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Magnesium in PDB 5a0y: Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y was solved by T.Wagner, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.35 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.227, 118.300, 122.560, 90.00, 91.90, 90.00
R / Rfree (%) 11.1 / 12.9

Other elements in 5a0y:

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Potassium (K) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution (pdb code 5a0y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 5a0y

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Magnesium binding site 1 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg551

b:18.6
occ:1.00
 O A:HOH2285 2.0 19.2 1.0
O A:HOH2281 2.0 20.1 1.0
O A:HOH2670 2.1 20.8 1.0
O D:HOH2174 4.0 41.5 1.0
O A:HOH2362 4.2 31.7 1.0
OE2 A:GLU134 4.2 19.3 1.0
O D:HOH2175 4.3 21.0 1.0
OE1 A:GLU134 4.3 18.0 1.0
O A:HOH2329 4.4 24.0 1.0
CG D:PRO54 4.7 11.4 1.0
CD A:GLU134 4.8 16.5 1.0

Magnesium binding site 2 out of 16 in 5a0y

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Magnesium binding site 2 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg553

b:11.8
occ:0.48
 O A:HOH2672 2.0 22.8 1.0
O A:HOH2621 2.0 32.1 1.0
O A:HOH2671 2.0 25.9 1.0
O A:HOH2631 2.1 24.4 1.0
O A:HOH2619 2.1 19.2 1.0
O A:HOH2617 2.1 22.6 1.0
O A:HOH2616 4.2 15.1 1.0
OD2 A:ASP521 4.4 13.9 1.0
O A:ASP516 4.5 12.5 1.0
OD1 A:ASP516 4.5 26.1 1.0
O A:HOH2627 4.6 16.6 1.0
O A:HOH2629 4.6 31.8 1.0
CG A:ASP521 4.7 11.2 1.0
CB A:ASP521 4.7 9.6 1.0
CB A:ASP516 4.8 17.6 1.0

Magnesium binding site 3 out of 16 in 5a0y

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Magnesium binding site 3 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg562

b:18.4
occ:1.00
 O A:HOH2149 2.3 23.1 1.0
O A:HOH2684 2.3 15.7 1.0
O A:HOH2682 2.3 24.3 1.0
O A:HOH2685 2.4 15.1 1.0
O A:HOH2152 2.5 15.2 1.0
O A:HOH2683 3.6 35.7 1.0
O D:HOH2318 3.9 39.0 1.0
O A:HOH2150 4.1 37.2 1.0
O D:HOH2281 4.2 12.7 1.0
O A:GLY52 4.2 11.1 1.0
OD1 D:ASN517 4.3 10.3 1.0
O D:HOH2538 4.5 42.5 1.0
O D:ALA179 4.7 10.9 1.0
NZ D:LYS164 4.8 9.6 1.0
CA D:ALA179 4.8 10.7 1.0
O D:PRO178 4.9 11.3 1.0
O A:ARG51 5.0 9.7 1.0
C A:GLY52 5.0 9.5 1.0

Magnesium binding site 4 out of 16 in 5a0y

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Magnesium binding site 4 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg563

b:23.1
occ:1.00
 O A:LYS11 2.2 18.1 1.0
O A:HOH2035 2.2 31.9 1.0
O A:HOH2034 2.2 23.9 1.0
O A:PHE14 2.4 18.4 1.0
O A:HOH2050 2.4 30.2 1.0
O A:HOH2036 2.4 31.9 1.0
C A:LYS11 3.2 16.9 1.0
C A:PHE14 3.5 17.5 1.0
CA A:LYS11 3.8 15.6 1.0
CA A:GLU15 3.8 23.4 1.0
O A:GLU15 4.0 20.4 1.0
C A:GLU15 4.1 19.7 1.0
N A:GLU15 4.1 19.7 1.0
CB A:LYS11 4.2 17.0 1.0
N A:LYS12 4.4 16.6 1.0
O A:GLU16 4.5 17.8 1.0
O A:HOH2023 4.5 34.6 1.0
O A:HOH2033 4.5 28.7 1.0
N A:PHE14 4.6 15.8 1.0
CA A:PHE14 4.6 15.7 1.0
CA A:LYS12 4.8 18.0 1.0
C A:LYS12 4.9 17.6 1.0
CD A:GLU15 5.0 62.3 1.0
O A:LEU10 5.0 14.4 1.0
N A:GLU16 5.0 17.8 1.0

Magnesium binding site 5 out of 16 in 5a0y

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Magnesium binding site 5 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg444

b:25.9
occ:1.00
 O B:HOH2551 2.0 34.3 1.0
O B:HOH2400 2.0 21.6 1.0
O B:HOH2552 2.1 35.8 1.0
O B:HOH2401 2.1 21.6 1.0
O B:HOH2550 2.1 32.6 1.0
ND2 B:ASN250 4.1 17.7 1.0
OD1 B:ASP254 4.1 17.4 1.0
OD2 B:ASP254 4.1 16.3 1.0
O B:HOH2407 4.1 34.8 1.0
O B:HOH2038 4.3 35.2 1.0
O B:HOH2403 4.4 37.8 1.0
CG B:ASP254 4.5 15.6 1.0

