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5B1B
Biol. Unit 1
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (694 KB)
Biol.Unit 2 (693 KB)
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Title
:
BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE AT 1.6 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
:
1.60
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, Proton Pump, Heme
(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
(13, 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: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
11b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
11c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
11d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
11e: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVe)
11f: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVf)
11g: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVg)
11h: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVh)
12a: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCa)
12b: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIME... (PSCb)
13a: N-ACETYL-SERINE (SACa)
13b: N-ACETYL-SERINE (SACb)
14a: TRISTEAROYLGLYCEROL (TGLa)
14b: TRISTEAROYLGLYCEROL (TGLb)
14c: TRISTEAROYLGLYCEROL (TGLc)
14d: TRISTEAROYLGLYCEROL (TGLd)
14e: TRISTEAROYLGLYCEROL (TGLe)
14f: TRISTEAROYLGLYCEROL (TGLf)
15a: PHOSPHOTHREONINE (TPOa)
15b: PHOSPHOTHREONINE (TPOb)
16a: UNKNOWN ATOM OR ION (UNXa)
16b: UNKNOWN ATOM OR ION (UNXb)
17a: ZINC ION (ZNa)
17b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CDL
2
Ligand/Ion
CARDIOLIPIN
2
CHD
5
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
PGV
4
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
12
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
13
SAC
1
Mod. Amino Acid
N-ACETYL-SERINE
14
TGL
3
Ligand/Ion
TRISTEAROYLGLYCEROL
15
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
16
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
17
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
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: AG2 (SOFTWARE)
29: AH3 (SOFTWARE)
30: AH4 (SOFTWARE)
31: AH5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:31 , SER A:34 , ILE A:37 , ARG A:38 , TYR A:54 , VAL A:58 , HIS A:61 , ALA A:62 , MET A:65 , VAL A:70 , ILE A:73 , GLY A:125 , TRP A:126 , TYR A:371 , PHE A:377 , HIS A:378 , SER A:382 , MET A:390 , PHE A:393 , MET A:417 , PHE A:425 , GLN A:428 , ARG A:438 , ARG A:439 , TYR A:440 , VAL A:465 , HOH A:727 , HOH A:756 , HOH A:774
binding site for residue HEA A 601
02
AC2
SOFTWARE
TRP A:126 , TRP A:236 , VAL A:243 , TYR A:244 , ILE A:247 , HIS A:290 , HIS A:291 , THR A:309 , ILE A:312 , THR A:316 , GLY A:317 , GLY A:352 , GLY A:355 , ILE A:356 , LEU A:358 , ALA A:359 , ASP A:364 , HIS A:368 , VAL A:373 , HIS A:376 , PHE A:377 , VAL A:380 , LEU A:381 , ARG A:438 , HOH A:720 , HOH A:765 , HOH A:803 , HOH A:857 , ILE B:34
