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Sodium 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
Magnesium (Mg) 13 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 9 binding sites of Sodium where determined in the Methyl-Coenzyme M Reductase in the Mcr-RED1-Silent State in Complex with Coenzyme M, PDB code: 1hbu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 1hbu

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Sodium binding site 1 out of 9 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 Sodium with other atoms in the Na 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:Na1559

b:28.1
occ:1.00
 O A:HOH2025 2.3 29.8 1.0
O A:PHE14 2.3 22.1 1.0
O A:HOH2032 2.4 31.9 1.0
O A:HOH2044 2.4 26.8 1.0
O A:LYS11 2.4 24.9 1.0
O A:HOH2034 2.4 33.7 1.0
C A:LYS11 3.4 23.0 1.0
C A:PHE14 3.5 20.2 1.0
CA A:LYS11 3.9 21.2 1.0
O A:GLU15 3.9 20.7 1.0
CA A:GLU15 4.0 21.1 1.0
C A:GLU15 4.1 20.9 1.0
N A:GLU15 4.2 22.0 1.0
O A:HOH2017 4.2 57.4 1.0
CB A:LYS11 4.3 21.6 1.0
O A:HOH2023 4.4 38.1 1.0
O A:GLU16 4.4 22.1 1.0
O A:HOH2013 4.5 43.1 1.0
N A:LYS12 4.5 23.3 1.0
N A:PHE14 4.6 21.7 1.0
O A:HOH2016 4.6 54.9 1.0
CA A:PHE14 4.6 22.4 1.0
CA A:LYS12 4.9 23.2 1.0
N A:GLU16 5.0 20.0 1.0

Sodium binding site 2 out of 9 in 1hbu

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Sodium binding site 2 out of 9 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 Sodium with other atoms in the Na 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:Na1560

b:31.1
occ:1.00
 O D:HOH2434 2.3 32.1 1.0
O D:HOH2131 2.4 34.3 1.0
O D:HOH2265 2.4 29.8 1.0
O D:ARG270 2.4 17.8 1.0
O1 A:GOL1553 2.4 36.7 1.0
O A:HOH2266 3.1 23.4 1.0
C D:ARG270 3.3 14.6 1.0
C1 A:GOL1553 3.4 38.0 1.0
CA D:ARG270 3.6 13.9 1.0
O2 A:GOL1553 3.7 38.0 1.0
CG D:ARG270 3.7 17.4 1.0
O E:HOH2075 3.7 46.1 1.0
NH1 A:ARG225 3.9 14.3 1.0
C2 A:GOL1553 4.1 38.5 1.0
O D:VAL269 4.2 11.3 1.0
CB D:ARG270 4.4 15.7 1.0
O D:TP71551 4.4 28.8 1.0
OE2 A:GLU275 4.5 21.7 1.0
O E:HOH2085 4.5 28.9 1.0
N D:AGM271 4.6 15.1 1.0
O2P D:TP71551 4.6 37.9 1.0
CE1 A:MHS257 4.6 27.8 1.0
N D:ARG270 4.8 13.9 1.0
CZ A:ARG225 4.8 16.3 1.0
C D:VAL269 4.9 12.3 1.0

Sodium binding site 3 out of 9 in 1hbu

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Sodium binding site 3 out of 9 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 Sodium with other atoms in the Na 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:Na1561

b:21.1
occ:1.00
 O A:HOH2427 2.3 26.4 1.0
O A:HOH2428 2.3 26.6 1.0
OG1 A:THR547 2.4 17.1 1.0
O A:THR547 2.4 14.7 1.0
O A:ALA544 2.4 19.4 1.0
O A:PRO548 2.4 22.2 1.0
C A:THR547 3.2 16.1 1.0
C A:PRO548 3.3 22.5 1.0
C A:ALA544 3.4 19.9 1.0
CB A:THR547 3.5 16.9 1.0
CA A:ALA544 3.6 19.3 1.0
CA A:THR547 3.8 15.3 1.0
N A:THR547 3.9 14.3 1.0
N A:PRO548 3.9 19.2 1.0
CB A:ALA544 4.0 19.9 1.0
N A:ALA549 4.1 24.8 1.0
O A:HOH2429 4.1 29.5 1.0
CA A:PRO548 4.2 21.4 1.0
CA A:ALA549 4.3 25.4 1.0
O A:HOH2424 4.4 47.2 1.0
O A:HOH2425 4.6 61.1 1.0
N A:LEU545 4.6 20.1 1.0
CG2 A:THR547 4.7 18.7 1.0
O A:ARG543 4.8 14.3 1.0
N A:ALA544 4.9 17.3 1.0

