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Sodium 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
Magnesium (Mg) 4 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 8 in 1hbo

Go back to Sodium Binding Sites List in 1hbo
Sodium binding site 1 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1557

b:31.1
occ:1.00
 O A:LYS11 2.3 26.7 1.0
O A:HOH2023 2.3 35.1 1.0
O A:HOH2037 2.3 30.3 1.0
O A:PHE14 2.3 25.5 1.0
O A:HOH2028 2.4 34.1 1.0
O A:HOH2034 2.4 33.9 1.0
C A:LYS11 3.4 26.6 1.0
C A:PHE14 3.5 24.4 1.0
O A:GLU15 3.8 25.2 1.0
CA A:GLU15 3.8 24.4 1.0
CA A:LYS11 3.9 25.3 1.0
C A:GLU15 4.0 23.7 1.0
N A:GLU15 4.1 23.9 1.0
CB A:LYS11 4.4 25.9 1.0
O A:HOH2022 4.4 43.6 1.0
O A:GLU16 4.4 26.0 1.0
N A:PHE14 4.5 23.7 1.0
N A:LYS12 4.6 26.2 1.0
O A:HOH2013 4.6 43.0 1.0
CA A:PHE14 4.6 24.1 1.0
O A:HOH2015 4.7 61.0 1.0
CA A:LYS12 4.9 25.9 1.0
N A:GLU16 4.9 23.7 1.0

Sodium binding site 2 out of 8 in 1hbo

Go back to Sodium Binding Sites List in 1hbo
Sodium binding site 2 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1558

b:30.8
occ:1.00
 O A:HOH2430 2.3 31.2 1.0
O A:HOH2255 2.4 27.0 1.0
O A:ARG270 2.4 20.5 1.0
O D:HOH2265 3.2 27.5 1.0
C A:ARG270 3.3 18.8 1.0
CA A:ARG270 3.6 18.7 1.0
O B:HOH2080 3.6 33.4 1.0
NH1 D:ARG225 3.7 21.8 1.0
CG A:ARG270 3.8 20.2 1.0
O A:VAL269 4.2 16.1 1.0
OXT A:TP71551 4.2 19.9 0.6
CB A:ARG270 4.3 19.1 1.0
OE2 D:GLU275 4.5 20.7 1.0
N A:AGM271 4.5 16.2 1.0
CE1 D:MHS257 4.7 30.9 1.0
O1P A:TP71551 4.7 24.2 0.6
N A:ARG270 4.7 20.2 1.0
O B:HOH2091 4.8 28.7 1.0
CZ D:ARG225 4.8 21.8 1.0
C A:VAL269 4.9 19.6 1.0
C A:TP71551 5.0 21.4 0.6

Sodium binding site 3 out of 8 in 1hbo

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Sodium binding site 3 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1559

b:25.4
occ:1.00
 O A:HOH2420 2.3 32.3 1.0
O A:HOH2421 2.4 29.6 1.0
OG1 A:THR547 2.4 18.7 1.0
O A:THR547 2.4 19.5 1.0
O A:ALA544 2.4 19.6 1.0
O A:PRO548 2.4 24.8 1.0
C A:THR547 3.2 18.9 1.0
C A:PRO548 3.4 24.3 1.0
C A:ALA544 3.4 20.6 1.0
CB A:THR547 3.6 18.1 1.0
CA A:ALA544 3.8 20.2 1.0
CA A:THR547 3.8 17.9 1.0
N A:THR547 3.9 16.7 1.0
N A:PRO548 3.9 21.0 1.0
O A:HOH2419 4.0 33.8 1.0
N A:ALA549 4.1 25.9 1.0
O A:HOH2414 4.1 58.1 1.0
CA A:PRO548 4.2 23.1 1.0
CB A:ALA544 4.3 22.5 1.0
O A:HOH2418 4.3 46.4 1.0
CA A:ALA549 4.4 26.2 1.0
N A:LEU545 4.6 20.6 1.0
CG2 A:THR547 4.7 19.8 1.0
O A:ARG543 5.0 17.6 1.0

Sodium binding site 4 out of 8 in 1hbo

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Sodium binding site 4 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1560

b:22.2
occ:1.00
 O A:HOH2106 2.3 23.4 1.0
O A:THR62 2.4 21.2 1.0
O A:ILE60 2.4 22.5 1.0
O D:HOH2160 2.4 18.2 1.0
O A:HOH2108 3.0 25.2 1.0
O A:HOH2109 3.1 19.6 1.0
O A:PRO58 3.1 24.0 1.0
C A:THR62 3.4 21.5 1.0
C A:ILE60 3.6 20.2 1.0
N A:THR62 3.8 21.0 1.0
C A:GLY61 3.8 22.5 1.0
C A:PRO58 3.9 21.5 1.0
O D:HOH2163 4.0 17.2 1.0
O A:GLY61 4.0 22.3 1.0
CA A:THR62 4.2 19.7 1.0
N A:PRO63 4.2 20.7 1.0
CA A:PRO63 4.2 20.7 1.0
N A:ILE60 4.2 21.4 1.0
CA A:GLY61 4.4 22.0 1.0
O D:ALA144 4.4 15.9 1.0
CA A:PRO58 4.4 21.0 1.0
N A:GLY61 4.5 22.0 1.0
O D:HOH2162 4.5 20.5 1.0
N A:LEU64 4.5 19.9 1.0
CA A:ILE60 4.5 21.5 1.0
O A:HOH2101 4.6 22.8 1.0
C A:ASP59 4.7 22.8 1.0
O A:ASN57 4.7 18.2 1.0
N A:ASP59 4.8 21.0 1.0
C A:PRO63 5.0 21.3 1.0
CA A:ASP59 5.0 23.2 1.0

