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5D4H
Asym. Unit
Info
Asym.Unit (374 KB)
Biol.Unit 1 (366 KB)
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(1)
Title
:
HIGH-RESOLUTION NITRITE COMPLEX OF A COPPER NITRITE REDUCTASE DETERMINED BY SYNCHROTRON RADIATION CRYSTALLOGRAPHY
Authors
:
Y. Fukuda, K. M. Tse, T. Nakane, T. Nakatsu, M. Suzuki, M. Sugahara, S. In T. Masuda, F. Yumoto, N. Matsugaki, E. Nango, K. Tono, Y. Joti, T. Kames C. Song, T. Hatsui, M. Yabashi, O. Nureki, M. E. P. Murphy, T. Inoue, S. I E. Mizohata
Date
:
07 Aug 15 (Deposition) - 09 Mar 16 (Release) - 22 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Copper, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Fukuda, K. M. Tse, T. Nakane, T. Nakatsu, M. Suzuki, M. Sugahara, S. Inoue, T. Masuda, F. Yumoto, N. Matsugaki, E. Nango, K. Tono, Y. Joti T. Kameshima, C. Song, T. Hatsui, M. Yabashi, O. Nureki, M. E. Murphy, T. Inoue, S. Iwata, E. Mizohata
Redox-Coupled Proton Transfer Mechanism In Nitrite Reductas Revealed By Femtosecond Crystallography
Proc. Natl. Acad. Sci. Usa V. 113 2928 2016
[
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Hetero Components
(4, 33)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
2e: COPPER (II) ION (CUe)
2f: COPPER (II) ION (CUf)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
4a: NITRITE ION (NO2a)
4b: NITRITE ION (NO2b)
4c: NITRITE ION (NO2c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
2
Ligand/Ion
ACETIC ACID
2
CU
6
Ligand/Ion
COPPER (II) ION
3
GOL
22
Ligand/Ion
GLYCEROL
4
NO2
3
Ligand/Ion
NITRITE ION
[
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Sites
(33, 33)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:95 , CYS A:136 , HIS A:145 , MET A:150
binding site for residue CU A 501
02
AC2
SOFTWARE
ASP A:98 , HIS A:100 , HIS A:135 , NO2 A:503 , HIS C:306
binding site for residue CU A 502
03
AC3
SOFTWARE
ASP A:98 , HIS A:100 , HIS A:135 , CU A:502 , HOH A:603 , HIS C:255 , ILE C:257 , HIS C:306 , LEU C:308
binding site for residue NO2 A 503
04
AC4
SOFTWARE
HIS A:255 , ILE A:257 , HIS A:306 , LEU A:308 , HOH A:710 , ASP B:98 , HIS B:100 , HIS B:135 , CU B:502 , HOH B:606
binding site for residue NO2 A 504
05
AC5
SOFTWARE
ILE A:52 , ASP A:53 , ASP A:54 , VAL A:224 , HOH A:676 , HOH A:814
binding site for residue GOL A 505
06
AC6
SOFTWARE
TYR A:193 , THR A:216 , HIS A:217 , GLU A:313 , LEU A:314 , HOH A:722 , ARG B:211
binding site for residue GOL A 506
07
AC7
SOFTWARE
VAL A:142 , HOH A:603 , HOH A:644 , HOH A:702 , ALA C:302 , HOH C:796
binding site for residue GOL A 507
08
AC8
SOFTWARE
LEU A:213 , ARG A:250 , HOH A:602 , HOH A:621 , HOH A:759 , ARG C:253 , ASN C:307 , GLU C:310 , HOH C:610
binding site for residue GOL A 508
09
AC9
SOFTWARE
ASP A:230 , LYS A:231 , HOH A:607 , HOH A:631 , HOH A:686 , HOH A:741
binding site for residue GOL A 509
10
AD1
SOFTWARE
GLY A:229 , ASP A:230 , ALA A:232 , THR A:234 , LYS A:321 , HOH A:615 , HOH A:620 , HOH A:774
