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5G0R
Asym. Unit
Info
Asym.Unit (868 KB)
Biol.Unit 1 (856 KB)
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(1)
Title
:
METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENSIS EXPOSED TO 3-NITROOXYPROPANOL
Authors
:
T. Wagner
Date
:
22 Mar 16 (Deposition) - 13 Apr 16 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Transferase, Methyl-Coenzymem, Methyl-Coenzymem Reductase Exposed To 3-Nitrooxypropanol, Posttranslational Modification, Binding Sites, Catalysis, Coenzymes, Disulfides, Hydrogen, Ligands, Mesna, Metalloporphyrins, Methane, Methanobacterium, Nickel, Oxidation- Reduction, Oxdoreductases, Phosphothreonine, Thioglycine, 3- Nitrooxypropanol, Inhibitor, Greenhouse Gas
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. C. Duin, T. Wagner, S. Shima, D. Prakash, B. Cronin, D. R. Yanez-Ruiz S. Duval, R. Rumbeli, R. T. Stemmler, R. K. Thauer, M. Kindermann
Mode Of Action Uncovered For The Specific Reduction Of Methane Emissions From Ruminants By The Small Molecule 3-Nitrooxypropanol.
Proc. Natl. Acad. Sci. Usa V. 113 6172 2016
[
close entry info
]
Hetero Components
(12, 41)
Info
All Hetero Components
01a: 5-METHYL-ARGININE (AGMa)
01b: 5-METHYL-ARGININE (AGMb)
02a: CHLORIDE ION (CLa)
02b: CHLORIDE ION (CLb)
02c: CHLORIDE ION (CLc)
03a: DIDEHYDROASPARTATE (DYAa)
03b: DIDEHYDROASPARTATE (DYAb)
04a: FACTOR 430 (F43a)
04b: FACTOR 430 (F43b)
05a: THIOGLYCIN (GL3a)
05b: THIOGLYCIN (GL3b)
06a: POTASSIUM ION (Ka)
08a: 2-METHYL-GLUTAMINE (MGNa)
08b: 2-METHYL-GLUTAMINE (MGNb)
07a: MAGNESIUM ION (MGa)
07b: MAGNESIUM ION (MGb)
07c: MAGNESIUM ION (MGc)
07d: MAGNESIUM ION (MGd)
07e: MAGNESIUM ION (MGe)
07f: MAGNESIUM ION (MGf)
07g: MAGNESIUM ION (MGg)
07h: MAGNESIUM ION (MGh)
07i: MAGNESIUM ION (MGi)
07j: MAGNESIUM ION (MGj)
07k: MAGNESIUM ION (MGk)
07l: MAGNESIUM ION (MGl)
07m: MAGNESIUM ION (MGm)
07n: MAGNESIUM ION (MGn)
08o: MAGNESIUM ION (MGo)
08p: MAGNESIUM ION (MGp)
08q: MAGNESIUM ION (MGq)
08r: MAGNESIUM ION (MGr)
09a: N1-METHYLATED HISTIDINE (MHSa)
09b: N1-METHYLATED HISTIDINE (MHSb)
10a: SODIUM ION (NAa)
10b: SODIUM ION (NAb)
10c: SODIUM ION (NAc)
11a: S-METHYLCYSTEINE (SMCa)
11b: S-METHYLCYSTEINE (SMCb)
12a: COENZYME B (TP7a)
12b: COENZYME B (TP7b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
2
CL
3
Ligand/Ion
CHLORIDE ION
3
DYA
2
Mod. Amino Acid
DIDEHYDROASPARTATE
4
F43
2
Ligand/Ion
FACTOR 430
5
GL3
2
Mod. Amino Acid
THIOGLYCIN
6
K
1
Ligand/Ion
POTASSIUM ION
7
MG
18
Ligand/Ion
MAGNESIUM ION
8
MGN
2
Mod. Amino Acid
2-METHYL-GLUTAMINE
9
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
10
NA
3
Ligand/Ion
SODIUM ION
11
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
12
TP7
2
Ligand/Ion
COENZYME B
[
close Hetero Component info
]
Sites
(28, 28)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:2258 , HOH A:2261 , HOH A:2630 , HOH A:2631
BINDING SITE FOR RESIDUE MG A 551
02
AC2
SOFTWARE
HOH A:2576 , HOH A:2579 , HOH A:2589 , HOH A:2632 , HOH A:2633 , HOH A:2634
BINDING SITE FOR RESIDUE MG A 553
03
AC3
SOFTWARE
ALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:2267 , HOH A:2271 , HOH A:2272 , HOH A:2273 , HOH A:2375 , 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 , HOH D:2395 , HOH D:2451 , 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:2145 , HOH F:2167
BINDING SITE FOR RESIDUE F43 A 554
04
AC4
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , PHE A:330 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:2411 , HOH A:2419 , HOH A:2563 , TYR B:367 , GLY B:369 , HIS B:379 , ILE B:380 , HOH B:2452 , HOH B:2453 , HOH B:2454 , ARG D:225 , LYS D:256 , MHS D:257
BINDING SITE FOR RESIDUE TP7 A 557
05
AC5
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 1550
