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3D1I
Biol. Unit 1
Info
Asym.Unit (380 KB)
Biol.Unit 1, α-C (1.0 MB)
Biol.Unit 1 (1.0 MB)
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(1)
Title
:
STRUCTURE OF THE THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE IN A COMPLEX WITH NITRITE
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
:
06 May 08 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
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, 78)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
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)
3b: SODIUM ION (NAb)
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)
6a: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6a)
6b: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6b)
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
18
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PG6
6
Ligand/Ion
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
[
close Hetero Component info
]
Sites
(32, 32)
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)
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:1232 , HOH A:1233
BINDING SITE FOR RESIDUE CA A 526
02
AC2
SOFTWARE
PRO A:116 , HEC A:1006 , HEC A:1007 , HOH A:1048 , HOH A:1327 , HOH A:1386
BINDING SITE FOR RESIDUE CA A 527
03
AC3
SOFTWARE
ARG A:131 , TYR A:303 , HIS A:361 , HEC A:1004 , HOH A:1013 , HOH A:1359
BINDING SITE FOR RESIDUE NO2 A 528
04
AC4
SOFTWARE
HOH A:1404 , HOH A:1405
BINDING SITE FOR RESIDUE NA A 529
05
AC5
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:1696 , HOH B:1697
BINDING SITE FOR RESIDUE CA B 526
06
AC6
SOFTWARE
PRO B:116 , HEC B:1006 , HEC B:1007 , HOH B:1512 , HOH B:1789 , HOH B:1845 , HOH B:2002
BINDING SITE FOR RESIDUE CA B 527
07
AC7
SOFTWARE
ARG B:131 , TYR B:303 , HIS B:361 , HEC B:1004 , HOH B:1431 , HOH B:1818
BINDING SITE FOR RESIDUE NO2 B 528
08
AC8
SOFTWARE
HOH B:1863 , HOH B:1864 , HOH B:1994
BINDING SITE FOR RESIDUE NA B 529
09
AC9
SOFTWARE
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 , NO2 A:528 , HEC A:1006 , HOH A:1013 , HOH A:1028 , HOH A:1145 , HOH A:1146 , HOH A:1152 , HOH A:1362
BINDING SITE FOR RESIDUE HEC A 1004
10
BC1
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 , ALA A:290 , MET A:384 , LYS A:386 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:1003 , HOH A:1116 , HOH A:1229 , HOH A:1250 , HOH A:1445 , HOH A:1523 , HOH A:1531
BINDING SITE FOR RESIDUE HEC A 1005
11
BC2
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 , LYS A:188 , LEU A:225 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , CA A:527 , HEC A:1004 , HEC A:1007 , HOH A:1017 , HOH A:1035 , HOH A:1140
BINDING SITE FOR RESIDUE HEC A 1006
12
BC3
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 , PRO A:403 , ARG A:404 , ILE A:427 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , CA A:527 , HEC A:1006 , HOH A:1140 , HOH A:1141 , HOH A:1149 , HOH A:1153 , HOH A:1327 , HOH A:1353
BINDING SITE FOR RESIDUE HEC A 1007
13
BC4
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 , HOH A:1413 , HOH A:1459 , HOH A:1461
BINDING SITE FOR RESIDUE HEC A 1008
14
BC5
SOFTWARE
CYS A:14 , PHE A:15 , HIS A:18 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , THR A:59 , ILE A:193 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HEC A:1001 , HEC A:1003 , HOH A:1087 , HOH A:1335 , HOH A:1471
BINDING SITE FOR RESIDUE HEC A 1002
15
BC6