binding site for residue GOL A 510
11
AD2
SOFTWARE
PHE A:24 , VAL A:25 , LYS A:174 , ILE A:175 , HOH A:671
binding site for residue GOL A 511
12
AD3
SOFTWARE
LYS A:174 , THR A:234 , HOH A:617
binding site for residue GOL A 512
13
AD4
SOFTWARE
GLU A:46 , LYS A:48
binding site for residue GOL A 513
14
AD5
SOFTWARE
TRP A:326 , THR A:332 , SER A:333
binding site for residue GOL A 514
15
AD6
SOFTWARE
HOH A:847
binding site for residue GOL A 515
16
AD7
SOFTWARE
GLY A:140 , MET A:141 , VAL A:142 , PRO A:143 , TRP A:144 , GLU C:313
binding site for residue ACY A 516
17
AD8
SOFTWARE
HIS B:95 , CYS B:136 , HIS B:145 , MET B:150
binding site for residue CU B 501
18
AD9
SOFTWARE
HIS A:306 , NO2 A:504 , HOH A:710 , ASP B:98 , HIS B:100 , HIS B:135
binding site for residue CU B 502
19
AE1
SOFTWARE
HIS B:255 , ILE B:257 , HIS B:306 , HOH B:706 , ASP C:98 , HIS C:100 , HIS C:135 , CU C:502 , HOH C:609
binding site for residue NO2 B 503
20
AE2
SOFTWARE
ALA A:302 , PRO B:139 , VAL B:142 , HOH B:633 , HOH B:676 , HOH B:748
binding site for residue GOL B 504
21
AE3
SOFTWARE
VAL B:59 , VAL B:147 , SER B:148 , PHE B:183 , TYR B:184 , THR B:206 , HOH B:619 , HOH B:704
binding site for residue GOL B 505
22
AE4
SOFTWARE
TRP B:326 , THR B:332 , SER B:333 , HOH B:625 , HOH B:831 , HOH B:908
binding site for residue GOL B 506
23
AE5
SOFTWARE
TYR B:193 , THR B:216 , HIS B:217 , VAL B:224 , GLU B:313 , LEU B:314 , ARG C:211
binding site for residue GOL B 507
24
AE6
SOFTWARE
GLU A:313 , GLY B:140 , MET B:141 , VAL B:142 , PRO B:143 , TRP B:144 , MET B:210
binding site for residue ACY B 508
25
AE7
SOFTWARE
HIS C:95 , CYS C:136 , HIS C:145 , MET C:150
binding site for residue CU C 501
26
AE8
SOFTWARE
HIS B:306 , NO2 B:503 , HOH B:706 , ASP C:98 , HIS C:100 , HIS C:135
binding site for residue CU C 502
27
AE9
SOFTWARE
THR A:212 , LEU A:213 , THR A:214 , THR B:212 , LEU B:213 , THR B:214 , THR C:212 , LEU C:213 , THR C:214 , HOH C:604 , HOH C:606 , HOH C:610
binding site for residue GOL C 503
28
AF1
SOFTWARE
HOH B:687 , PRO C:139 , VAL C:142 , HOH C:603 , HOH C:628
binding site for residue GOL C 504
29
AF2
SOFTWARE
TRP C:326 , THR C:332 , SER C:333 , GOL C:509
binding site for residue GOL C 505
30
AF3
SOFTWARE
ALA C:27 , HIS C:28 , GLN C:30 , HOH C:607 , HOH C:756
binding site for residue GOL C 506
31
AF4
SOFTWARE
GLN C:15 , HIS C:26 , HIS C:28 , LYS C:37 , VAL C:39 , VAL C:74 , VAL C:75 , HOH C:615 , HOH C:767
binding site for residue GOL C 507
32
AF5
SOFTWARE
ARG A:211 , THR C:216 , HIS C:217 , VAL C:224 , GLU C:313 , LEU C:314 , HOH C:602 , HOH C:665
binding site for residue GOL C 508
33
AF6
SOFTWARE
ALA A:105 , TRP C:326 , GOL C:505 , HOH C:622
binding site for residue GOL C 509
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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Pfam Domains
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Asym.Unit (374 KB)
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