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Magnesium in PDB 1hbm: Methyl-Coenzyme M Reductase Enzyme Product Complex

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase Enzyme Product Complex, PDB code: 1hbm was solved by U.Ermler, W.Grabarse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.000, 118.300, 122.800, 90.00, 92.00, 90.00
R / Rfree (%) 16.4 / 19.3

Other elements in 1hbm:

The structure of Methyl-Coenzyme M Reductase Enzyme Product Complex also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Methyl-Coenzyme M Reductase Enzyme Product Complex (pdb code 1hbm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Methyl-Coenzyme M Reductase Enzyme Product Complex, PDB code: 1hbm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1hbm

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Magnesium binding site 1 out of 5 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1250

b:19.1
occ:1.00
 O C:HOH2027 2.1 19.5 1.0
OE2 C:GLU30 2.1 17.4 1.0
O C:HOH2055 2.1 19.4 1.0
O C:HOH2152 2.1 16.9 1.0
O C:HOH2058 2.1 20.1 1.0
CD C:GLU30 3.2 15.1 1.0
OE1 C:GLU30 3.6 15.6 1.0
O C:HOH2057 4.0 18.3 1.0
O C:HOH2151 4.1 27.5 1.0
O C:ILE31 4.2 18.3 1.0
O C:HOH2060 4.2 39.2 1.0
NZ C:LYS135 4.2 24.5 1.0
O C:HOH2025 4.4 31.9 1.0
OE2 C:GLU139 4.4 16.1 1.0
CG C:GLU30 4.5 15.4 1.0
NZ C:LYS27 4.5 14.7 1.0
O C:HOH2061 4.6 19.8 1.0
O C:HOH2090 4.7 45.4 1.0
CE C:LYS135 4.9 22.0 1.0

Magnesium binding site 2 out of 5 in 1hbm

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Magnesium binding site 2 out of 5 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1249

b:17.2
occ:1.00
 O F:HOH2044 2.1 18.7 1.0
O F:HOH2048 2.1 18.9 1.0
O F:HOH2018 2.1 16.3 1.0
OE2 F:GLU30 2.1 15.9 1.0
O F:HOH2143 2.1 17.0 1.0
CD F:GLU30 3.1 13.7 1.0
OE1 F:GLU30 3.4 13.9 1.0
O F:HOH2046 4.0 19.6 1.0
O F:ILE31 4.1 17.6 1.0
NZ F:LYS135 4.1 19.2 1.0
O F:HOH2144 4.2 45.2 1.0
O F:HOH2017 4.3 40.2 1.0
OE2 F:GLU139 4.4 16.9 1.0
O F:HOH2051 4.4 20.8 1.0
CG F:GLU30 4.4 14.2 1.0
O F:HOH2050 4.5 58.5 1.0
NZ F:LYS27 4.6 15.6 1.0
C F:ILE31 5.0 16.8 1.0

Magnesium binding site 3 out of 5 in 1hbm

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Magnesium binding site 3 out of 5 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1250

b:33.0
occ:1.00
 O E:HOH2036 2.1 33.3 1.0
O E:HOH2100 2.1 32.0 1.0
O E:HOH2037 2.1 35.1 1.0
O E:HOH2101 2.1 32.6 1.0
OD2 E:ASP77 4.0 25.4 1.0
OD1 E:ASP77 4.3 25.2 1.0
CA E:GLY80 4.4 16.9 1.0
CG E:ASP77 4.6 25.0 1.0

Magnesium binding site 4 out of 5 in 1hbm

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Magnesium binding site 4 out of 5 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1251

b:29.6
occ:1.00
 O A:HOH2021 2.1 28.8 1.0
O A:HOH2058 2.1 28.2 1.0
O A:HOH2019 2.1 28.5 1.0
O A:HOH2018 2.1 32.2 1.0
O A:HOH2040 2.1 28.2 1.0
O A:HOH2059 3.9 24.8 1.0
O A:GLU15 4.2 16.0 1.0
O A:HOH2037 4.3 49.0 1.0
OE2 A:GLU20 4.3 15.0 1.0
O A:HOH2020 4.5 35.5 1.0
C A:GLU15 4.9 15.7 1.0
CA A:GLU16 4.9 16.6 1.0

Magnesium binding site 5 out of 5 in 1hbm

Go back to Magnesium Binding Sites List in 1hbm
Magnesium binding site 5 out of 5 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1252

b:31.6
occ:1.00
 O A:HOH2025 2.1 33.1 1.0
O A:HOH2330 2.1 31.9 1.0
O A:HOH2053 2.1 33.6 1.0
CB A:GLU19 4.3 16.7 1.0
O A:GLU387 4.4 14.1 1.0
O A:GLU19 4.5 14.6 1.0
OE1 A:GLU387 4.5 28.8 1.0
CG A:GLU19 4.8 17.6 1.0

Reference:

W.Grabarse, F.Mahlert, E.C.Duin, M.Goubeaud, S.Shima, R.K.Thauer, V.Lamzin, U.Ermler. On the Mechanism of Biological Methane Formation: Structural Evidence For Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding J.Mol.Biol. V. 309 315 2001.
ISSN: ISSN 0022-2836
PubMed: 11491299
DOI: 10.1006/JMBI.2001.4647
Page generated: Mon Dec 14 05:59:03 2020

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