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Sodium in PDB 1hbm: Methyl-Coenzyme M Reductase Enzyme Product Complex

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase Enzyme Product Complex, PDB code: 1hbm 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 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.000, 118.300, 122.800, 90.00, 92.00, 90.00
R / Rfree (%) 16.4 / 19.3

Other elements in 1hbm:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 5 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Methyl-Coenzyme M Reductase Enzyme Product Complex (pdb code 1hbm). 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 Enzyme Product Complex, PDB code: 1hbm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 1hbm

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Sodium binding site 1 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1556

b:24.9
occ:1.00
 O A:HOH2027 2.3 26.9 1.0
O A:LYS11 2.3 19.8 1.0
O A:PHE14 2.3 19.2 1.0
O A:HOH2035 2.3 30.6 1.0
O A:HOH2044 2.4 21.8 1.0
O A:HOH2036 2.4 28.4 1.0
C A:LYS11 3.4 18.9 1.0
C A:PHE14 3.5 17.2 1.0
O A:GLU15 3.9 16.0 1.0
CA A:GLU15 3.9 16.4 1.0
CA A:LYS11 4.0 17.4 1.0
C A:GLU15 4.1 15.7 1.0
N A:GLU15 4.1 17.3 1.0
O A:HOH2026 4.3 31.6 1.0
CB A:LYS11 4.4 17.8 1.0
O A:HOH2024 4.5 31.1 1.0
N A:LYS12 4.5 17.6 1.0
N A:PHE14 4.5 17.6 1.0
O A:GLU16 4.6 19.6 1.0
CA A:PHE14 4.6 18.3 1.0
CA A:LYS12 4.9 18.7 1.0
N A:GLU16 5.0 16.2 1.0
C A:LYS12 5.0 18.6 1.0

Sodium binding site 2 out of 9 in 1hbm

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Sodium binding site 2 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1557

b:22.6
occ:1.00
 O D:HOH2437 2.3 25.9 1.0
O A:HOH2420 2.4 11.4 1.0
O A:HOH2261 2.4 18.9 1.0
O A:ARG270 2.4 13.7 1.0
O3 D:GOL1553 2.4 30.0 1.0
O D:HOH2273 3.3 20.1 1.0
C A:ARG270 3.4 11.2 1.0
C3 D:GOL1553 3.6 29.5 1.0
CA A:ARG270 3.6 11.9 1.0
O D:HOH2423 3.7 23.1 1.0
CG A:ARG270 3.8 10.4 1.0
O1 D:GOL1553 3.9 24.3 1.0
C1 D:GOL1553 4.0 27.7 1.0
NH1 D:ARG225 4.1 10.3 1.0
O A:VAL269 4.2 9.0 1.0
C2 D:GOL1553 4.4 29.0 1.0
CB A:ARG270 4.4 10.7 1.0
OE2 D:GLU275 4.4 14.6 1.0
CE1 D:MHS257 4.4 13.5 1.0
OXT A:SHT1551 4.5 11.0 1.0
O D:HOH2422 4.6 24.0 1.0
O1P A:SHT1551 4.6 11.1 1.0
N A:AGM271 4.6 10.6 1.0
N A:ARG270 4.8 12.3 1.0
C A:VAL269 5.0 12.6 1.0

Sodium binding site 3 out of 9 in 1hbm

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Sodium binding site 3 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1558

b:20.9
occ:1.00
 O A:HOH2410 2.3 25.1 1.0
O A:HOH2407 2.3 24.3 1.0
O A:THR547 2.4 15.8 1.0
OG1 A:THR547 2.4 15.8 1.0
O A:PRO548 2.4 20.3 1.0
O A:ALA544 2.4 17.1 1.0
C A:THR547 3.2 16.0 1.0
C A:PRO548 3.3 20.3 1.0
C A:ALA544 3.4 17.7 1.0
CB A:THR547 3.6 15.3 1.0
CA A:ALA544 3.7 17.4 1.0
CA A:THR547 3.8 15.3 1.0
N A:PRO548 3.9 17.5 1.0
N A:THR547 3.9 14.2 1.0
N A:ALA549 4.0 21.4 1.0
O D:HOH2413 4.1 26.7 1.0
CA A:PRO548 4.1 19.3 1.0
CB A:ALA544 4.2 19.0 1.0
CA A:ALA549 4.3 22.3 1.0
O D:HOH2419 4.6 40.7 1.0
O A:HOH2205 4.6 50.4 1.0
N A:LEU545 4.6 18.0 1.0
CG2 A:THR547 4.7 16.8 1.0
O A:ARG543 4.9 13.7 1.0
O D:HOH2208 5.0 38.0 1.0
N A:ALA544 5.0 16.3 1.0

