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Magnesium in PDB 1hbu: Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M, PDB code: 1hbu 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 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.100, 116.500, 121.800, 90.00, 91.80, 90.00
R / Rfree (%) 16.2 / 21.1

Other elements in 1hbu:

The structure of Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M 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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M (pdb code 1hbu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M, PDB code: 1hbu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 1hbu

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Magnesium binding site 1 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1558

b:39.0
occ:1.00
O A:HOH2164 2.1 40.9 1.0
O A:HOH2165 2.1 41.3 1.0
OE1 A:GLU117 2.1 37.2 1.0
O A:VAL124 2.2 28.9 1.0
CD A:GLU117 3.3 34.9 1.0
C A:VAL124 3.3 26.5 1.0
N A:VAL124 3.3 26.3 1.0
CA A:VAL124 3.8 26.0 1.0
OE2 A:GLU117 3.8 37.5 1.0
CB A:VAL124 4.1 25.4 1.0
C A:GLU123 4.4 27.0 1.0
N A:THR125 4.4 24.7 1.0
CA A:GLU123 4.5 26.7 1.0
CG A:GLU117 4.5 31.5 1.0
CB A:GLU123 4.6 25.5 1.0
O A:HOH2085 4.6 61.2 1.0
CG2 A:THR125 4.7 23.4 1.0
CA A:THR125 4.8 25.0 1.0
CG1 A:VAL124 5.0 24.7 1.0

Magnesium binding site 2 out of 13 in 1hbu

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Magnesium binding site 2 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1563

b:54.5
occ:1.00
O A:HOH2194 2.1 52.7 1.0
O A:HOH2195 2.1 52.5 1.0
O D:HOH2036 3.4 24.1 0.5
OD1 A:ASP177 3.9 31.7 1.0
OD2 A:ASP177 4.2 26.2 1.0
CG A:ASP177 4.4 27.3 1.0
O A:HOH2174 4.8 43.5 1.0

Magnesium binding site 3 out of 13 in 1hbu

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Magnesium binding site 3 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1564

b:43.8
occ:1.00
O A:HOH2045 2.1 38.2 1.0
O A:HOH2063 2.9 40.2 1.0
OE1 A:GLU20 3.9 17.7 1.0
O A:LYS22 4.1 21.6 1.0
CG A:GLU16 4.4 21.5 1.0
O A:HOH2018 4.5 45.8 1.0
OE2 A:GLU16 4.5 23.4 1.0
C A:LYS22 4.9 21.4 1.0
O A:HOH2064 4.9 53.2 1.0
CD A:GLU16 5.0 23.2 1.0

Magnesium binding site 4 out of 13 in 1hbu

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Magnesium binding site 4 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1565

b:46.2
occ:1.00
O A:HOH2018 2.1 45.8 1.0
O A:HOH2059 2.1 43.3 1.0
O A:HOH2019 2.1 45.1 1.0
O A:HOH2040 2.1 45.9 1.0
O A:GLU15 4.1 20.7 1.0
OE2 A:GLU20 4.2 19.1 1.0
O A:HOH2035 4.4 71.5 1.0
C A:GLU15 4.7 20.9 1.0
O A:HOH2050 4.7 56.5 1.0
CA A:GLU16 4.8 20.6 1.0

Magnesium binding site 5 out of 13 in 1hbu

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Magnesium binding site 5 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1566

b:31.4
occ:1.00
O A:HOH2173 2.1 35.7 1.0
O A:HOH2055 2.1 32.7 1.0
O A:HOH2024 2.1 32.0 1.0
O A:HOH2340 2.1 33.5 1.0
O A:HOH2338 4.2 24.8 0.5
OE1 A:GLU387 4.3 36.1 1.0
CB A:GLU19 4.3 20.6 1.0
O A:GLU387 4.4 20.1 1.0
O A:GLU19 4.6 18.8 1.0
CG A:GLU19 4.8 23.0 1.0