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 , HEC A:1002 , HEC A:1005 , HOH A:1304 , HOH A:1347 , HOH A:1388 , HOH A:1434 , HOH A:1546 , HOH A:1567 , THR B:68 , HOH B:1472
BINDING SITE FOR RESIDUE HEC A 1003
16
BC7
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 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HEC A:1002 , HOH A:1089 , HOH A:1114 , HOH A:1470 , HOH A:1472
BINDING SITE FOR RESIDUE HEC A 1001
17
BC8
SOFTWARE
LYS A:431 , HIS A:435 , HOH A:1408 , HOH A:1446
BINDING SITE FOR RESIDUE PG4 A 1009
18
BC9
SOFTWARE
TYR A:309 , LEU A:311 , GLY A:314 , ARG A:348 , ALA A:355 , HOH A:1247 , HOH A:1298
BINDING SITE FOR RESIDUE PG6 A 1010
19
CC1
SOFTWARE
GLN A:138 , PHE A:139 , HOH A:1273 , HOH A:1536 , HOH A:1537
BINDING SITE FOR RESIDUE PG4 A 1011
20
CC2
SOFTWARE
ARG A:153 , THR A:157 , ASN A:222
BINDING SITE FOR RESIDUE PG4 A 1012
21
CC3
SOFTWARE
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 , VAL B:301 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , NO2 B:528 , HEC B:1006 , HOH B:1431 , HOH B:1492 , HOH B:1609 , HOH B:1610 , HOH B:1616 , HOH B:1940
BINDING SITE FOR RESIDUE HEC B 1004
22
CC4
SOFTWARE
CYS B:66 , HIS B:70 , GLN B:73 , LEU B:225 , ASN B:226 , CYS B:227 , CYS B:230 , HIS B:231 , ALA B:290 , MET B:384 , LYS B:386 , TYR B:395 , THR B:396 , HIS B:398 , HEC B:1003 , HEC B:1006 , HOH B:1580 , HOH B:1693 , HOH B:1714 , HOH B:1904 , HOH B:1968
BINDING SITE FOR RESIDUE HEC B 1005
23
CC5
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 , LYS B:188 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , CA B:527 , HEC B:1004 , HEC B:1005 , HEC B:1007 , HOH B:1481 , HOH B:1499 , HOH B:1604 , HOH B:2002
BINDING SITE FOR RESIDUE HEC B 1006
24
CC6
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 , PRO B:403 , ARG B:404 , ILE B:427 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , CA B:527 , HEC B:1006 , HOH B:1604 , HOH B:1605 , HOH B:1613 , HOH B:1617 , HOH B:1789 , HOH B:1812 , HOH B:2002
BINDING SITE FOR RESIDUE HEC B 1007
25
CC7
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 , PG4 B:1012 , HOH B:1872 , HOH B:1924 , HOH B:1954
BINDING SITE FOR RESIDUE HEC B 1008
26
CC8
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 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HEC B:1001 , HEC B:1003 , HOH B:1551 , HOH B:1796
BINDING SITE FOR RESIDUE HEC B 1002
27
CC9
SOFTWARE
THR A:68 , 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 , HEC B:1002 , HEC B:1005 , HOH B:1440 , HOH B:1767 , HOH B:1807 , HOH B:1847 , HOH B:1893 , HOH B:1928
BINDING SITE FOR RESIDUE HEC B 1003
28
DC1
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 , HEC B:1002 , HOH B:1553 , HOH B:1578 , HOH B:1796 , HOH B:1912 , HOH B:1916 , HOH B:1932
BINDING SITE FOR RESIDUE HEC B 1001
29
DC2
SOFTWARE
THR B:94 , HIS B:435 , HOH B:1867 , HOH B:1905
BINDING SITE FOR RESIDUE PG4 B 1009
30
DC3
SOFTWARE
LEU B:311 , ASP B:313 , GLY B:314 , ARG B:348 , ALA B:355 , HOH B:1711 , HOH B:1934 , HOH B:1935
BINDING SITE FOR RESIDUE PG6 B 1010
31
DC4
SOFTWARE
PHE B:172
BINDING SITE FOR RESIDUE PG4 B 1011
32
DC5
SOFTWARE
TRP B:142 , PHE B:367 , SER B:370 , VAL B:371 , HIS B:372 , PHE B:490 , HIS B:491 , ASN B:492 , PRO B:493 , ASP B:494 , HEC B:1008 , HOH B:1963
BINDING SITE FOR RESIDUE PG4 B 1012
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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
[
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Exons
(0, 0)
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Pfam Domains
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