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Magnesium in PDB 7b2h: Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon

Enzymatic activity of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon

All present enzymatic activity of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h was solved by T.Wagner, O.N.Lemaire, S.Engilberge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.719, 116.386, 123.07, 90, 92.36, 90
R / Rfree (%) 17.7 / 20.4

Other elements in 7b2h:

The structure of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Xenon (Xe) 12 atoms
Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon (pdb code 7b2h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 7b2h

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Magnesium binding site 1 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:72.4
occ:1.00
 O A:HOH885 2.1 73.1 1.0
O A:HOH901 2.3 74.3 1.0
OE1 A:GLU20 2.6 58.0 1.0
CD A:GLU20 3.8 58.6 1.0
CG A:GLU16 4.1 63.4 1.0
OE2 A:GLU20 4.3 58.6 1.0
O A:LYS22 4.8 62.6 1.0

Magnesium binding site 2 out of 15 in 7b2h

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Magnesium binding site 2 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:99.4
occ:1.00
 OE2 A:GLU19 2.9 57.8 1.0
CD A:GLU19 3.8 58.3 1.0
OE1 A:GLU19 4.2 58.9 1.0

Magnesium binding site 3 out of 15 in 7b2h

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Magnesium binding site 3 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:80.8
occ:1.00
 O D:HOH886 2.4 64.1 1.0
OE2 D:GLU275 2.4 37.7 1.0
O D:HOH722 2.8 60.1 1.0
O A:VAL269 3.0 34.8 1.0
CD D:GLU275 3.3 35.3 1.0
O A:ARG270 3.4 35.6 1.0
OE1 D:GLU275 3.6 36.1 1.0
C A:ARG270 3.9 34.3 1.0
O D:HOH817 3.9 30.9 1.0
C A:VAL269 4.0 35.6 1.0
CA A:ARG270 4.1 34.3 1.0
CD2 D:TYR266 4.3 31.4 1.0
CB A:ALA272 4.4 28.7 1.0
N A:ALA272 4.4 30.9 1.0
N A:ARG270 4.6 35.0 1.0
CG1 A:VAL269 4.6 35.5 1.0
NH2 D:ARG225 4.6 33.2 1.0
O A:HOH893 4.7 58.0 1.0
O A:HOH743 4.7 31.9 1.0
CE2 D:TYR266 4.7 34.3 1.0
CG D:GLU275 4.7 33.5 1.0
N A:AGM271 4.8 31.9 1.0
CG D:TYR266 4.9 32.2 1.0

Magnesium binding site 4 out of 15 in 7b2h

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Magnesium binding site 4 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:97.5
occ:1.00
 OD1 A:ASP356 2.9 85.6 1.0
OD2 A:ASP356 3.2 84.6 1.0
CG A:ASP356 3.4 84.0 1.0
CB A:ASP356 4.9 80.5 1.0

Magnesium binding site 5 out of 15 in 7b2h

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Magnesium binding site 5 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:80.5
occ:1.00
 O B:HOH687 2.2 76.8 1.0
O B:HOH673 2.3 70.2 1.0
OD1 B:ASP271 2.3 66.8 1.0
CG B:ASP271 3.2 65.0 1.0
OD2 B:ASP271 3.4 66.0 1.0
OE1 B:GLU274 4.1 87.5 1.0
O B:HOH747 4.5 76.5 1.0
CB B:ASP271 4.6 61.9 1.0
CA B:ASP271 4.9 58.4 1.0

Magnesium binding site 6 out of 15 in 7b2h

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Magnesium binding site 6 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:76.6
occ:1.00
 OD1 B:ASP147 2.4 64.8 1.0
O F:HOH717 2.7 53.5 1.0
CG B:ASP147 3.3 64.3 1.0
OD2 B:ASP147 3.7 65.5 1.0
O B:VAL148 4.0 48.5 1.0
O B:HOH683 4.2 48.5 1.0
O B:ASP147 4.3 56.2 1.0
O F:LEU248 4.3 64.0 1.0
C F:LEU248 4.6 63.1 1.0
C B:ASP147 4.6 56.1 1.0
CB B:ASP147 4.6 62.4 1.0
CA B:ASP147 4.7 58.9 1.0
C B:VAL148 4.8 49.8 1.0
CA B:SER149 4.8 51.3 1.0

