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3X2Q
Biol. Unit 2
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (662 KB)
Biol.Unit 2 (669 KB)
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Title
:
X-RAY STRUCTURE OF CYANIDE-BOUND BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY OXIDIZED STATE AT 2.0 ANGSTROM RESOLUTION
Authors
:
N. Yano, K. Muramoto, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, S. Yoshikawa, T. Tsukihara
Date
:
26 Dec 14 (Deposition) - 10 Jun 15 (Release) - 10 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M (1x)
Biol. Unit 2: N,O,P,Q,R,S,T,U,V,W,X,Y,Z (1x)
Keywords
:
Oxidoreductase, Respiratory Chain, Electron Transport, Heme, Iron, Mitochondorial Inner Membrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Yano, K. Muramoto, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, S. Yoshikawa, T. Tsukihara
X-Ray Structure Of Cyanide-Bound Bovine Heart Cytochrome C Oxidase In The Fully Oxidized State At 2. 0 A Resolution.
Acta Crystallogr. , Sect. F V. 71 726 2015
[
close entry info
]
Hetero Components
(14, 27)
Info
All Hetero Components
01a: CARDIOLIPIN (CDLa)
01b: CARDIOLIPIN (CDLb)
01c: CARDIOLIPIN (CDLc)
01d: CARDIOLIPIN (CDLd)
02a: CHOLIC ACID (CHDa)
02b: CHOLIC ACID (CHDb)
02c: CHOLIC ACID (CHDc)
02d: CHOLIC ACID (CHDd)
02e: CHOLIC ACID (CHDe)
02f: CHOLIC ACID (CHDf)
04a: DINUCLEAR COPPER ION (CUAa)
04b: DINUCLEAR COPPER ION (CUAb)
03a: COPPER (II) ION (CUa)
04b: COPPER (II) ION (CUb)
05a: CYANIDE ION (CYNa)
05b: CYANIDE ION (CYNb)
06a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
06b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
06c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
06d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
07a: N-FORMYLMETHIONINE (FMEa)
07b: N-FORMYLMETHIONINE (FMEb)
07c: N-FORMYLMETHIONINE (FMEc)
07d: N-FORMYLMETHIONINE (FMEd)
08a: HEME-A (HEAa)
08b: HEME-A (HEAb)
08c: HEME-A (HEAc)
08d: HEME-A (HEAd)
09a: MAGNESIUM ION (MGa)
09b: MAGNESIUM ION (MGb)
10a: SODIUM ION (NAa)
10b: SODIUM ION (NAb)
11a: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKa)
11b: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKb)
11c: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKc)
11d: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKd)
11e: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKe)
11f: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKf)
12a: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
12b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
12c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
12d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
12e: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVe)
