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5B1A
Biol. Unit 2
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Asym.Unit (1.4 MB)
Biol.Unit 1 (697 KB)
Biol.Unit 2 (701 KB)
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Title
:
BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY OXIDIZED STATE AT 1.5 ANGSTROM RESOLUTION
Authors
:
N. Yano, K. Muramoto, A. Shimada, S. Takemura, J. Baba, H. Fujisawa, M. M K. Shinzawa-Itoh, E. Yamashita, T. Tsukihara, S. Yoshikawa
Date
:
01 Dec 15 (Deposition) - 14 Sep 16 (Release) - 23 Nov 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
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, Proton Pump, Heme, Respiratory Chain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Yano, K. Muramoto, A. Shimada, S. Takemura, J. Baba, H. Fujisawa, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, T. Tsukihara, S. Yoshikawa
The Mg2+-Containing Water Cluster Of Mammalian Cytochrome C Oxidase Collects Four Pumping Proton Equivalents In Each Catalytic Cycle.
J. Biol. Chem. V. 291 23882 2016
[
close entry info
]
Hetero Components
(14, 28)
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)
02g: CHOLIC ACID (CHDg)
02h: CHOLIC ACID (CHDh)
04a: DINUCLEAR COPPER ION (CUAa)
04b: DINUCLEAR COPPER ION (CUAb)
03a: COPPER (II) ION (CUa)
04b: COPPER (II) ION (CUb)
05a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
05b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
05c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
05d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
06a: N-FORMYLMETHIONINE (FMEa)
06b: N-FORMYLMETHIONINE (FMEb)
06c: N-FORMYLMETHIONINE (FMEc)
06d: N-FORMYLMETHIONINE (FMEd)
07a: HEME-A (HEAa)
07b: HEME-A (HEAb)
07c: HEME-A (HEAc)
07d: HEME-A (HEAd)
08a: MAGNESIUM ION (MGa)
08b: MAGNESIUM ION (MGb)
09a: SODIUM ION (NAa)
09b: SODIUM ION (NAb)
10a: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKa)
10b: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKb)
10c: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKc)
10d: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKd)
10e: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKe)
10f: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKf)
11a: PEROXIDE ION (PERa)
11b: PEROXIDE ION (PERb)
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
4
Ligand/Ion
CHOLIC ACID
3
CU
-1
Ligand/Ion
COPPER (II) ION
4
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
5
DMU
2
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
6
FME
2
Mod. Amino Acid
N-FORMYLMETHIONINE
7
HEA
2
Ligand/Ion
HEME-A
8
MG
-1
Ligand/Ion
MAGNESIUM ION
9
NA
-1
Ligand/Ion
SODIUM ION
10
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
11
PER
1
Ligand/Ion
PEROXIDE ION
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
(33, 33)
Info
All Sites
01: AD2 (SOFTWARE)
02: AD7 (SOFTWARE)
03: AD8 (SOFTWARE)
04: AE4 (SOFTWARE)
05: AE5 (SOFTWARE)
06: AF1 (SOFTWARE)
07: AF2 (SOFTWARE)
08: AF3 (SOFTWARE)
09: AF4 (SOFTWARE)
10: AF5 (SOFTWARE)
11: AF6 (SOFTWARE)
12: AF7 (SOFTWARE)
13: AF8 (SOFTWARE)
14: AF9 (SOFTWARE)
15: AG1 (SOFTWARE)
16: AG2 (SOFTWARE)
17: AG3 (SOFTWARE)
18: AG4 (SOFTWARE)
19: AG5 (SOFTWARE)
20: AG6 (SOFTWARE)
21: AG7 (SOFTWARE)
22: AG8 (SOFTWARE)
23: AG9 (SOFTWARE)
24: AH1 (SOFTWARE)
25: AH2 (SOFTWARE)
26: AH3 (SOFTWARE)