Magnesium binding site 7 out of 15 in 7b2h

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Magnesium binding site 7 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:103.2
occ:1.00
 OD2 B:ASP13 2.2 81.4 1.0
CG B:ASP13 3.0 81.5 1.0
OE2 B:GLU427 3.1 86.3 1.0
OD1 B:ASP13 3.2 82.9 1.0
CD B:GLU427 4.1 84.3 1.0
NZ B:LYS430 4.2 92.8 1.0
CB B:ASP13 4.4 79.7 1.0
CL B:CL512 4.5 64.3 1.0
NE2 B:GLN210 4.6 57.9 1.0
OE1 B:GLU427 4.8 86.0 1.0
CE B:LYS430 4.8 92.0 1.0
ND2 B:ASN207 4.9 67.5 1.0

Magnesium binding site 8 out of 15 in 7b2h

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Magnesium binding site 8 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:86.3
occ:1.00
 O B:HOH679 2.3 88.6 1.0
O B:LYS3 2.5 56.3 1.0
C B:LYS3 3.6 54.6 1.0
OE2 B:GLU5 4.0 65.4 1.0
CG B:GLU5 4.1 63.3 1.0
N B:PHE4 4.4 52.8 1.0
CA B:PHE4 4.4 51.8 1.0
CA B:LYS3 4.5 57.0 1.0
O B:ALA2 4.6 56.0 1.0
CD B:GLU5 4.6 64.6 1.0
O B:HOH676 4.7 54.0 1.0
C B:PHE4 4.8 52.6 1.0
N B:GLU5 5.0 54.4 1.0

Magnesium binding site 9 out of 15 in 7b2h

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Magnesium binding site 9 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:69.4
occ:1.00
 O D:LYS11 2.1 68.5 1.0
O D:PHE14 2.2 67.1 1.0
C D:LYS11 3.1 68.3 1.0
C D:PHE14 3.5 66.8 1.0
CA D:LYS11 3.5 63.2 1.0
O D:GLU15 3.6 71.7 1.0
CB D:LYS11 3.9 62.6 1.0
O D:GLU16 3.9 68.5 1.0
C D:GLU15 4.0 73.2 1.0
CA D:GLU15 4.1 75.8 1.0
N D:GLU15 4.2 71.0 1.0
N D:LYS12 4.3 70.5 1.0
CA D:PHE14 4.6 65.0 1.0
N D:PHE14 4.6 66.2 1.0
CG D:LYS11 4.7 62.8 1.0
N D:GLU16 4.7 71.6 1.0
CA D:LYS12 4.8 73.0 1.0
O D:LEU10 4.8 53.2 1.0
C D:GLU16 4.8 70.0 1.0
N D:LYS11 4.9 57.9 1.0

Magnesium binding site 10 out of 15 in 7b2h

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Magnesium binding site 10 out of 15 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg608

b:64.1
occ:1.00
 OE2 D:GLU383 2.3 71.4 1.0
CD D:GLU383 3.5 69.0 1.0
O D:HOH848 3.6 70.0 1.0
OE1 D:GLU383 4.1 69.7 1.0
OE1 D:GLU387 4.5 78.7 1.0
CG D:GLU383 4.6 65.2 1.0

Reference:

C.J.Hahn, O.N.Lemaire, J.Kahnt, S.Engilberge, G.Wegener, T.Wagner. Crystal Structure of A Key Enzyme For Anaerobic Ethane Activation. Science V. 373 118 2021.
ISSN: ESSN 1095-9203
PubMed: 34210888
DOI: 10.1126/SCIENCE.ABG1765
Page generated: Wed Oct 2 10:18:29 2024

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