12f: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVf)
12g: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVg)
12h: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVh)
13a: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCa)
13b: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCb)
14a: N-ACETYL-SERINE (SACa)
14b: N-ACETYL-SERINE (SACb)
15a: TRISTEAROYLGLYCEROL (TGLa)
15b: TRISTEAROYLGLYCEROL (TGLb)
15c: TRISTEAROYLGLYCEROL (TGLc)
15d: TRISTEAROYLGLYCEROL (TGLd)
15e: TRISTEAROYLGLYCEROL (TGLe)
15f: TRISTEAROYLGLYCEROL (TGLf)
16a: PHOSPHOTHREONINE (TPOa)
16b: PHOSPHOTHREONINE (TPOb)
17a: UNKNOWN ATOM OR ION (UNXa)
17b: UNKNOWN ATOM OR ION (UNXb)
18a: ZINC ION (ZNa)
18b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CDL
2
Ligand/Ion
CARDIOLIPIN
2
CHD
3
Ligand/Ion
CHOLIC ACID
3
CU
-1
Ligand/Ion
COPPER (II) ION
4
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
5
CYN
1
Ligand/Ion
CYANIDE ION
6
DMU
2
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
7
FME
2
Mod. Amino Acid
N-FORMYLMETHIONINE
8
HEA
2
Ligand/Ion
HEME-A
9
MG
-1
Ligand/Ion
MAGNESIUM ION
10
NA
-1
Ligand/Ion
SODIUM ION
11
PEK
3
Ligand/Ion
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
12
PGV
4
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
13
PSC
1
Ligand/Ion
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
14
SAC
1
Mod. Amino Acid
N-ACETYL-SERINE
15
TGL
3
Ligand/Ion
TRISTEAROYLGLYCEROL
16
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
17
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
18
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: BC2 (SOFTWARE)
02: BC6 (SOFTWARE)
03: BC7 (SOFTWARE)
04: CC5 (SOFTWARE)
05: CC6 (SOFTWARE)
06: CC9 (SOFTWARE)
07: DC1 (SOFTWARE)
08: DC2 (SOFTWARE)
09: DC3 (SOFTWARE)
10: DC4 (SOFTWARE)
11: DC5 (SOFTWARE)
12: DC6 (SOFTWARE)
13: DC7 (SOFTWARE)
14: DC8 (SOFTWARE)
15: DC9 (SOFTWARE)
16: EC1 (SOFTWARE)
17: EC2 (SOFTWARE)
18: EC3 (SOFTWARE)
19: EC4 (SOFTWARE)
20: EC5 (SOFTWARE)
21: EC6 (SOFTWARE)
22: EC7 (SOFTWARE)
23: EC8 (SOFTWARE)
24: EC9 (SOFTWARE)
25: FC1 (SOFTWARE)
26: FC2 (SOFTWARE)
27: FC3 (SOFTWARE)
28: FC4 (SOFTWARE)
29: FC5 (SOFTWARE)
30: FC6 (SOFTWARE)
31: FC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC2
SOFTWARE
MET A:271 , TRP A:275 , GLN B:59 , GLU B:62 , THR B:63 , THR B:66 , HOH B:466 , HOH B:476 , HOH B:516 , PEK P:309 , ARG T:14 , ARG T:17 , GLY T:22
BINDING SITE FOR RESIDUE CHD B 302
02
BC6
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , TRP C:99 , HIS C:103 , PGV C:307 , LEU P:127 , CDL T:102
BINDING SITE FOR RESIDUE CHD C 305
03
BC7
SOFTWARE
LYS C:157 , HIS C:158 , GLN C:161 , ALA F:1 , ARG G:17 , GLY G:22 , CDL G:103 , GLN O:59 , CHD O:302 , HOH O:481