Sodium binding site 4 out of 9 in 1hbu

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Sodium binding site 4 out of 9 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 Sodium with other atoms in the Na 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:Na1562

b:17.9
occ:1.00
 O A:HOH2106 2.3 20.2 1.0
O A:ILE60 2.3 17.5 1.0
O A:THR62 2.4 17.5 1.0
O D:HOH2165 2.4 14.0 1.0
O A:HOH2109 2.9 18.6 1.0
O A:PRO58 3.1 19.2 1.0
O A:HOH2108 3.1 26.2 1.0
C A:THR62 3.4 18.0 1.0
C A:ILE60 3.6 17.5 1.0
N A:THR62 3.8 18.2 1.0
C A:PRO58 3.8 20.1 1.0
C A:GLY61 3.9 19.5 1.0
O D:HOH2167 4.0 12.1 1.0
O A:GLY61 4.2 18.4 1.0
CA A:THR62 4.2 17.0 1.0
N A:PRO63 4.2 17.8 1.0
N A:ILE60 4.3 20.0 1.0
CA A:PRO63 4.3 18.5 1.0
O D:ALA144 4.3 14.7 1.0
CA A:PRO58 4.4 19.3 1.0
O D:HOH2166 4.4 17.9 1.0
N A:GLY61 4.4 18.1 1.0
O A:HOH2101 4.4 19.0 1.0
CA A:GLY61 4.4 18.5 1.0
N A:LEU64 4.5 18.5 1.0
CA A:ILE60 4.5 18.9 1.0
O A:ASN57 4.6 16.5 1.0
N A:ASP59 4.6 19.0 1.0
C A:ASP59 4.7 20.8 1.0
CA A:ASP59 4.9 20.5 1.0
C A:PRO63 4.9 19.3 1.0

Sodium binding site 5 out of 9 in 1hbu

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Sodium binding site 5 out of 9 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 Sodium with other atoms in the Na 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
B:Na1445

b:21.4
occ:1.00
 O B:HOH2381 2.4 28.4 1.0
O B:ASN441 2.4 21.6 1.0
C B:ASN441 3.5 22.9 1.0
CB B:ASN441 3.9 21.0 1.0
CA B:ASN441 4.0 21.2 1.0
O B:HOH2384 4.5 20.6 1.0
ND2 B:ASN441 4.6 20.2 1.0
N B:GLU442 4.6 23.3 1.0
CG B:ASN441 4.8 20.6 1.0
CA B:GLU442 4.9 25.4 1.0

Sodium binding site 6 out of 9 in 1hbu

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Sodium binding site 6 out of 9 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 Sodium with other atoms in the Na 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:Na1448

b:33.7
occ:1.00
 O B:HOH2128 2.3 32.8 1.0
O B:HOH2148 2.4 38.2 1.0
O B:HOH2149 2.4 34.8 1.0
O B:HOH2144 2.4 38.5 1.0
O B:THR101 2.4 24.1 1.0
O B:ASP99 2.4 27.2 1.0
C B:THR101 3.5 22.4 1.0
C B:ASP99 3.6 25.0 1.0
N B:THR101 3.6 21.4 1.0
C B:ASP100 3.8 22.4 1.0
O B:HOH2143 3.8 26.8 1.0
CA B:ASP100 4.0 22.7 1.0
CA B:THR101 4.0 21.6 1.0
OD1 B:ASN102 4.0 29.3 1.0
NZ B:LYS90 4.2 27.0 1.0
N B:ASP100 4.2 23.3 1.0
CB B:THR101 4.5 21.1 1.0
OD2 B:ASP99 4.5 23.7 1.0
O B:ASP100 4.5 22.0 1.0
N B:ASP99 4.5 30.3 1.0
C B:ASP98 4.5 33.6 1.0
CE B:LYS90 4.5 26.1 1.0
N B:ASN102 4.6 21.6 1.0
CA B:ASP98 4.6 34.1 1.0
CA B:ASP99 4.7 27.1 1.0
OD2 B:ASP98 4.8 24.1 0.0
CG B:ASN102 4.9 27.9 1.0
O B:ASP98 4.9 35.3 1.0
CA B:ASN102 4.9 22.4 1.0

