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3POT
Asym. Unit
Info
Asym.Unit (877 KB)
Biol.Unit 1 (866 KB)
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(1)
Title
:
STRUCTURAL ANALYSIS OF A NI(III)-METHYL SPECIES IN METHYL-COENZYME M REDUCTASE FROM METHANOTHERMOBACTER MARBURGENSIS
Authors
:
P. E. Cedervall, C. M. Wilmot
Date
:
23 Nov 10 (Deposition) - 13 Apr 11 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Metal-Binding, Nickel, Methyl-Coenzyme M Reductase, Methanogenesis, Methylation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. E. Cedervall, M. Dey, X. Li, R. Sarangi, B. Hedman, S. W. Ragsdale, C. M. Wilmot
Structural Analysis Of A Ni-Methyl Species In Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis.
J. Am. Chem. Soc. V. 133 5626 2011
[
close entry info
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Hetero Components
(13, 34)
Info
All Hetero Components
01a: IODOMETHANE (06Ca)
01b: IODOMETHANE (06Cb)
02a: 5-METHYL-ARGININE (AGMa)
02b: 5-METHYL-ARGININE (AGMb)
03a: 1-THIOETHANESULFONIC ACID (COMa)
03b: 1-THIOETHANESULFONIC ACID (COMb)
04a: 1,2-ETHANEDIOL (EDOa)
05a: FACTOR 430 (F43a)
05b: FACTOR 430 (F43b)
06a: THIOGLYCIN (GL3a)
06b: THIOGLYCIN (GL3b)
07a: POTASSIUM ION (Ka)
09a: 2-METHYL-GLUTAMINE (MGNa)
09b: 2-METHYL-GLUTAMINE (MGNb)
08a: MAGNESIUM ION (MGa)
08b: MAGNESIUM ION (MGb)
08c: MAGNESIUM ION (MGc)
08d: MAGNESIUM ION (MGd)
08e: MAGNESIUM ION (MGe)
08f: MAGNESIUM ION (MGf)
08g: MAGNESIUM ION (MGg)
08h: MAGNESIUM ION (MGh)
08i: MAGNESIUM ION (MGi)
08j: MAGNESIUM ION (MGj)
08k: MAGNESIUM ION (MGk)
08l: MAGNESIUM ION (MGl)
10a: N1-METHYLATED HISTIDINE (MHSa)
10b: N1-METHYLATED HISTIDINE (MHSb)
11a: S-METHYLCYSTEINE (SMCa)
11b: S-METHYLCYSTEINE (SMCb)
12a: COENZYME B (TP7a)
12b: COENZYME B (TP7b)
13a: O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)... (TXZa)
13b: O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)... (TXZb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
06C
2
Ligand/Ion
IODOMETHANE
2
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
3
COM
2
Ligand/Ion
1-THIOETHANESULFONIC ACID
4
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
5
F43
2
Ligand/Ion
FACTOR 430
6
GL3
2
Mod. Amino Acid
THIOGLYCIN
7
K
1
Ligand/Ion
POTASSIUM ION
8
MG
12
Ligand/Ion
MAGNESIUM ION
9
MGN
2
Mod. Amino Acid
2-METHYL-GLUTAMINE
10
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
11
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
12
TP7
2
Ligand/Ion
COENZYME B
13
TXZ
2
Ligand/Ion
O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)-L-THREONINE
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:850 , HOH A:3425 , HOH D:899
BINDING SITE FOR RESIDUE MG A 551
02
AC2
SOFTWARE
HOH A:600 , HOH A:725 , HOH A:1212 , HOH A:1508 , HOH A:1856 , HOH A:2090
BINDING SITE FOR RESIDUE MG A 552
03
AC3
SOFTWARE
HOH A:1159 , HOH A:1212 , HOH A:1456 , HOH A:1481 , HOH A:1508 , HOH A:1968
BINDING SITE FOR RESIDUE MG A 553
04
AC4
SOFTWARE
HOH A:1037 , HOH A:1115 , HOH A:3449 , HOH A:3450
BINDING SITE FOR RESIDUE MG A 554
05
AC5
SOFTWARE
ALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:577 , HOH A:615 , HOH A:619 , HOH A:624 , HOH A:671 , HOH A:747 , GLY D:326 , GLY D:327 , VAL D:328 , GLY D:329 , PHE D:330 , THR D:331 , GLN D:332 , TYR D:333 , PHE D:396 , GLY D:397 , GLY D:442 , PHE D:443 , COM D:555 , 06C D:556 , HOH D:626 , SER E:365 , ILE E:366 , TYR E:367 , LEU F:117 , SER F:118 , GLY F:119 , LYS F:153 , SER F:154 , VAL F:155 , HIS F:156 , HIS F:158 , HOH F:262
BINDING SITE FOR RESIDUE F43 A 555
06
AC6
SOFTWARE
TYR A:333 , PHE A:443 , TYR A:444 , HOH A:733 , PHE B:361 , TYR B:367 , LEU C:117 , ARG C:120 , F43 D:552
BINDING SITE FOR RESIDUE COM A 556
07
AC7
SOFTWARE
ARG A:270 , MET A:324 , PHE A:330 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:613 , HOH A:628 , HOH A:637 , HOH A:715 , HOH A:726 , GLY B:368 , GLY B:369 , HIS B:379 , ILE B:380 , ARG D:225 , LYS D:256 , MHS D:257
BINDING SITE FOR RESIDUE TXZ A 557
08
AC8
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , SER A:325 , PHE A:330 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:613 , HOH A:628 , HOH A:637 , HOH A:715 , HOH A:726 , TYR B:367 , GLY B:368 , GLY B:369 , HIS B:379 , ILE B:380 , ARG D:225 , LYS D:256 , MHS D:257
BINDING SITE FOR RESIDUE TP7 A 558
09
AC9
SOFTWARE
TYR A:333 , TYR B:367 , F43 D:552
BINDING SITE FOR RESIDUE 06C A 559
10
BC1
SOFTWARE
ARG A:102 , SER A:215 , ARG A:216 , CYS A:218 , ARG D:102 , SER D:215 , ARG D:216 , CYS D:218
BINDING SITE FOR RESIDUE K A 561
11
BC2
SOFTWARE
HOH B:1103 , HOH B:1305 , HOH B:2344 , HOH B:3452 , HOH B:3453
BINDING SITE FOR RESIDUE MG B 444
12
BC3
SOFTWARE
ASP B:271 , HOH B:670 , HOH B:976 , HOH B:1040 , HOH B:1911 , HOH B:2168
BINDING SITE FOR RESIDUE MG B 445
13
BC4
SOFTWARE
GLU C:30 , HOH C:726 , HOH C:3417 , HOH C:3418 , HOH C:3419 , HOH C:3420
BINDING SITE FOR RESIDUE MG C 250
14
BC5
SOFTWARE
HOH A:3614 , HOH C:1328 , HOH C:1849
BINDING SITE FOR RESIDUE MG C 251
15
BC6
SOFTWARE
HOH D:1211 , HOH D:1613 , HOH D:3428 , HOH D:3429 , HOH D:3430 , HOH E:1573
BINDING SITE FOR RESIDUE MG D 551
16
BC7
SOFTWARE
GLY A:326 , GLY A:327 , VAL A:328 , GLY A:329 , PHE A:330 , THR A:331 , GLN A:332 , TYR A:333 , PHE A:396 , GLY A:397 , GLY A:442 , PHE A:443 , COM A:556 , 06C A:559 , HOH A:609 , SER B:365 , ILE B:366 , TYR B:367 , LEU C:117 , SER C:118 , GLY C:119 , ARG C:120 , LYS C:153 , SER C:154 , VAL C:155 , HIS C:156 , HIS C:158 , HOH C:264 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243 , HOH D:582 , HOH D:610 , HOH D:619 , HOH D:640 , HOH D:649 , HOH D:700
BINDING SITE FOR RESIDUE F43 D 552
17
BC8
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:568 , HOH D:580 , HOH D:606 , HOH D:607 , HOH D:716 , PHE E:362 , TYR E:367 , GLY E:368 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE TP7 D 553
18
BC9
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , MET D:324 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:568 , HOH D:580 , HOH D:606 , HOH D:607 , HOH D:716 , PHE E:362 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE TXZ D 554
19
CC1
SOFTWARE
F43 A:555 , TYR D:333 , PHE D:443 , TYR D:444 , HOH D:713 , PHE E:361 , SER E:365 , TYR E:367 , LEU F:117 , ARG F:120