Magnesium binding site 6 out of 13 in 1hbu

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Magnesium binding site 6 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1447

b:37.8
occ:1.00
O B:HOH2292 2.1 39.3 1.0
O B:HOH2291 2.1 39.1 1.0
O B:HOH2290 2.1 35.5 1.0
O B:HOH2288 2.1 36.6 1.0
OD1 B:ASP271 2.1 25.1 1.0
CG B:ASP271 3.1 21.5 1.0
OD2 B:ASP271 3.4 20.8 1.0
O B:HOH2135 4.2 46.0 1.0
OE1 B:GLU274 4.4 36.9 1.0
CB B:ASP271 4.5 19.4 1.0
O B:SER267 4.7 16.2 1.0
CA B:ASP271 4.7 18.0 1.0
N B:ASP271 4.8 17.0 1.0
OE2 B:GLU274 4.9 37.3 1.0
CD B:GLU274 5.0 35.5 1.0

Magnesium binding site 7 out of 13 in 1hbu

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Magnesium binding site 7 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1449

b:91.5
occ:1.00
O B:HOH2153 2.1 91.1 1.0
OE2 B:GLU104 3.2 29.5 0.7
OE1 B:GLU104 3.5 31.2 0.7
CD B:GLU104 3.7 29.5 0.7
OE2 B:GLU104 3.8 25.9 0.3
OE1 B:GLN421 4.0 33.2 1.0
O B:GLN421 4.5 25.8 1.0
CB B:GLN421 4.6 27.4 1.0
O B:HOH2186 4.7 47.0 1.0
CD B:GLU104 4.8 26.4 0.3
CD B:GLN421 4.9 31.9 1.0
CG B:GLN421 4.9 29.9 1.0

Magnesium binding site 8 out of 13 in 1hbu

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Magnesium binding site 8 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1250

b:22.9
occ:1.00
OE2 C:GLU30 2.1 20.0 1.0
O C:HOH2027 2.1 22.1 1.0
O C:HOH2053 2.1 22.6 1.0
O C:HOH2144 2.1 23.8 1.0
O C:HOH2056 2.1 22.9 1.0
CD C:GLU30 3.2 19.0 1.0
OE1 C:GLU30 3.5 19.9 1.0
O C:HOH2052 3.9 30.2 1.0
O C:HOH2145 4.2 28.2 1.0
NZ C:LYS135 4.2 22.5 1.0
O C:ILE31 4.2 22.2 1.0
O C:HOH2058 4.2 37.5 1.0
OE2 C:GLU139 4.2 20.9 1.0
NZ C:LYS27 4.4 18.1 1.0
O C:HOH2023 4.4 45.2 1.0
CG C:GLU30 4.5 19.1 1.0
O C:HOH2059 4.5 21.9 1.0
O C:HOH2084 4.6 51.1 1.0
OD2 C:ASP33 5.0 25.9 1.0
CE C:LYS135 5.0 21.1 1.0

Magnesium binding site 9 out of 13 in 1hbu

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Magnesium binding site 9 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1557

b:45.6
occ:1.00
O D:HOH2185 2.1 47.1 1.0
O D:HOH2186 2.1 45.0 1.0
O D:HOH2187 2.1 46.9 1.0
OE1 D:GLU175 2.4 31.2 1.0
CD D:GLU175 3.4 27.6 1.0
OE2 D:GLU175 3.8 27.8 1.0
CG D:GLU175 4.7 24.8 1.0

Magnesium binding site 10 out of 13 in 1hbu

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Magnesium binding site 10 out of 13 in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M


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 in the Mcr-RED1-Silent State in Complex with Coenzyme M within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1446

b:39.1
occ:1.00
O E:HOH2276 2.1 40.9 1.0
O E:HOH2273 2.1 36.7 1.0
OD1 E:ASP271 2.1 26.2 1.0
O E:HOH2275 3.1 45.6 1.0
CG E:ASP271 3.2 23.8 1.0
OD2 E:ASP271 3.6 23.8 1.0
OE1 E:GLU274 3.9 38.6 0.0
CB E:ASP271 4.5 22.1 1.0
O E:SER267 4.6 15.7 1.0
N E:ASP271 4.7 19.5 1.0
CA E:ASP271 4.7 19.9 1.0
CB E:ALA270 4.8 17.7 1.0
CD E:GLU274 5.0 35.4 0.0

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 05:59:08 2020

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