Sodium binding site 7 out of 9 in 1hbu

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Sodium binding site 7 out of 9 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 Sodium with other atoms in the Na 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
D:Na1558

b:28.0
occ:1.00
 O D:HOH2025 2.3 26.8 1.0
O D:HOH2017 2.3 32.8 1.0
O D:HOH2011 2.4 32.3 1.0
O D:LYS11 2.4 25.4 1.0
O D:HOH2020 2.4 29.1 1.0
O D:PHE14 2.4 24.7 1.0
C D:LYS11 3.4 24.8 1.0
C D:PHE14 3.5 24.1 1.0
CA D:LYS11 3.9 24.2 1.0
CA D:GLU15 3.9 26.1 1.0
O D:GLU15 3.9 27.3 1.0
N D:GLU15 4.1 25.8 1.0
C D:GLU15 4.1 26.4 1.0
CB D:LYS11 4.3 23.7 1.0
O D:GLU16 4.5 24.3 1.0
N D:PHE14 4.6 23.0 1.0
N D:LYS12 4.6 25.4 1.0
O D:HOH2004 4.6 58.6 1.0
CA D:PHE14 4.6 24.3 1.0
O D:HOH2010 4.7 35.4 1.0
CA D:LYS12 5.0 25.0 1.0
O D:HOH2012 5.0 52.6 1.0
O D:LEU10 5.0 20.7 1.0

Sodium binding site 8 out of 9 in 1hbu

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Sodium binding site 8 out of 9 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 Sodium with other atoms in the Na 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
D:Na1559

b:32.5
occ:1.00
 O D:HOH2438 2.3 33.5 1.0
O A:HOH2261 2.4 29.6 1.0
O A:ARG270 2.4 18.6 1.0
O3 D:GOL1554 2.4 38.5 1.0
O D:HOH2272 3.1 23.1 1.0
C A:ARG270 3.4 16.7 1.0
CA A:ARG270 3.6 17.3 1.0
C1 D:GOL1554 3.6 37.9 1.0
CG A:ARG270 3.7 16.9 1.0
O1 D:GOL1554 3.7 37.0 1.0
NH1 D:ARG225 3.8 16.3 1.0
O B:HOH2085 3.8 46.1 1.0
C3 D:GOL1554 3.8 38.2 1.0
O A:VAL269 4.1 15.8 1.0
CB A:ARG270 4.3 16.9 1.0
C2 D:GOL1554 4.4 38.7 1.0
OE2 D:GLU275 4.4 18.6 1.0
OXT A:TP71551 4.5 28.3 1.0
N A:AGM271 4.5 15.0 1.0
O B:HOH2094 4.6 29.8 1.0
N A:ARG270 4.7 17.2 1.0
CE1 D:MHS257 4.7 24.4 1.0
CZ D:ARG225 4.8 17.1 1.0
O1P A:TP71551 4.8 37.8 1.0
C A:VAL269 4.8 19.1 1.0
OE1 D:GLU275 4.9 12.8 1.0

Sodium binding site 9 out of 9 in 1hbu

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Sodium binding site 9 out of 9 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 Sodium with other atoms in the Na 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:Na1560

b:21.0
occ:1.00
 O A:HOH2177 2.3 18.1 1.0
O D:HOH2091 2.4 27.7 1.0
O D:THR62 2.4 19.7 1.0
O D:ILE60 2.4 19.2 1.0
O D:PRO58 2.4 22.1 1.0
O D:HOH2092 2.9 30.7 1.0
O D:HOH2093 3.1 25.6 1.0
C D:THR62 3.4 20.7 1.0
C D:PRO58 3.5 20.9 1.0
C D:ILE60 3.5 20.0 1.0
N D:THR62 3.8 19.6 1.0
C D:GLY61 3.9 20.9 1.0
O D:GLY61 4.1 22.3 1.0
O A:HOH2181 4.1 17.9 1.0
N D:ILE60 4.1 22.2 1.0
CA D:THR62 4.2 19.4 1.0
C D:ASP59 4.2 23.2 1.0
N D:PRO63 4.2 20.4 1.0
CA D:PRO63 4.3 19.9 1.0
CA D:PRO58 4.3 20.8 1.0
O D:HOH2098 4.3 17.4 1.0
O A:ALA144 4.4 13.8 1.0
N D:ASP59 4.4 20.2 1.0
CA D:ILE60 4.4 21.6 1.0
N D:GLY61 4.5 19.8 1.0
CA D:ASP59 4.5 22.9 1.0
CA D:GLY61 4.5 20.1 1.0
N D:LEU64 4.6 18.1 1.0
O D:ASN57 4.7 18.0 1.0
O D:HOH2086 4.7 22.0 1.0
O D:ASP59 4.8 21.6 1.0
C D:PRO63 5.0 19.4 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: Sun Oct 6 18:43:12 2024

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