Magnesium in PDB 1hbn: Methyl-Coenzyme M Reductase

The structure of Methyl-Coenzyme M Reductase, PDB code: 1hbn 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)	30.00 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.720, 116.883, 122.582, 90.00, 92.02, 90.00
R / Rfree (%)	12.4 / 19

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

Nickel	(Ni)	2 atoms
Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	10 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Methyl-Coenzyme M Reductase (pdb code 1hbn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Methyl-Coenzyme M Reductase, PDB code: 1hbn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1558 b:35.7 occ:1.00 O A:HOH2192 2.1 37.7 1.0 O A:HOH2193 2.1 38.5 1.0 OE1 A:GLU117 2.1 36.5 1.0 O A:VAL124 2.2 23.7 1.0 CD A:GLU117 3.3 35.7 1.0 C A:VAL124 3.3 20.8 1.0 N A:VAL124 3.4 20.2 1.0 OE2 A:GLU117 3.7 38.9 1.0 CA A:VAL124 3.8 20.0 1.0 CB A:VAL124 4.0 18.6 1.0 N A:THR125 4.5 21.1 1.0 O A:HOH2097 4.5 45.8 1.0 C A:GLU123 4.5 22.1 1.0 CG A:GLU117 4.6 29.4 1.0 CA A:GLU123 4.7 24.5 1.0 CG2 A:THR125 4.9 24.4 1.0 CA A:THR125 4.9 21.8 1.0 CB A:GLU123 4.9 28.5 1.0 CG1 A:VAL124 5.0 18.7 1.0

Magnesium binding site 2 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1563 b:41.0 occ:1.00 O A:HOH2230 2.1 37.9 1.0 O D:HOH2049 2.1 44.5 1.0 O A:HOH2432 2.1 38.5 1.0 O D:HOH2102 3.9 40.1 1.0 O A:HOH2232 4.2 30.3 1.0 OD1 A:ASN517 4.2 16.9 1.0 O D:GLY52 4.3 17.8 1.0 CA A:ALA179 4.6 18.2 1.0 O A:ALA179 4.6 18.0 1.0 NZ A:LYS164 4.7 16.2 1.0 O A:PRO178 4.7 18.4 1.0 O D:HOH2048 4.7 46.6 1.0 C A:ALA179 5.0 16.8 1.0

Magnesium binding site 3 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1564 b:48.0 occ:1.00 O A:HOH2227 2.1 47.9 1.0 O A:HOH2228 2.1 49.8 1.0 O D:HOH2101 3.0 32.0 0.5 O D:HOH2047 3.1 21.8 0.5 OD2 A:ASP177 4.1 25.6 1.0 OD1 A:ASP177 4.1 31.8 1.0 O D:HOH2048 4.5 46.6 1.0 CG A:ASP177 4.5 26.2 1.0 CB A:ALA179 4.8 19.4 1.0 O D:HOH2102 4.9 40.1 1.0

Magnesium binding site 4 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1565 b:34.1 occ:1.00 O A:HOH2048 2.1 29.8 1.0 O A:HOH2065 2.8 32.2 1.0 O A:HOH2075 3.4 44.4 1.0 OE1 A:GLU20 3.8 17.4 1.0 O A:LYS22 4.1 17.6 1.0 CG A:GLU16 4.5 17.0 1.0 OE2 A:GLU16 4.5 18.6 1.0 O A:HOH2019 4.6 27.8 1.0 C A:LYS22 4.9 16.4 1.0 CD A:GLU20 5.0 15.9 1.0

Magnesium binding site 5 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1566 b:27.0 occ:1.00 O A:HOH2022 2.1 30.2 1.0 O A:HOH2066 2.1 27.4 1.0 O A:HOH2019 2.1 27.8 1.0 O A:HOH2044 2.1 26.0 1.0 O A:HOH2021 2.1 32.5 1.0 O A:GLU15 4.2 18.5 1.0 OE2 A:GLU20 4.3 19.1 1.0 O A:HOH2039 4.3 44.7 1.0 O A:HOH2020 4.5 37.9 1.0 CA A:GLU16 4.8 15.3 1.0 C A:GLU15 4.9 17.6 1.0 O A:HOH2018 5.0 51.0 1.0