BINDING SITE FOR RESIDUE PEK C 306
04
CC5
SOFTWARE
LEU C:127 , LEU C:131 , SER C:135 , LEU C:250 , VAL C:254 , PEK C:306 , LEU G:23 , SER G:27 , LEU G:30 , CYS G:31 , ASN G:34 , HIS G:38 , PHE N:282 , ASP N:300 , SER N:307 , ILE N:311 , ALA O:77 , LEU O:78 , LEU O:81 , TYR O:85 , CHD P:308
BINDING SITE FOR RESIDUE CDL G 103
05
CC6
SOFTWARE
SER G:2 , ALA G:3 , LYS G:5 , HIS G:8 , HOH G:227 , PHE N:282 , LYS P:77 , ARG P:80 , ILE P:84 , PHE P:98 , TRP P:240
BINDING SITE FOR RESIDUE PEK G 104
06
CC9
SOFTWARE
HIS N:240 , HIS N:290 , HIS N:291 , HEA N:603 , CU N:604
BINDING SITE FOR RESIDUE CYN N 601
07
DC1
SOFTWARE
THR N:31 , SER N:34 , ILE N:37 , ARG N:38 , TYR N:54 , VAL N:58 , HIS N:61 , ALA N:62 , MET N:65 , VAL N:70 , ILE N:73 , GLY N:125 , TRP N:126 , TYR N:371 , PHE N:377 , HIS N:378 , SER N:382 , VAL N:386 , PHE N:393 , MET N:417 , PHE N:425 , GLN N:428 , ARG N:438 , ARG N:439 , TYR N:440 , MET N:468 , HOH N:725 , HOH N:729 , HOH N:746
BINDING SITE FOR RESIDUE HEA N 602
08
DC2
SOFTWARE
TRP N:126 , TRP N:236 , VAL N:243 , TYR N:244 , HIS N:290 , HIS N:291 , THR N:309 , ILE N:312 , ALA N:313 , THR N:316 , GLY N:317 , GLY N:352 , LEU N:353 , GLY N:355 , ILE N:356 , LEU N:358 , ALA N:359 , ASP N:364 , HIS N:368 , VAL N:373 , HIS N:376 , PHE N:377 , VAL N:380 , LEU N:381 , ARG N:438 , CYN N:601 , HOH N:733 , HOH N:751 , HOH N:756 , HOH N:761 , ILE O:72
BINDING SITE FOR RESIDUE HEA N 603
09
DC3
SOFTWARE
HIS N:240 , HIS N:290 , HIS N:291 , CYN N:601
BINDING SITE FOR RESIDUE CU N 604
10
DC4
SOFTWARE
HIS N:368 , ASP N:369 , GLU O:198 , HOH O:431 , HOH O:432 , HOH O:433
BINDING SITE FOR RESIDUE MG N 605
11
DC5
SOFTWARE
GLU N:40 , GLN N:43 , GLY N:45 , SER N:441 , HOH N:701
BINDING SITE FOR RESIDUE NA N 606
12
DC6
SOFTWARE
ASN N:406 , THR N:408 , TRP N:409 , ILE N:412 , PHE Q:87 , PRO Z:12 , GLN Z:15 , LEU Z:19
BINDING SITE FOR RESIDUE PGV N 607
13
DC7
SOFTWARE
PHE N:94 , PRO N:95 , ARG N:96 , MET N:97 , HOH N:795 , HIS P:9 , THR P:28 , ASN P:50 , MET P:54 , TRP P:57 , TRP P:58 , GLU P:64 , HIS P:71 , LEU P:79 , GLY P:82 , GLU P:90 , PHE P:93
BINDING SITE FOR RESIDUE PGV N 608
14
DC8
SOFTWARE
ASN N:422 , PHE N:426 , PHE N:430 , LEU N:433 , LEU O:7 , LEU O:28 , PHE O:32 , SER O:35 , SER O:36 , ARG V:43
BINDING SITE FOR RESIDUE TGL N 609
15
DC9
SOFTWARE
THR N:17 , LEU N:18 , LEU N:20 , PHE N:22 , TRP N:81 , LEU N:113 , PHE N:400 , ILE Y:11 , PRO Y:12 , PHE Y:13 , SER Y:14 , ARG Y:20 , MET Y:24 , PHE Y:28 , PHE Y:29
BINDING SITE FOR RESIDUE TGL N 610
16
EC1
SOFTWARE
HIS O:161 , CYS O:196 , GLU O:198 , CYS O:200 , HIS O:204 , MET O:207
BINDING SITE FOR RESIDUE CUA O 301
17
EC2
SOFTWARE