Sodium binding site 5 out of 8 in 1hbo

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Sodium binding site 5 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1445

b:26.8
occ:1.00
 O B:ASN441 2.4 26.3 1.0
O B:HOH2376 2.4 31.9 1.0
C B:ASN441 3.5 25.8 1.0
CB B:ASN441 3.8 25.3 1.0
CA B:ASN441 4.0 24.9 1.0
O B:HOH2375 4.5 22.1 1.0
ND2 B:ASN441 4.5 24.4 1.0
N B:GLU442 4.6 25.6 1.0
CG B:ASN441 4.7 25.2 1.0
CA B:GLU442 5.0 26.4 1.0

Sodium binding site 6 out of 8 in 1hbo

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Sodium binding site 6 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1447

b:37.4
occ:1.00
 O B:HOH2143 2.3 39.4 1.0
O B:HOH2142 2.3 41.2 1.0
O B:HOH2123 2.3 38.5 1.0
O B:HOH2137 2.4 40.9 1.0
O B:THR101 2.4 27.7 1.0
O B:ASP99 2.4 29.1 1.0
C B:THR101 3.5 24.5 1.0
C B:ASP99 3.6 26.6 1.0
N B:THR101 3.6 22.2 1.0
C B:ASP100 3.8 23.2 1.0
O B:HOH2138 3.9 29.0 1.0
OD1 B:ASN102 3.9 33.3 1.0
CA B:ASP100 3.9 23.2 1.0
CA B:THR101 4.0 22.9 1.0
N B:ASP100 4.2 24.4 1.0
O B:ASP100 4.4 23.2 1.0
N B:ASP99 4.5 31.8 1.0
NZ B:LYS90 4.5 28.3 1.0
N B:ASN102 4.5 24.9 1.0
CB B:THR101 4.5 21.6 1.0
C B:ASP98 4.5 34.4 1.0
OD2 B:ASP99 4.6 26.1 1.0
OD2 B:ASP98 4.6 40.0 0.0
CE B:LYS90 4.7 26.6 1.0
CA B:ASP99 4.7 28.6 1.0
CA B:ASP98 4.7 35.4 1.0
CG B:ASN102 4.8 31.1 1.0
CA B:ASN102 4.9 25.4 1.0
O B:ASP98 5.0 35.8 1.0

Sodium binding site 7 out of 8 in 1hbo

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Sodium binding site 7 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1556

b:32.5
occ:1.00
 O D:HOH2025 2.3 31.1 1.0
O D:HOH2017 2.3 35.9 1.0
O D:HOH2020 2.3 34.3 1.0
O D:LYS11 2.4 28.3 1.0
O D:PHE14 2.4 26.6 1.0
C D:LYS11 3.5 27.5 1.0
C D:PHE14 3.5 25.0 1.0
CA D:LYS11 3.9 25.8 1.0
CA D:GLU15 3.9 26.4 1.0
O D:GLU15 3.9 27.6 1.0
C D:GLU15 4.1 25.8 1.0
N D:GLU15 4.2 26.6 1.0
CB D:LYS11 4.3 26.9 1.0
O D:HOH2013 4.4 36.1 1.0
O D:GLU16 4.5 25.7 1.0
N D:LYS12 4.6 26.6 1.0
N D:PHE14 4.7 23.9 1.0
CA D:PHE14 4.7 24.3 1.0
O D:HOH2008 4.9 50.6 1.0

Sodium binding site 8 out of 8 in 1hbo

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Sodium binding site 8 out of 8 in the Methyl-Coenzyme M Reductase Mcr-RED1-Silent


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 Mcr-RED1-Silent within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1557

b:23.4
occ:1.00
 O D:HOH2093 2.3 28.1 1.0
O A:HOH2172 2.4 20.5 1.0
O D:THR62 2.4 22.5 1.0
O D:ILE60 2.4 21.1 1.0
O D:PRO58 2.4 22.8 1.0
O D:HOH2094 2.8 26.3 1.0
O D:HOH2095 3.2 20.2 1.0
C D:THR62 3.4 22.3 1.0
C D:PRO58 3.5 19.5 1.0
C D:ILE60 3.5 20.5 1.0
N D:THR62 3.8 21.8 1.0
C D:GLY61 3.9 23.4 1.0
O A:HOH2174 4.0 18.4 1.0
N D:ILE60 4.1 22.0 1.0
O D:GLY61 4.1 25.7 1.0
N D:PRO63 4.1 21.7 1.0
CA D:PRO63 4.2 20.6 1.0
CA D:THR62 4.2 21.7 1.0
C D:ASP59 4.3 23.2 1.0
N D:ASP59 4.3 21.1 1.0
CA D:PRO58 4.3 18.3 1.0
CA D:ASP59 4.4 22.3 1.0
N D:GLY61 4.4 21.3 1.0
CA D:ILE60 4.4 20.6 1.0
CA D:GLY61 4.5 21.4 1.0
O A:ALA144 4.5 15.5 1.0
O D:HOH2099 4.5 20.5 1.0
N D:LEU64 4.6 17.3 1.0
O D:ASN57 4.7 15.8 1.0
O D:HOH2087 4.8 21.8 1.0
O D:ASP59 4.9 22.9 1.0
C D:PRO63 5.0 19.8 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 18:41:20 2024

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