binding site for residue HEA A 602
03
AC3
SOFTWARE
HIS A:240 , HIS A:290 , HIS A:291
binding site for residue CU A 603
04
AC4
SOFTWARE
HIS A:368 , ASP A:369 , GLU B:198 , HOH B:432 , HOH B:467 , HOH B:540
binding site for residue MG A 604
05
AC5
SOFTWARE
GLU A:40 , GLY A:45 , SER A:441 , HOH A:848
binding site for residue NA A 605
06
AC6
SOFTWARE
PHE A:94 , PRO A:95 , ARG A:96 , MET A:97 , HIS A:151 , HOH A:755 , HIS C:9 , GLY C:20 , THR C:28 , ASN C:50 , MET C:54 , TRP C:57 , TRP C:58 , GLU C:64 , HIS C:71 , GLY C:82 , GLU C:90 , PEK C:303 , HOH C:492
binding site for residue PGV A 606
07
AC7
SOFTWARE
ASN A:406 , THR A:408 , ARG A:480 , HOH A:701 , HOH A:705 , HOH A:758 , HOH A:900 , HOH A:963 , PHE D:87 , HIS K:10 , GLN M:15 , LEU M:19 , HOH M:220
binding site for residue PGV A 607
08
AC8
SOFTWARE
ASN A:422 , PHE A:426 , PHE A:430 , LEU A:433 , LEU B:7 , LEU B:28 , VAL B:31 , PHE B:32 , SER B:35 , SER B:36 , LEU B:39
binding site for residue TGL B 301
09
AC9
SOFTWARE
HIS B:161 , CYS B:196 , GLU B:198 , CYS B:200 , HIS B:204 , MET B:207
binding site for residue CUA B 302
10
AD1
SOFTWARE
MET A:271 , TRP A:275 , GLN B:59 , GLU B:62 , THR B:63 , HOH B:445 , HOH B:446 , HOH B:457 , ARG T:14 , ARG T:17 , PHE T:21 , GLY T:22 , PEK T:103
binding site for residue CHD B 303
11
AD2
SOFTWARE
PHE A:321 , HIS A:328 , ILE B:41 , HIS B:52 , MET B:56 , ASP B:57 , VAL B:61 , HOH B:472 , THR E:7 , ASP E:8 , PHE E:11 , HOH E:290 , ARG I:10 , ALA I:14
binding site for residue PSC B 304
12
AD3
SOFTWARE
SER C:29 , MET C:33 , PHE C:37 , SER J:46 , TYR J:48 , CYS J:49 , TRP J:52 , HOH J:237
binding site for residue DMU C 301
13
AD4
SOFTWARE
HIS A:151 , PGV A:606 , HOH A:903 , HOH A:973 , TRP C:34 , TYR C:181 , TYR C:182 , ALA C:184 , PHE C:186 , THR C:187 , ILE C:188 , PHE C:198 , GLY C:202 , HOH C:566 , TRP G:62 , THR G:68 , PHE G:69 , PHE G:70 , HIS G:71 , ASN G:76 , HOH G:239
binding site for residue PEK C 303
14
AD5
SOFTWARE
MET C:54 , TRP C:58 , VAL C:61 , SER C:65 , THR C:66 , ILE C:210 , PHE C:214 , ARG C:221 , HIS C:226 , PHE C:227 , THR C:228 , HIS C:231 , HIS C:232 , PHE C:233 , GLY C:234 , CDL C:305 , HOH C:426 , HOH C:440 , HOH C:498 , HOH F:231
binding site for residue PGV C 304
15
AD6
SOFTWARE
MET C:51 , LEU C:52 , MET C:54 , TYR C:55 , ARG C:59 , ILE C:62 , ARG C:63 , PHE C:67 , THR C:213 , PHE C:220 , ARG C:221 , LYS C:224 , HIS C:226 , PGV C:304 , HOH C:413 , HOH C:529 , LYS J:8
binding site for residue CDL C 305
16
AD7
SOFTWARE
ARG C:156 , GLN C:161 , PHE C:164 , LEU C:223 , HOH C:496 , PHE J:1
binding site for residue CHD C 306
17
AD8
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , HOH A:716 , TRP C:99 , HIS C:103 , HOH C:446 , HOH C:463 , HOH C:493 , HOH C:513 , HOH C:523 , HOH C:533 , LEU P:127
binding site for residue CHD C 307