Magnesium binding site 6 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1447 b:36.1 occ:1.00 O B:HOH2316 2.1 38.7 1.0 O B:HOH2312 2.1 33.8 1.0 O B:HOH2317 2.1 36.8 1.0 OD1 B:ASP271 2.1 24.2 1.0 O B:HOH2314 2.1 38.1 1.0 CG B:ASP271 3.1 18.9 1.0 OD2 B:ASP271 3.3 20.0 1.0 O B:HOH2144 4.0 45.6 1.0 CB B:ASP271 4.4 16.3 1.0 OE1 B:GLU274 4.5 42.3 1.0 O B:SER267 4.5 15.2 1.0 CA B:ASP271 4.8 14.8 1.0 N B:ASP271 4.8 14.7 1.0

Magnesium binding site 7 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1449 b:49.8 occ:1.00 O B:HOH2068 2.1 49.6 1.0 O B:HOH2401 2.1 49.2 1.0 O B:HOH2171 2.1 51.1 1.0 O B:HOH2170 2.1 52.5 1.0 OE2 B:GLU104 3.8 35.5 0.7 O B:HOH2403 4.1 43.7 1.0 OE2 B:GLU104 4.2 27.7 0.3 O B:GLN421 4.2 22.2 1.0 OE1 B:GLU104 4.3 37.2 0.7 OE1 B:GLN421 4.3 28.8 1.0 CD B:GLU104 4.5 34.9 0.7 O B:HOH2069 4.6 54.1 1.0 CB B:GLN421 4.7 20.9 1.0

Magnesium binding site 8 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1250 b:18.4 occ:1.00 O C:HOH2066 2.1 19.2 1.0 O C:HOH2179 2.1 19.1 1.0 O C:HOH2062 2.1 20.6 1.0 OE2 C:GLU30 2.1 18.8 1.0 O C:HOH2172 2.1 20.7 1.0 CD C:GLU30 3.1 18.1 1.0 OE1 C:GLU30 3.4 19.4 1.0 O C:HOH2063 3.9 24.4 1.0 NZ C:LYS135 4.0 23.2 1.0 O C:ILE31 4.1 17.3 1.0 O C:HOH2178 4.1 30.5 1.0 OE2 C:GLU139 4.2 18.2 1.0 O C:HOH2069 4.2 42.5 1.0 O C:HOH2028 4.3 39.4 1.0 O C:HOH2068 4.4 24.3 1.0 CG C:GLU30 4.5 17.4 1.0 NZ C:LYS27 4.5 19.0 1.0 O C:HOH2098 4.7 56.5 1.0 CE C:LYS135 5.0 22.3 1.0

Magnesium binding site 9 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1251 b:46.5 occ:1.00 O C:HOH2073 2.1 44.2 1.0 O C:HOH2074 3.3 37.9 0.5 O C:HOH2231 4.1 41.8 1.0 O C:HOH2234 4.1 27.7 1.0 OE1 C:GLU197 4.3 22.1 0.0 OD2 C:ASP35 4.3 23.7 1.0 O C:HOH2067 4.4 27.4 0.5 O C:PRO198 4.4 21.0 1.0 OD1 C:ASP35 4.7 24.2 1.0 CG C:ASP35 5.0 21.7 1.0 NZ C:LYS38 5.0 29.6 1.0 CB C:GLU197 5.0 25.9 1.0

Magnesium binding site 10 out of 18 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1557 b:39.4 occ:1.00 O D:HOH2121 2.1 40.9 1.0 O D:HOH2226 2.1 42.1 1.0 O D:HOH2227 2.1 39.7 1.0 O D:HOH2223 2.1 41.5 1.0 OE1 D:GLU175 2.4 27.1 1.0 CD D:GLU175 3.5 21.4 1.0 O D:HOH2222 3.5 43.7 1.0 OE2 D:GLU175 3.9 23.2 1.0 CG D:GLU175 4.7 18.6 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