BINDING SITE FOR RESIDUE COM D 555
20
CC2
SOFTWARE
F43 A:555 , TYR D:333 , TYR E:367
BINDING SITE FOR RESIDUE 06C D 556
21
CC3
SOFTWARE
TYR D:348
BINDING SITE FOR RESIDUE EDO D 558
22
CC4
SOFTWARE
HOH E:1993 , HOH E:2253 , HOH E:3439 , HOH E:3440
BINDING SITE FOR RESIDUE MG E 444
23
CC5
SOFTWARE
HOH C:3555 , ASP E:147 , HOH E:1070 , HOH E:1373 , HOH E:3557
BINDING SITE FOR RESIDUE MG E 445
24
CC6
SOFTWARE
GLU F:30 , HOH F:635 , HOH F:648 , HOH F:3422 , HOH F:3423 , HOH F:3424
BINDING SITE FOR RESIDUE MG F 250
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d3pota2 (A:270-549)
1b: SCOP_d3potb2 (B:189-443)
1c: SCOP_d3potd2 (D:270-549)
1d: SCOP_d3pote2 (E:189-443)
2a: SCOP_d3pota1 (A:2-269)
2b: SCOP_d3potb1 (B:2-188)
2c: SCOP_d3potd1 (D:2-269)
2d: SCOP_d3pote1 (E:2-188)
3a: SCOP_d3potc_ (C:)
3b: SCOP_d3potf_ (F:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Superfamily
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Family
:
automated matches
(2)
Protein domain
:
automated matches
(2)
Methanothermobacter marburgensis [TaxId: 145263]
(1)
1a
d3pota2
A:270-549
1b
d3potb2
B:189-443
1c
d3potd2
D:270-549
1d
d3pote2
E:189-443
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Methyl-coenzyme M reductase subunits
(42)
Family
:
automated matches
(2)
Protein domain
:
automated matches
(2)
Methanothermobacter marburgensis [TaxId: 145263]
(1)
2a
d3pota1
A:2-269
2b
d3potb1
B:2-188
2c
d3potd1
D:2-269
2d
d3pote1
E:2-188
Family
:
Methyl-coenzyme M reductase gamma chain
(14)
Protein domain
:
Methyl-coenzyme M reductase gamma chain
(14)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(12)
3a
d3potc_
C:
3b
d3potf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_MCR_alpha_3potD01 (D:316-441)
1b: PFAM_MCR_alpha_3potD02 (D:316-441)
2a: PFAM_MCR_alpha_N_3potD03 (D:2-268)
2b: PFAM_MCR_alpha_N_3potD04 (D:2-268)
3a: PFAM_MCR_beta_3potE01 (E:189-442)
3b: PFAM_MCR_beta_3potE02 (E:189-442)
4a: PFAM_MCR_beta_N_3potE03 (E:6-187)
4b: PFAM_MCR_beta_N_3potE04 (E:6-187)
5a: PFAM_MCR_gamma_3potF01 (F:2-247)
5b: PFAM_MCR_gamma_3potF02 (F:2-247)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: MCR_alpha]
(8)
Family
:
MCR_alpha
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
1a
MCR_alpha-3potD01
D:316-441
1b
MCR_alpha-3potD02
D:316-441
Clan
:
no clan defined [family: MCR_alpha_N]
(8)
Family
:
MCR_alpha_N
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
2a
MCR_alpha_N-3potD03
D:2-268
2b
MCR_alpha_N-3potD04
D:2-268
Clan
:
no clan defined [family: MCR_beta]
(8)
Family
:
MCR_beta
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
3a
MCR_beta-3potE01
E:189-442
3b
MCR_beta-3potE02
E:189-442
Clan
:
no clan defined [family: MCR_beta_N]
(8)
Family
:
MCR_beta_N
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
4a
MCR_beta_N-3potE03
E:6-187
4b
MCR_beta_N-3potE04
E:6-187
Clan
:
no clan defined [family: MCR_gamma]
(8)
Family
:
MCR_gamma
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
5a
MCR_gamma-3potF01
F:2-247
5b
MCR_gamma-3potF02
F:2-247
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