06
AC6
SOFTWARE
HOH A:2136 , HOH A:2138 , HOH A:2635 , ASN B:441 , HOH D:2257 , HOH D:2283
BINDING SITE FOR RESIDUE MG A 562
07
AC7
SOFTWARE
LYS A:11 , PHE A:14 , HOH A:2033 , HOH A:2034 , HOH A:2035 , HOH A:2046
BINDING SITE FOR RESIDUE MG A 563
08
AC8
SOFTWARE
PRO A:58 , ILE A:60 , THR A:62 , HOH A:2148 , HOH A:2155 , HOH A:2163
BINDING SITE FOR RESIDUE NA A 564
09
AC9
SOFTWARE
HOH B:2368 , HOH B:2369 , HOH B:2509 , HOH B:2510 , HOH B:2511
BINDING SITE FOR RESIDUE MG B 444
10
BC1
SOFTWARE
GLU C:30 , HOH C:2053 , HOH C:2054 , HOH C:2064 , HOH C:2158 , HOH F:2055
BINDING SITE FOR RESIDUE MG C 250
11
BC2
SOFTWARE
HOH C:2231 , HOH C:2236 , HOH C:2261 , HOH C:2262 , HOH C:2263
BINDING SITE FOR RESIDUE MG C 251
12
BC3
SOFTWARE
HOH D:2505 , HOH D:2507 , HOH D:2508 , HOH D:2518 , HOH E:2062 , HOH E:2181
BINDING SITE FOR RESIDUE MG D 551
13
BC4
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 , HOH A:2456 , HOH A:2457 , HOH A:2514 , SER B:365 , ILE B:366 , TYR B:367 , LEU C:117 , SER C:118 , GLY C:119 , LYS C:153 , SER C:154 , VAL C:155 , HIS C:156 , HIS C:158 , HOH C:2133 , HOH C:2175 , HOH C:2176 , HOH C:2177 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243 , HOH D:2247
BINDING SITE FOR RESIDUE F43 D 552
14
BC5
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , HOH A:2393 , ARG D:270 , LEU D:320 , MET D:324 , SER D:325 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:2353 , HOH D:2360 , HOH D:2491 , TYR E:367 , GLY E:369 , HIS E:379 , ILE E:380 , HOH E:2366 , HOH E:2367
BINDING SITE FOR RESIDUE TP7 D 556
15
BC6
SOFTWARE
LYS D:11 , PHE D:14 , HOH D:2034 , HOH D:2035 , HOH D:2037 , HOH D:2049
BINDING SITE FOR RESIDUE MG D 557
16
BC7
SOFTWARE
HOH A:2265 , HOH A:2268 , PRO D:58 , ILE D:60 , THR D:62 , HOH D:2166
BINDING SITE FOR RESIDUE NA D 558
17
BC8
SOFTWARE
HOH E:2327 , HOH E:2328 , HOH E:2407 , HOH E:2408
BINDING SITE FOR RESIDUE MG E 444
18
BC9
SOFTWARE
ASP E:147 , HOH E:2218 , HOH E:2219 , HOH E:2220 , HOH E:2409
BINDING SITE FOR RESIDUE MG E 445
19
CC1
SOFTWARE
HOH A:2390 , HOH E:2234 , HOH E:2260 , HOH E:2261 , HOH E:2410 , HOH E:2411 , HOH E:2412
BINDING SITE FOR RESIDUE MG E 446
20
CC2
SOFTWARE
HOH C:2052 , GLU F:30 , HOH F:2056 , HOH F:2057 , HOH F:2068 , HOH F:2155
BINDING SITE FOR RESIDUE MG F 250
21
CC3
SOFTWARE
ARG B:235 , LEU C:248
BINDING SITE FOR RESIDUE CL B 1444
22
CC4
SOFTWARE
ARG E:235 , HOH E:2139 , LEU F:248
BINDING SITE FOR RESIDUE CL E 1444
23
CC5
SOFTWARE
GLY A:61 , HIS D:131
BINDING SITE FOR RESIDUE CL A 1551
24
CC6
SOFTWARE
HOH A:2636 , HOH A:2637 , HOH A:2638 , HOH B:2290 , HOH B:2322 , HOH B:2323
BINDING SITE FOR RESIDUE MG A 1500
25
CC7
SOFTWARE
ASP E:99 , THR E:101 , HOH E:2162 , HOH E:2182 , HOH E:2183 , HOH E:2413
BINDING SITE FOR RESIDUE MG E 1500
26
CC8
SOFTWARE
HOH D:2411 , HOH D:2412 , HOH D:2539 , HOH D:2540 , HOH D:2541 , HOH D:2542
BINDING SITE FOR RESIDUE MG D 1500
27
CC9
SOFTWARE
HOH A:2301 , HOH A:2302 , HOH A:2640
BINDING SITE FOR RESIDUE MG A 1501
28
DC1
SOFTWARE
HIS A:131 , GLY D:61
BINDING SITE FOR RESIDUE NA A 1502
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
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Note:
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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Info
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Sorry, no Info available
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CATH Domains
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Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Info
all PFAM domains
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Sorry, no Info available
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)
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