27: AH4 (SOFTWARE)
28: AH5 (SOFTWARE)
29: AH6 (SOFTWARE)
30: AH7 (SOFTWARE)
31: AH8 (SOFTWARE)
32: AH9 (SOFTWARE)
33: AI1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AD2
SOFTWARE
MET A:271 , TRP A:275 , GLN B:59 , GLU B:62 , THR B:63 , HOH B:419 , HOH B:444 , HOH B:468 , PEK P:308 , ARG T:14 , ARG T:17 , GLY T:22
binding site for residue CHD B 303
02
AD7
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , HOH A:723 , TRP C:99 , HIS C:103 , HOH C:415 , HOH C:418 , HOH C:432 , HOH C:506 , HOH C:508 , HOH C:520 , LEU P:127
binding site for residue CHD C 305
03
AD8
SOFTWARE
LYS C:157 , HIS C:158 , GLN C:161 , TYR C:172 , HOH C:425 , HOH C:481 , ALA F:1 , ARG G:17 , PHE G:21 , GLY G:22 , CDL G:102 , SER N:279 , ILE N:311 , GLN O:59 , CHD O:302
binding site for residue PEK C 306
04
AE4
SOFTWARE
LEU C:127 , LEU C:131 , TYR C:253 , VAL C:254 , TRP C:258 , PEK C:306 , SER G:27 , LEU G:30 , CYS G:31 , ASN G:34 , LEU G:37 , HIS G:38 , PEK G:103 , HOH G:205 , HOH G:209 , HOH G:258 , HOH G:267 , PHE N:282 , ILE N:286 , SER N:307 , ILE N:311 , ILE O:74 , ALA O:77 , LEU O:78 , HOH O:488
binding site for residue CDL G 102
05
AE5
SOFTWARE
SER G:2 , ALA G:3 , LYS G:5 , GLY G:6 , HIS G:8 , CDL G:102 , LYS P:77 , ARG P:80 , TYR P:81 , THR P:95 , PHE P:98 , TRP P:240 , VAL P:247
binding site for residue PEK G 103
06
AF1
SOFTWARE
ALA N:24 , MET N:28 , 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 , GLY N:125 , TRP N:126 , TYR N:371 , PHE N:377 , HIS N:378 , SER N:382 , VAL N:386 , MET N:417 , PHE N:425 , GLN N:428 , ARG N:438 , ARG N:439 , HOH N:718 , HOH N:739 , HOH N:776
binding site for residue HEA N 601
07
AF2
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 , 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 , PER N:606 , HOH N:706 , HOH N:747 , HOH N:771 , HOH N:787
binding site for residue HEA N 602
08
AF3
SOFTWARE
HIS N:240 , HIS N:290 , HIS N:291 , PER N:606
binding site for residue CU N 603
09
AF4
SOFTWARE
HIS N:368 , ASP N:369 , GLU O:198 , HOH O:439 , HOH O:479 , HOH O:548
binding site for residue MG N 604
10
AF5
SOFTWARE
GLU N:40 , GLY N:45 , SER N:441 , HOH N:835
binding site for residue NA N 605
11
AF6
SOFTWARE
HIS N:240 , VAL N:243 , HIS N:291 , HEA N:602 , CU N:603
binding site for residue PER N 606
12
AF7
SOFTWARE
PHE N:94 , PRO N:95 , ARG N:96 , MET N:97 , HOH N:728 , HIS P:9 , GLY P:20 , ASN P:50 , MET P:54 , TRP P:57 , TRP P:58 , GLU P:64 , HIS P:71 , GLY P:82 , SER P:89 , HOH P:486 , PEK T:101
binding site for residue PGV N 607
13
AF8
SOFTWARE
ASN N:422 , PHE N:426 , PHE N:430 , LEU N:433 , HOH N:866 , LEU O:7 , LEU O:28 , PHE O:32 , SER O:35 , ARG V:43
binding site for residue TGL N 608
14
AF9
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
15
AG1
SOFTWARE
PEK C:306 , ARG G:14 , ARG G:17 , GLY G:22 , MET N:271 , GLU O:62 , THR O:63 , HOH O:425 , HOH O:431 , HOH O:451 , HOH O:459 , HOH O:471
binding site for residue CHD O 302
16
AG2
SOFTWARE
PHE N:321 , HIS N:328 , MET O:56 , ASP O:57 , GLU O:60 , TRP O:65 , HOH O:532 , GLU R:6 , ASP R:8 , ARG V:10 , HOH V:170
binding site for residue PSC O 303
17
AG3
SOFTWARE
ALA G:1 , PHE N:237 , ASP N:298 , TRP P:99 , HIS P:103 , ALA P:107 , CHD P:307 , HOH P:403 , HOH P:412 , HOH P:523 , ASN U:24 , HOH U:135
binding site for residue PGV P 301
18
AG4
