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3UU9
Biol. Unit 1
Info
Asym.Unit (218 KB)
Biol.Unit 1 (597 KB)
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(1)
Title
:
STRUCTURE OF THE FREE TVNIRB FORM OF THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE
Authors
:
A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, A. V. Tikhonov, P. V. Dorovatovskii, V. O. Popov
Date
:
28 Nov 11 (Deposition) - 25 Jan 12 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Tyr-Cys (Ce2-S) Bond, Tyr-Gln (Ce1-Cg) Bond, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, A. V. Tikhonov, T. N. Safonova, K. M. Boyko, P. V. Dorovatovskii, V. O. Popov
Covalent Modifications Of The Catalytic Tyrosine In Octahae Cytochrome C Nitrite Reductase And Their Effect On The Enzyme Activity.
Acta Crystallogr. , Sect. D V. 68 144 2012
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Hetero Components
(2, 90)
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)
4a: TETRAETHYLENE GLYCOL (PG4a)
4b: TETRAETHYLENE GLYCOL (PG4b)
4c: TETRAETHYLENE GLYCOL (PG4c)
4d: TETRAETHYLENE GLYCOL (PG4d)
4e: TETRAETHYLENE GLYCOL (PG4e)
4f: TETRAETHYLENE GLYCOL (PG4f)
4g: TETRAETHYLENE GLYCOL (PG4g)
4h: TETRAETHYLENE GLYCOL (PG4h)
4i: TETRAETHYLENE GLYCOL (PG4i)
4j: TETRAETHYLENE GLYCOL (PG4j)
4k: TETRAETHYLENE GLYCOL (PG4k)
4l: TETRAETHYLENE GLYCOL (PG4l)
4m: TETRAETHYLENE GLYCOL (PG4m)
4n: TETRAETHYLENE GLYCOL (PG4n)
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
PG4
42
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(35, 35)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , ALA A:179 , 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 , HEC A:603 , HOH A:715 , HOH A:756 , HOH A:759 , HOH A:788 , HOH A:1000
BINDING SITE FOR RESIDUE HEC A 601
02
AC2
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:295 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:603 , HEC A:607 , HOH A:928
BINDING SITE FOR RESIDUE HEC A 602
03
AC3
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 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , HEC A:601 , HEC A:602 , HEC A:604 , CA A:610 , HOH A:709 , HOH A:731 , HOH A:1048
BINDING SITE FOR RESIDUE HEC A 603
04
AC4
SOFTWARE
HIS A:300 , GLU A:363 , PHE A:367 , HIS A:372 , VAL A:377 , 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 , HEC A:603 , CA A:610 , HOH A:711 , HOH A:817 , HOH A:820 , HOH A:845 , HOH A:1043 , HOH A:1048
BINDING SITE FOR RESIDUE HEC A 604
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 , HOH A:806 , HOH A:1006
BINDING SITE FOR RESIDUE HEC A 605
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 , 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:607 , HEC A:608 , HOH A:805 , HOH A:999 , HOH A:1060
BINDING SITE FOR RESIDUE HEC A 606
07
AC7
SOFTWARE
LYS A:29 , HIS A:30 , VAL A:33 , HIS A:37 , ALA A:65 , CYS A:66 , CYS A:69 , HIS A:70 , CYS A:227 , HIS A:231 , ALA A:236 , HEC A:602 , HEC A:606 , HOH A:1035 , HOH A:1135 , HIS B:37 , THR B:68
BINDING SITE FOR RESIDUE HEC A 607
08
AC8
SOFTWARE
GLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , ALA A:41 , HIS A:44 , VAL A:45 , 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 , HEC A:606 , HOH A:814 , HOH A:819 , HOH A:1050
BINDING SITE FOR RESIDUE HEC A 608
09
AC9
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:718 , HOH A:732
BINDING SITE FOR RESIDUE CA A 609
10
BC1
SOFTWARE
PRO A:116 , HEC A:603 , HEC A:604 , HOH A:711 , HOH A:761 , HOH A:822
BINDING SITE FOR RESIDUE CA A 610
11
BC2
SOFTWARE
GLY A:314 , ARG A:348 , PG4 A:612
BINDING SITE FOR RESIDUE PG4 A 611
12
BC3
SOFTWARE
LEU A:311 , GLY A:314 , ARG A:348 , ALA A:355 , PG4 A:611 , HOH A:852
