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3LG1
Biol. Unit 1
Info
Asym.Unit (224 KB)
Biol.Unit 1 (610 KB)
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(1)
Title
:
STRUCTURE OF THE THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE REDUCED BY SODIUM BOROHYDRIDE (IN COMPLEX WITH SULFITE)
Authors
:
A. A. Trofimov, K. M. Polyakov, K. M. Boyko, A. A. Filimonenkov, P. V. Dorovatovsky, T. V. Tikhonova, V. O. Popov
Date
:
19 Jan 10 (Deposition) - 29 Dec 10 (Release) - 15 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Alpha Protein, Eight Hemes C, 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
[
close entry info
]
Hetero Components
(4, 129)
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)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
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)
5a: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6a)
5b: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6b)
5c: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6c)
5d: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6d)
5e: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6e)
5f: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6f)
5g: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6g)
5h: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6h)
5i: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6i)
5j: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6j)
5k: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6k)
5l: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-ME... (PG6l)
6a: SULFITE ION (SO3a)
6b: SULFITE ION (SO3b)
6c: SULFITE ION (SO3c)
6d: SULFITE ION (SO3d)
6e: SULFITE ION (SO3e)
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
30
Ligand/Ion
TETRAETHYLENE GLYCOL
5
PG6
36
Ligand/Ion
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
6
SO3
15
Ligand/Ion
SULFITE ION
[
close Hetero Component info
]
Sites
(53, 53)
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)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (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 , SO3 A:526 , HOH A:568 , HOH A:692 , HOH A:693 , HOH A:699 , HOH A:940 , HOH A:943 , HEC A:1006
BINDING SITE FOR RESIDUE HEC A 1004
02
AC2
SOFTWARE
HIS A:70 , GLN A:73 , LEU A:225 , ASN A:226 , CYS A:227 , CYS A:230 , HIS A:231 , ALA A:290 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HOH A:665 , HOH A:775 , HOH A:798 , HOH A:866 , HOH A:870 , HOH A:892 , HOH A:964 , HOH A:980 , HEC A:1003
BINDING SITE FOR RESIDUE HEC A 1005
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 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , CA A:528 , HOH A:558 , HOH A:575 , HOH A:686 , HEC A:1004 , HEC A:1007
BINDING SITE FOR RESIDUE HEC A 1006
04
AC4
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:686 , HOH A:687 , HOH A:688 , HOH A:700 , HOH A:883 , HEC A:1006 , HOH A:1025
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 , 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:541 , HOH A:640 , HOH A:715 , HOH A:871 , HOH A:878 , HOH A:890 , HOH A:894
BINDING SITE FOR RESIDUE HEC A 1008
06
AC6