Magnesium binding site 6 out of 16 in 5a0y

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Magnesium binding site 6 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg445

b:20.9
occ:0.23
 OD1 B:ASP271 1.9 18.3 1.0
O B:HOH2423 2.1 23.8 1.0
O B:HOH2426 2.1 38.7 1.0
O B:HOH2427 2.1 41.4 1.0
O B:HOH2553 2.3 45.2 1.0
O B:HOH2409 2.7 30.9 1.0
CG B:ASP271 2.9 16.2 1.0
OD2 B:ASP271 3.3 17.0 1.0
O B:HOH2410 3.6 38.4 1.0
O B:HOH2220 4.2 35.0 1.0
CB B:ASP271 4.3 14.6 1.0
OE1 B:GLU274 4.4 38.9 0.4
O B:SER267 4.5 13.1 1.0
CA B:ASP271 4.5 13.7 1.0
N B:ASP271 4.6 13.1 1.0
OE2 B:GLU274 4.7 39.2 0.4
CD B:GLU274 4.8 36.5 0.4
CB B:ALA270 5.0 15.0 1.0
OE2 B:GLU274 5.0 38.2 0.6

Magnesium binding site 7 out of 16 in 5a0y

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Magnesium binding site 7 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg250

b:16.1
occ:1.00
 OE2 C:GLU30 2.1 14.7 1.0
O C:HOH2182 2.1 18.1 1.0
O C:HOH2067 2.1 16.5 1.0
O C:HOH2066 2.1 16.1 1.0
O C:HOH2076 2.1 16.2 1.0
CD C:GLU30 3.1 14.2 1.0
OE1 C:GLU30 3.4 14.6 1.0
NZ C:LYS135 3.9 24.0 1.0
O C:HOH2077 4.0 17.7 1.0
O C:ILE31 4.1 15.6 1.0
O C:HOH2068 4.1 27.6 1.0
O C:HOH2085 4.2 32.2 1.0
OE2 C:GLU139 4.2 15.2 1.0
O C:HOH2082 4.4 20.9 1.0
CG C:GLU30 4.4 13.6 1.0
O C:HOH2025 4.4 30.6 1.0
NZ C:LYS27 4.5 15.9 1.0
CE C:LYS135 4.9 22.8 1.0

Magnesium binding site 8 out of 16 in 5a0y

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Magnesium binding site 8 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg251

b:12.2
occ:0.27
 O C:HOH2286 2.0 16.1 0.3
O C:HOH2285 2.1 31.5 1.0
O C:HOH2287 2.1 16.3 0.4
O C:HOH2264 2.2 26.3 1.0
O C:HOH2256 2.3 14.9 0.3
O A:HOH2542 4.0 33.8 1.0
O C:HOH2255 4.1 22.4 1.0
O C:HOH2260 4.2 32.1 1.0
O C:HOH2263 4.5 22.1 1.0
OD1 C:ASP226 4.7 16.4 1.0
NE C:ARG225 4.8 15.8 1.0
CD C:ARG225 4.9 15.0 1.0

Magnesium binding site 9 out of 16 in 5a0y

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Magnesium binding site 9 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg551

b:20.5
occ:1.00
 O D:HOH2569 2.0 23.5 1.0
O D:HOH2536 2.0 29.2 1.0
O D:HOH2533 2.0 19.6 1.0
O D:HOH2546 2.1 21.4 1.0
O D:HOH2535 2.1 21.1 1.0
O D:HOH2532 4.1 15.8 1.0
OD1 D:ASP516 4.4 22.2 1.0
O D:HOH2541 4.4 35.8 1.0
O D:ASP516 4.5 11.4 1.0
OD2 D:ASP521 4.5 12.8 1.0
O D:HOH2543 4.6 18.0 1.0
CG D:ASP521 4.7 10.1 1.0
O D:HOH2544 4.7 31.9 1.0
CB D:ASP521 4.7 8.5 1.0
CB D:ASP516 4.8 15.2 1.0
CG D:ASP516 5.0 20.4 1.0

Magnesium binding site 10 out of 16 in 5a0y

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Magnesium binding site 10 out of 16 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg557

b:21.3
occ:1.00
 O D:LYS11 2.2 17.7 1.0
O D:HOH2038 2.3 18.9 1.0
O D:HOH2039 2.4 27.3 1.0
O D:PHE14 2.4 17.4 1.0
O D:HOH2037 2.4 29.5 1.0
O D:HOH2053 2.4 26.7 1.0
C D:LYS11 3.3 16.2 1.0
C D:PHE14 3.5 17.4 1.0
CA D:LYS11 3.8 15.7 1.0
CA D:GLU15 3.9 26.9 1.0
O D:GLU15 4.0 18.7 1.0
C D:GLU15 4.1 19.9 1.0
N D:GLU15 4.2 19.6 1.0
CB D:LYS11 4.2 17.0 1.0
N D:LYS12 4.5 16.7 1.0
N D:PHE14 4.5 14.9 1.0
O D:GLU16 4.5 16.0 1.0
O D:HOH2040 4.6 28.8 1.0
CA D:PHE14 4.6 16.2 1.0
CA D:LYS12 4.8 18.0 1.0
OE1 D:GLU15 4.9 88.9 1.0
O D:HOH2054 4.9 34.1 1.0
C D:LYS12 4.9 16.8 1.0
O D:LEU10 4.9 13.9 1.0
CD D:GLU15 4.9 82.7 1.0
N D:GLU16 5.0 16.1 1.0

Reference:

T.Wagner, J.Kahnt, U.Ermler, S.Shima. Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. V. 55 10630 2016.
ISSN: ISSN 1433-7851
PubMed: 27467699
DOI: 10.1002/ANIE.201603882
Page generated: Sun Sep 29 00:13:55 2024

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