BINDING SITE FOR RESIDUE PG4 A 612
13
BC4
SOFTWARE
GLN A:138 , PHE A:139 , TRP A:142
BINDING SITE FOR RESIDUE PG4 A 613
14
BC5
SOFTWARE
ARG A:171 , SER A:174
BINDING SITE FOR RESIDUE PG4 A 614
15
BC6
SOFTWARE
HIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , 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 , HEC B:603 , HOH B:732 , HOH B:770 , HOH B:773 , HOH B:803 , HOH B:1012
BINDING SITE FOR RESIDUE HEC B 601
16
BC7
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 , TYR B:395 , THR B:396 , HIS B:398 , HEC B:603 , HEC B:607 , HOH B:862 , HOH B:942 , HOH B:1107
BINDING SITE FOR RESIDUE HEC B 602
17
BC8
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 , LEU B:225 , MET B:229 , MET B:295 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , GLN B:400 , HEC B:601 , HEC B:602 , HEC B:604 , CA B:610 , NA B:621 , HOH B:728 , HOH B:746
BINDING SITE FOR RESIDUE HEC B 603
18
BC9
SOFTWARE
HIS B:300 , GLU B:363 , 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 , HEC B:603 , CA B:610 , NA B:621 , HOH B:729 , HOH B:832 , HOH B:835 , HOH B:860 , HOH B:1055
BINDING SITE FOR RESIDUE HEC B 604
19
CC1
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 , PG4 B:616 , HOH B:821 , HOH B:1018 , HOH B:1100 , HOH B:1122
BINDING SITE FOR RESIDUE HEC B 605
20
CC2
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 , HEC B:607 , HEC B:608 , HOH B:820 , HOH B:1011
BINDING SITE FOR RESIDUE HEC B 606
21
CC3
SOFTWARE
HIS A:37 , LYS B:29 , HIS B:30 , 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:602 , HEC B:606 , HOH B:720 , HOH B:1047 , HOH B:1114 , HOH B:1115 , HOH B:1150
BINDING SITE FOR RESIDUE HEC B 607
22
CC4
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:606 , HOH B:829 , HOH B:834 , HOH B:945 , HOH B:1011 , HOH B:1079
BINDING SITE FOR RESIDUE HEC B 608
23
CC5
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:733 , HOH B:747
BINDING SITE FOR RESIDUE CA B 609
24
CC6
SOFTWARE
PRO B:116 , HEC B:603 , HEC B:604 , HOH B:729 , HOH B:775 , HOH B:837
BINDING SITE FOR RESIDUE CA B 610
25
CC7
SOFTWARE
LEU B:311 , ARG B:348 , ALA B:355 , PG4 B:612 , HOH B:867
BINDING SITE FOR RESIDUE PG4 B 611
26
CC8
SOFTWARE
GLY B:314 , ARG B:348 , PG4 B:611 , HOH B:1076
BINDING SITE FOR RESIDUE PG4 B 612
27
CC9
SOFTWARE
GLN B:138 , PHE B:139 , TRP B:142
BINDING SITE FOR RESIDUE PG4 B 613
28
DC1
SOFTWARE
ARG B:171 , PHE B:172 , SER B:174
BINDING SITE FOR RESIDUE PG4 B 614
29
DC2
SOFTWARE
THR B:94 , SER B:95 , HIS B:435 , HOH B:703
BINDING SITE FOR RESIDUE PG4 B 615
30
DC3
SOFTWARE
ASN B:375 , GLY B:376 , ASP B:381 , CYS B:414 , HEC B:605
BINDING SITE FOR RESIDUE PG4 B 616
31
DC4
SOFTWARE
ARG B:153 , THR B:157 , HOH B:1034
BINDING SITE FOR RESIDUE PG4 B 617
32
DC5
SOFTWARE
ARG B:374 , HOH B:933
BINDING SITE FOR RESIDUE PG4 B 618
33
DC6
SOFTWARE
HIS B:107 , GLY B:108 , ALA B:177 , THR B:178 , ALA B:179 , HOH B:1014 , HOH B:1073
BINDING SITE FOR RESIDUE PG4 B 619
34
DC7
SOFTWARE
PHE B:333 , LYS B:506 , HOH B:1070
BINDING SITE FOR RESIDUE PG4 B 620
35
DC8
SOFTWARE
SER B:84 , ARG B:401 , THR B:402 , HEC B:603 , HEC B:604
BINDING SITE FOR RESIDUE NA B 621
[
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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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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)
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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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CATH Domains
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Pfam Domains
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