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 , 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:632 , HOH A:891 , 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:837 , HEC A:1002 , HEC A:1005 , HOH A:1039 , THR B:68
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 , HOH A:635 , HOH A:663 , HOH A:814 , HOH A:891 , HOH A:925 , HEC A:1002 , HOH A:1019 , HOH A:1022
BINDING SITE FOR RESIDUE HEC A 1001
09
AC9
SOFTWARE
PHE A:109 , ARG A:131 , TYR A:303 , GLN A:360 , HIS A:361 , HOH A:699 , HOH A:935 , HOH A:940 , HOH A:943 , HEC A:1004
BINDING SITE FOR RESIDUE SO3 A 526
10
BC1
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:778 , HOH A:779
BINDING SITE FOR RESIDUE CA A 527
11
BC2
SOFTWARE
PRO A:116 , HOH A:583 , HOH A:589 , HOH A:883 , HEC A:1006
BINDING SITE FOR RESIDUE CA A 528
12
BC3
SOFTWARE
GLU A:390 , HOH A:550 , HOH A:1049
BINDING SITE FOR RESIDUE NA A 529
13
BC4
SOFTWARE
THR A:94 , PG6 A:532 , HOH A:936
BINDING SITE FOR RESIDUE NA A 530
14
BC5
SOFTWARE
HOH A:879 , HOH A:906
BINDING SITE FOR RESIDUE NA A 531
15
BC6
SOFTWARE
THR A:94 , GLU A:115 , ASP A:428 , LYS A:431 , ASN A:432 , NA A:530 , PG4 A:533 , HOH A:893 , HOH A:931 , HOH A:1015
BINDING SITE FOR RESIDUE PG6 A 532
16
BC7
SOFTWARE
ARG A:404 , ASP A:428 , LYS A:431 , PG6 A:532 , HOH A:687 , HOH A:893 , HOH A:1015
BINDING SITE FOR RESIDUE PG4 A 533
17
BC8
SOFTWARE
ALA A:11 , ALA A:31 , ASN A:34 , HOH A:882
BINDING SITE FOR RESIDUE PG6 A 534
18
BC9
SOFTWARE
HOH A:603 , HOH A:688 , HOH A:842 , HOH A:883
BINDING SITE FOR RESIDUE NA A 535
19
CC1
SOFTWARE
GLU A:265 , ASP A:288 , HOH A:817 , HOH A:899 , HOH A:1027
BINDING SITE FOR RESIDUE NA A 536
20
CC2
SOFTWARE
HOH A:592 , HOH A:906 , HOH A:921 , HOH A:938 , HOH A:986
BINDING SITE FOR RESIDUE SO3 A 537
21
CC3
SOFTWARE
GLN A:138 , PHE A:139 , TRP A:142 , ASP A:494 , HOH A:884 , HOH A:962
BINDING SITE FOR RESIDUE PG6 A 539
22
CC4
SOFTWARE
ARG A:60 , ASP A:62 , GLU A:64
BINDING SITE FOR RESIDUE PG4 A 540
23
CC5
SOFTWARE
ASN A:375 , GLY A:376 , HEC A:1008
BINDING SITE FOR RESIDUE PG4 A 541
24
CC6
SOFTWARE
ASN A:141 , GLN A:143 , LYS A:144 , ASP A:147 , THR A:157 , HOH A:922
BINDING SITE FOR RESIDUE PG6 A 542
25
CC7
SOFTWARE
LEU A:311 , GLY A:314 , ARG A:348 , ALA A:355
BINDING SITE FOR RESIDUE PG6 A 543
26
CC8
SOFTWARE
HIS A:107 , GLY A:108 , ALA A:179 , HOH A:646 , HOH A:706
BINDING SITE FOR RESIDUE PG6 A 544
27
CC9
SOFTWARE
VAL A:36 , HIS A:39 , ASP A:40 , ARG A:60
BINDING SITE FOR RESIDUE PG4 A 545
28
DC1
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 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , SO3 B:526 , HOH B:585 , HOH B:709 , HOH B:710 , HOH B:716 , HOH B:955 , HEC B:1006
BINDING SITE FOR RESIDUE HEC B 1004
29
DC2
SOFTWARE
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 , HOH B:683 , HOH B:792 , HOH B:815 , HOH B:882 , HOH B:886 , HOH B:908 , HEC B:1003 , HEC B:1006
BINDING SITE FOR RESIDUE HEC B 1005
30
DC3
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 , LEU B:225 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , CA B:528 , HOH B:575 , HOH B:592 , HOH B:703 , HEC B:1004 , HEC B:1005 , HEC B:1007
BINDING SITE FOR RESIDUE HEC B 1006
31
DC4
