Magnesium in PDB 1hbo: Methyl-Coenzyme M Reductase Mcr-RED1-Silent

The structure of Methyl-Coenzyme M Reductase Mcr-RED1-Silent, PDB code: 1hbo was solved by W.Grabarse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.700, 117.300, 122.400, 90.00, 92.00, 90.00
R / Rfree (%)	17.7 / 21.3

The structure of Methyl-Coenzyme M Reductase Mcr-RED1-Silent also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	8 atoms

The binding sites of Magnesium atom in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent (pdb code 1hbo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent, PDB code: 1hbo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1561 b:38.9 occ:1.00 O A:HOH2167 2.1 42.0 1.0 O A:HOH2336 2.1 38.5 1.0 CB A:GLU19 4.2 23.8 1.0 OE1 A:GLU387 4.4 36.4 1.0 O A:GLU387 4.5 21.7 1.0 CG A:GLU19 4.5 24.8 1.0 O A:HOH2334 4.6 26.2 0.5 O A:GLU19 4.7 23.5 1.0

Magnesium binding site 2 out of 4 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1562 b:44.6 occ:1.00 O A:HOH2051 2.1 42.8 1.0 O A:HOH2018 2.1 45.2 1.0 O A:HOH2017 2.1 43.8 1.0 O A:HOH2033 2.1 42.7 1.0 O A:HOH2053 3.8 35.5 1.0 O A:GLU15 4.1 25.2 1.0 OE2 A:GLU20 4.4 22.1 1.0 O A:HOH2016 4.7 50.2 1.0 CA A:GLU16 4.8 24.4 1.0 C A:GLU15 4.8 23.7 1.0

Magnesium binding site 3 out of 4 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1250 b:29.2 occ:1.00 O C:HOH2054 2.1 29.2 1.0 O C:HOH2025 2.1 29.7 1.0 OE2 C:GLU30 2.1 26.4 1.0 O C:HOH2057 2.1 32.2 1.0 O C:HOH2153 2.1 28.3 1.0 CD C:GLU30 3.2 24.5 1.0 OE1 C:GLU30 3.5 24.6 1.0 O C:HOH2052 3.9 34.2 1.0 O C:ILE31 4.1 28.1 1.0 NZ C:LYS135 4.1 31.8 1.0 O C:HOH2152 4.1 45.6 1.0 OE2 C:GLU139 4.3 26.9 1.0 O C:HOH2060 4.4 50.3 1.0 O C:HOH2022 4.4 41.1 1.0 CG C:GLU30 4.5 23.9 1.0 O C:HOH2061 4.5 29.9 1.0 NZ C:LYS27 4.6 22.9 1.0 O C:HOH2088 4.8 48.8 1.0 CE C:LYS135 4.9 30.2 1.0

Magnesium binding site 4 out of 4 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1249 b:26.2 occ:1.00 O F:HOH2049 2.1 27.1 1.0 O F:HOH2052 2.1 29.0 1.0 O F:HOH2022 2.1 24.8 1.0 OE2 F:GLU30 2.1 25.0 1.0 O F:HOH2142 2.1 25.1 1.0 CD F:GLU30 3.1 22.8 1.0 OE1 F:GLU30 3.3 21.4 1.0 O F:ILE31 4.0 25.1 1.0 O F:HOH2050 4.0 29.3 1.0 NZ F:LYS135 4.1 28.4 1.0 O F:HOH2143 4.2 52.7 1.0 O F:HOH2054 4.3 30.1 1.0 OE2 F:GLU139 4.4 23.3 1.0 CG F:GLU30 4.5 23.2 1.0 O F:HOH2023 4.5 57.8 1.0 NZ F:LYS27 4.6 24.9 1.0 C F:ILE31 5.0 25.3 1.0

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