIDUE PG6 B 527
38
EC2
SOFTWARE
GLN B:138 , PHE B:139 , TRP B:142 , HOH B:672
BINDING SITE FOR RESIDUE PG4 B 528
39
EC3
SOFTWARE
THR B:94 , LYS B:431 , HIS B:435 , HOH B:680 , HOH B:683 , HOH B:1020
BINDING SITE FOR RESIDUE PG6 B 529
40
EC4
SOFTWARE
ALA B:31 , ASN B:34 , HOH B:561 , HOH B:693 , HOH B:1114
BINDING SITE FOR RESIDUE PG6 B 530
41
EC5
SOFTWARE
ARG B:171 , PHE B:172 , SER B:174
BINDING SITE FOR RESIDUE PG4 B 531
42
EC6
SOFTWARE
ARG B:60 , ASP B:62
BINDING SITE FOR RESIDUE PG4 B 532
43
EC7
SOFTWARE
ARG B:153 , ASN B:222 , HOH B:1061
BINDING SITE FOR RESIDUE PG4 B 533
44
EC8
SOFTWARE
LYS B:336 , GLN B:340 , GLU B:470 , TYR B:473 , HOH B:951
BINDING SITE FOR RESIDUE PG4 B 534
45
EC9
SOFTWARE
GLN B:143 , CYS B:414 , HIS B:415 , GLU B:417
BINDING SITE FOR RESIDUE PG4 B 535
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:9-420,B:9-420)
;
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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
[
close PROSITE info
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Exons
(0, 0)
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