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

Protein crystallography data

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

Other elements in 1hbo:

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

Magnesium Binding Sites:

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 1hbo

Go back to Magnesium Binding Sites List in 1hbo
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 1hbo

Go back to Magnesium Binding Sites List in 1hbo
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 1hbo

Go back to Magnesium Binding Sites List in 1hbo
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 1hbo

Go back to Magnesium Binding Sites List in 1hbo
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

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 05:59:05 2020

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