PEK C:306 , ARG G:14 , ARG G:17 , PHE G:21 , GLY G:22 , MET N:271 , GLU O:62 , THR O:63 , HOH O:401 , HOH O:478 , HOH O:483 , HOH O:487
BINDING SITE FOR RESIDUE CHD O 302
18
EC3
SOFTWARE
PHE N:321 , ILE O:41 , HIS O:52 , MET O:56 , ASP O:57 , VAL O:61 , ILE O:64 , GLU R:6 , ASP R:8 , LEU R:41 , ARG V:10
BINDING SITE FOR RESIDUE PSC O 303
19
EC4
SOFTWARE
TRP P:34 , MET P:40 , SER T:61 , TRP T:62 , GLY T:63 , PHE T:69
BINDING SITE FOR RESIDUE DMU P 301
20
EC5
SOFTWARE
ALA G:1 , ASP N:298 , TRP P:99 , HIS P:103 , ALA P:107 , CHD P:308 , ASN U:22
BINDING SITE FOR RESIDUE PGV P 302
21
EC6
SOFTWARE
HIS N:151 , TYR P:181 , TYR P:182 , ALA P:184 , PHE P:186 , THR P:187 , ILE P:188 , PHE P:198 , TRP T:62 , THR T:68 , PHE T:69 , PHE T:70 , HIS T:71 , ASN T:76
BINDING SITE FOR RESIDUE PEK P 304
22
EC7
SOFTWARE
MET P:51 , MET P:54 , TRP P:58 , VAL P:61 , SER P:65 , THR P:66 , HIS P:71 , ILE P:209 , ILE P:210 , PHE P:214 , ARG P:221 , HIS P:226 , PHE P:227 , HIS P:231 , HIS P:232 , PHE P:233 , GLY P:234 , CDL P:306 , HOH P:420 , HOH P:431 , HOH P:438 , HOH P:468 , HOH S:206
BINDING SITE FOR RESIDUE PGV P 305
23
EC8
SOFTWARE
MET P:51 , LEU P:52 , TYR P:55 , TRP P:58 , ARG P:59 , ARG P:63 , PHE P:67 , THR P:213 , PHE P:220 , ARG P:221 , LYS P:224 , HIS P:226 , PGV P:305 , HOH P:468
BINDING SITE FOR RESIDUE CDL P 306
24
EC9
SOFTWARE
ARG P:156 , LEU P:160 , GLN P:161 , PHE P:164 , PHE P:219 , LEU P:223 , PHE W:1
BINDING SITE FOR RESIDUE CHD P 307
25
FC1
SOFTWARE
CDL G:103 , HIS N:233 , ASP N:300 , THR N:301 , TYR N:304 , TRP P:99 , HIS P:103 , PGV P:302
BINDING SITE FOR RESIDUE CHD P 308
26
FC2
SOFTWARE
SER A:279 , CHD B:302 , LYS P:157 , HIS P:158 , GLN P:161 , ILE P:165 , THR P:168 , HOH P:426 , HOH P:475 , ALA S:1 , ARG T:17 , GLY T:22 , CDL T:102
BINDING SITE FOR RESIDUE PEK P 309
27
FC3
SOFTWARE
TRP N:334 , GLY N:343 , LEU O:39 , LYS O:49 , ARG Q:73 , SER Q:74 , GLU Q:77 , TRP Q:78 , VAL Q:81 , HOH Q:308
BINDING SITE FOR RESIDUE TGL Q 201
28
FC4
SOFTWARE
CYS S:60 , CYS S:62 , CYS S:82 , CYS S:85
BINDING SITE FOR RESIDUE ZN S 101
29
FC5
SOFTWARE
LYS C:77 , ILE C:84 , VAL C:91 , THR C:95 , PHE C:98 , TRP C:240 , VAL C:247 , SER T:2 , ALA T:3 , LYS T:5 , GLY T:6 , HIS T:8
BINDING SITE FOR RESIDUE PEK T 101
30
FC6
SOFTWARE
ASP A:300 , SER A:307 , ILE A:311 , LEU B:78 , LEU B:81 , TYR B:85 , CHD C:305 , LEU P:127 , LEU P:131 , VAL P:142 , TRP P:258 , PEK P:309 , SER T:27 , LEU T:30 , CYS T:31 , ASN T:34 , LEU T:37 , HIS T:38 , HOH T:215
BINDING SITE FOR RESIDUE CDL T 102
31
FC7
SOFTWARE
PHE N:459 , TRP Q:98 , TYR Q:102 , LEU Z:27 , LEU Z:28 , GLY Z:31 , TRP Z:32 , TYR Z:35
BINDING SITE FOR RESIDUE DMU Z 101
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