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 , ILE B:427 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , HOH B:703 , HOH B:704 , HOH B:705 , HOH B:717 , HOH B:899 , HEC B:1006
BINDING SITE FOR RESIDUE HEC B 1007
32
DC5
SOFTWARE
ASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , PHE B:490 , HOH B:657 , HOH B:732 , HOH B:887 , HOH B:894 , HOH B:906 , HOH B:910
BINDING SITE FOR RESIDUE HEC B 1008
33
DC6
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 , HOH B:649 , HOH B:907 , HEC B:1001 , HEC B:1003
BINDING SITE FOR RESIDUE HEC B 1002
34
DC7
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 , HOH B:854 , HEC B:1002 , HEC B:1005 , HOH B:1015
BINDING SITE FOR RESIDUE HEC B 1003
35
DC8
SOFTWARE
GLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , HIS B:44 , VAL B:45 , ALA B:48 , SER B:49 , 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:652 , HOH B:681 , HOH B:831 , HOH B:907 , HOH B:941 , HOH B:997 , HEC B:1002
BINDING SITE FOR RESIDUE HEC B 1001
36
DC9
SOFTWARE
PHE B:109 , ARG B:131 , TYR B:303 , GLN B:360 , HIS B:361 , HOH B:716 , HOH B:951 , HOH B:955 , HOH B:958 , HEC B:1004
BINDING SITE FOR RESIDUE SO3 B 526
37
EC1
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:795 , HOH B:796
BINDING SITE FOR RESIDUE CA B 527
38
EC2
SOFTWARE
PRO B:116 , HOH B:600 , HOH B:606 , HOH B:899 , HEC B:1006
BINDING SITE FOR RESIDUE CA B 528
39
EC3
SOFTWARE
THR B:94 , PG6 B:531 , HOH B:952
BINDING SITE FOR RESIDUE NA B 529
40
EC4
SOFTWARE
HOH B:895 , HOH B:922
BINDING SITE FOR RESIDUE NA B 530
41
EC5
SOFTWARE
THR B:94 , GLU B:115 , ASP B:428 , LYS B:431 , ASN B:432 , NA B:529 , PG4 B:532 , HOH B:896 , HOH B:947 , HOH B:952
BINDING SITE FOR RESIDUE PG6 B 531
42
EC6
SOFTWARE
ARG B:404 , ASP B:428 , PG6 B:531 , HOH B:704 , HOH B:909
BINDING SITE FOR RESIDUE PG4 B 532
43
EC7
SOFTWARE
SER B:50 , HOH B:1012
BINDING SITE FOR RESIDUE SO3 B 533
44
EC8
SOFTWARE
PRO A:8 , MET B:12 , ALA B:31 , ASN B:34 , HOH B:898
BINDING SITE FOR RESIDUE PG6 B 534
45
EC9
SOFTWARE
HOH B:620 , HOH B:705 , HOH B:859 , HOH B:899
BINDING SITE FOR RESIDUE NA B 535
46
FC1
SOFTWARE
HOH B:609 , HOH B:922 , HOH B:1000
BINDING SITE FOR RESIDUE SO3 B 536
47
FC2
SOFTWARE
ARG B:171 , PHE B:172 , SER B:174
BINDING SITE FOR RESIDUE PG4 B 537
48
FC3
SOFTWARE
GLN B:138 , PHE B:139 , TRP B:142 , ASP B:494 , HOH B:1018
BINDING SITE FOR RESIDUE PG6 B 538
49
FC4
SOFTWARE
ARG B:60 , GLU B:64 , THR B:68
BINDING SITE FOR RESIDUE PG6 B 539
50
FC5
SOFTWARE
ASN B:375
BINDING SITE FOR RESIDUE PG4 B 540
51
FC6
SOFTWARE
ASN B:141 , GLN B:143 , LYS B:144 , ASP B:147 , THR B:157
BINDING SITE FOR RESIDUE PG6 B 541
52
FC7
SOFTWARE
LEU B:311 , GLY B:314 , ARG B:348 , ALA B:355 , HOH B:810
BINDING SITE FOR RESIDUE PG6 B 542
53
FC8
SOFTWARE
GLY B:308 , TYR B:309 , ARG B:316
BINDING SITE FOR RESIDUE PG4 B 543
[
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SAPs(SNPs)/Variants
(0, 0)
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(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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select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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