SOFTWARE
VAL P:61 , SER P:65 , THR P:66 , ILE P:210 , PHE P:214 , ARG P:221 , HIS P:226 , PHE P:227 , THR P:228 , HIS P:231 , PHE P:233 , GLY P:234 , CDL P:304 , HOH P:427 , HOH P:444 , HOH P:448 , HOH P:509
binding site for residue PGV P 303
19
AG5
SOFTWARE
THR P:48 , MET P:51 , MET P:54 , TYR P:55 , ARG P:59 , ILE P:62 , ARG P:63 , PHE P:67 , PHE P:220 , LYS P:224 , HIS P:226 , PGV P:303 , HOH P:408 , HOH P:502 , HOH P:515
binding site for residue CDL P 304
20
AG6
SOFTWARE
ARG P:156 , LEU P:160 , GLN P:161 , PHE P:164 , PHE P:219 , LEU P:223 , HOH P:510 , HOH P:571 , PHE W:1
binding site for residue CHD P 305
21
AG7
SOFTWARE
LEU N:110 , MET P:33 , PHE P:37 , HOH P:404 , SER W:46 , TYR W:48 , CYS W:49 , TRP W:52
binding site for residue DMU P 306
22
AG8
SOFTWARE
HIS N:233 , ASP N:300 , THR N:301 , TYR N:304 , HOH N:741 , HOH N:913 , TRP P:99 , HIS P:103 , PGV P:301 , HOH P:442 , HOH P:447 , HOH P:513 , HOH P:523
binding site for residue CHD P 307
23
AG9
SOFTWARE
SER A:279 , ILE A:311 , THR B:66 , CHD B:303 , LYS P:157 , HIS P:158 , GLN P:161 , THR P:168 , TYR P:172 , HOH P:436 , HOH P:441 , HOH P:476 , ALA S:1 , ARG T:17 , PHE T:21 , GLY T:22 , CDL T:103
binding site for residue PEK P 308
24
AH1
SOFTWARE
ASN N:406 , THR N:408 , TRP N:409 , ILE N:412 , PHE Q:87 , HOH Q:406 , HIS X:10 , HOH X:116 , GLN Z:15 , LEU Z:19 , SER Z:20
binding site for residue PGV Q 201
25
AH2
SOFTWARE
TRP N:334 , PHE N:414 , HOH N:707 , ILE O:42 , THR O:47 , HOH O:571 , ARG Q:73 , THR Q:75 , GLU Q:77 , TRP Q:78 , ARG V:16 , HIS V:20
binding site for residue TGL Q 202
26
AH3
SOFTWARE
CYS S:60 , CYS S:62 , CYS S:82 , CYS S:85
binding site for residue ZN S 101
27
AH4
SOFTWARE
HIS N:151 , ALA N:203 , PGV N:607 , TRP P:34 , TYR P:181 , TYR P:182 , ALA P:184 , PHE P:186 , THR P:187 , ILE P:188 , PHE P:198 , GLY P:205 , TRP T:62 , THR T:68 , PHE T:69 , PHE T:70 , HIS T:71 , ASN T:76 , HOH T:237
binding site for residue PEK T 101
28
AH5
SOFTWARE
LYS C:77 , ARG C:80 , TYR C:81 , PHE C:98 , TRP C:240 , VAL C:247 , SER T:2 , ALA T:3 , LYS T:5 , GLY T:6 , CDL T:103
binding site for residue PEK T 102
29
AH6
SOFTWARE
ILE A:286 , ASP A:300 , SER A:307 , ILE A:311 , HOH A:730 , ALA B:70 , ALA B:77 , TYR B:85 , HOH B:476 , LEU P:127 , LEU P:131 , SER P:135 , LEU P:138 , PEK P:308 , SER T:27 , LEU T:30 , CYS T:31 , ASN T:34 , LEU T:37 , HIS T:38 , PEK T:102 , HOH T:210 , HOH T:244
binding site for residue CDL T 103
30
AH7
SOFTWARE
PHE N:8 , TYR W:32 , ARG W:33 , THR W:37
binding site for residue CHD W 101
31
AH8
SOFTWARE
THR N:17 , LEU N:18 , PHE N:22 , TRP N:25 , LEU N:113 , PHE N:400 , PRO Y:12 , PHE Y:13 , SER Y:14 , ARG Y:20 , MET Y:24 , PHE Y:28 , PHE Y:29 , SER Y:31 , HOH Y:221 , HOH Y:225
binding site for residue TGL Y 101
32
AH9
SOFTWARE
TRP Q:98 , LEU Z:28 , GLY Z:31 , TRP Z:32 , TYR Z:35 , HIS Z:36 , HOH Z:206 , HOH Z:225
binding site for residue DMU Z 101
33
AI1
SOFTWARE
TRP N:236 , PHE N:238 , GLY N:239 , PRO N:241 , GLU N:242 , VAL N:243 , ILE N:245 , LEU N:246 , ILE N:247 , LEU N:248 , ILE N:280 , GLY N:284 , VAL N:287 , HIS N:290 , ILE N:312 , HEA N:602 , CU N:603 , PER N:606
binding site for Di-peptide HIS N 240 and TYR N 244
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SAPs(SNPs)/Variants
(0, 0)
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