18
AD9
SOFTWARE
LYS C:157 , HIS C:158 , GLN C:161 , ALA F:1 , ARG G:17 , PHE G:21 , CDL G:101 , CHD G:103 , ILE N:311 , GLN O:59
binding site for residue PEK C 308
19
AE1
SOFTWARE
THR C:95 , TRP C:99 , TYR C:102 , HIS C:103 , LEU C:106 , ALA C:107 , HOH C:448 , HOH C:466 , HOH C:495 , HOH C:512 , ASN H:24 , ALA T:1
binding site for residue PGV C 309
20
AE2
SOFTWARE
TRP A:334 , GLY A:343 , LEU B:39 , ILE B:42 , LYS B:49 , HOH B:572 , ARG D:73 , THR D:75 , GLU D:77 , TRP D:78 , HOH D:346 , HOH D:373 , ARG I:16
binding site for residue TGL D 201
21
AE3
SOFTWARE
CYS F:60 , CYS F:62 , CYS F:82 , CYS F:85
binding site for residue ZN F 101
22
AE4
SOFTWARE
ASN C:125 , LEU C:127 , LEU C:131 , PEK C:308 , HOH C:481 , TPO G:11 , SER G:27 , LEU G:30 , CYS G:31 , ASN G:34 , LEU G:37 , HIS G:38 , HOH G:216 , HOH G:258 , HOH G:267 , HOH G:271 , PHE N:282 , ILE N:286 , ASP N:300 , SER N:307 , ILE N:311 , LEU O:78 , LEU O:81
binding site for residue CDL G 101
23
AE5
SOFTWARE
SER G:2 , ALA G:3 , LYS G:5 , GLY G:6 , HIS G:8 , HOH G:246 , HOH G:259 , HOH G:270 , LYS P:77 , ARG P:80 , ILE P:84 , VAL P:91 , THR P:95 , PHE P:98 , TRP P:240 , VAL P:247
binding site for residue PEK G 102
24
AE6
SOFTWARE
PEK C:308 , ARG G:14 , ARG G:17 , PHE G:18 , PHE G:21 , GLY G:22 , HOH G:206 , HOH G:220 , HOH G:236 , MET N:271 , GLN O:59 , GLU O:62 , THR O:63 , HOH O:417
binding site for residue CHD G 103
25
AE7
SOFTWARE
TYR J:32 , ARG J:33 , MET J:36 , THR J:37
binding site for residue CHD J 101
26
AE8
SOFTWARE
THR A:17 , LEU A:21 , PHE A:22 , TRP A:25 , PHE A:400 , SER A:401 , ILE L:11 , PRO L:12 , PHE L:13 , SER L:14 , ARG L:20 , MET L:24 , SER L:31 , HOH L:239
binding site for residue TGL L 101
27
AE9
SOFTWARE
TRP D:98 , LEU M:28 , TRP M:32 , TYR M:35 , HIS M:36 , HOH M:215 , HOH M:226
binding site for residue DMU M 101
28
AG2
SOFTWARE
ALA G:1 , TRP P:99 , HIS P:103 , ALA P:107 , CHD P:307 , HOH P:403 , HOH P:418 , HOH P:461 , HOH P:470 , HOH P:536 , HOH P:545 , ASN U:24
binding site for residue PGV P 301
29
AH3
SOFTWARE
LYS C:77 , ARG C:80 , ILE C:84 , VAL C:91 , PHE C:98 , TRP C:240 , VAL C:247 , SER T:2 , ALA T:3 , LYS T:5 , GLY T:6 , HIS T:8 , TPO T:11 , HOH T:221
binding site for residue PEK T 102
30
AH4
SOFTWARE
SER A:279 , ILE A:311 , CHD B:303 , LYS P:157 , HIS P:158 , GLN P:161 , THR P:168 , TYR P:172 , ALA S:1 , ARG T:17 , GLY T:22 , CDL T:104 , HOH T:206
binding site for residue PEK T 103
31
AH5
SOFTWARE
ILE A:286 , ASP A:300 , SER A:307 , ILE A:311 , ALA B:77 , LEU B:78 , LEU B:81 , TYR B:85 , HOH C:446 , ASN P:125 , LEU P:127 , SER P:135 , TYR P:253 , SER T:27 , LEU T:30 , CYS T:31 , ASN T:34 , LEU T:37 , HIS T:38 , PEK T:103 , HOH T:223 , HOH T:250
binding site for residue CDL T 104
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SAPs(SNPs)/Variants
(0, 0)
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