Sodium binding site 4 out of 9 in 1hbm

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Sodium binding site 4 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1559

b:15.3
occ:1.00
 O A:HOH2110 2.3 16.3 1.0
O A:THR62 2.3 14.3 1.0
O A:ILE60 2.4 15.7 1.0
O D:HOH2172 2.4 11.9 1.0
O A:HOH2113 3.0 14.3 1.0
O A:PRO58 3.1 18.7 1.0
O A:HOH2112 3.1 20.5 1.0
C A:THR62 3.4 15.4 1.0
C A:ILE60 3.6 14.9 1.0
N A:THR62 3.8 14.8 1.0
C A:PRO58 3.9 17.0 1.0
C A:GLY61 3.9 16.5 1.0
O D:HOH2174 4.0 12.8 1.0
O A:GLY61 4.1 15.4 1.0
CA A:THR62 4.2 13.4 1.0
N A:PRO63 4.2 15.1 1.0
CA A:PRO63 4.3 15.4 1.0
N A:ILE60 4.3 15.4 1.0
O D:ALA144 4.4 11.0 1.0
CA A:GLY61 4.4 15.6 1.0
CA A:PRO58 4.4 15.9 1.0
N A:GLY61 4.4 15.4 1.0
O D:HOH2173 4.5 16.2 1.0
N A:LEU64 4.5 13.7 1.0
O A:HOH2104 4.5 15.8 1.0
CA A:ILE60 4.6 15.2 1.0
C A:ASP59 4.7 18.4 1.0
O A:ASN57 4.7 13.1 1.0
N A:ASP59 4.8 17.4 1.0
C A:PRO63 4.9 14.8 1.0
CA A:ASP59 5.0 18.3 1.0

Sodium binding site 5 out of 9 in 1hbm

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Sodium binding site 5 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1445

b:20.3
occ:1.00
 O B:ASN441 2.4 19.4 1.0
O B:HOH2368 2.4 24.0 1.0
C B:ASN441 3.5 21.0 1.0
CB B:ASN441 3.8 20.2 1.0
CA B:ASN441 4.0 19.7 1.0
O B:HOH2195 4.3 56.4 1.0
ND2 B:ASN441 4.5 17.4 1.0
O B:HOH2366 4.5 21.8 1.0
N B:GLU442 4.6 20.6 1.0
CG B:ASN441 4.7 19.5 1.0
CA B:GLU442 5.0 22.5 1.0

Sodium binding site 6 out of 9 in 1hbm

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Sodium binding site 6 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1447

b:28.9
occ:1.00
 O B:HOH2145 2.3 33.0 1.0
O B:HOH2147 2.3 31.6 1.0
O B:HOH2122 2.4 27.1 1.0
O B:HOH2140 2.4 33.3 1.0
O B:ASP99 2.4 23.4 1.0
O B:THR101 2.4 20.3 1.0
C B:THR101 3.5 19.1 1.0
C B:ASP99 3.6 20.5 1.0
N B:THR101 3.7 18.3 1.0
C B:ASP100 3.9 19.4 1.0
OD1 B:ASN102 3.9 25.3 1.0
CA B:ASP100 4.0 19.5 1.0
O B:HOH2130 4.0 26.3 1.0
CA B:THR101 4.1 18.4 1.0
N B:ASP100 4.3 19.4 1.0
NZ B:LYS90 4.3 22.0 1.0
OD2 B:ASP98 4.3 24.1 0.0
N B:ASP99 4.5 24.3 1.0
O B:ASP100 4.5 18.6 1.0
C B:ASP98 4.5 26.7 1.0
N B:ASN102 4.6 18.6 1.0
CB B:THR101 4.6 18.4 1.0
OD2 B:ASP99 4.6 19.3 1.0
CE B:LYS90 4.7 21.1 1.0
CA B:ASP99 4.7 22.3 1.0
CG B:ASN102 4.8 22.8 1.0
CA B:ASP98 4.8 27.8 1.0
CA B:ASN102 4.9 19.5 1.0
O B:ASP98 4.9 28.2 1.0

Sodium binding site 7 out of 9 in 1hbm

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Sodium binding site 7 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1557

b:26.5
occ:1.00
 O D:HOH2028 2.3 26.6 1.0
O D:HOH2017 2.3 31.7 1.0
O D:HOH2016 2.3 29.7 1.0
O D:HOH2022 2.4 28.2 1.0
O D:LYS11 2.4 23.7 1.0
O D:PHE14 2.4 21.9 1.0
C D:LYS11 3.5 23.2 1.0
C D:PHE14 3.5 21.5 1.0
O D:GLU15 3.9 22.0 1.0
CA D:LYS11 3.9 21.7 1.0
CA D:GLU15 3.9 22.2 1.0
C D:GLU15 4.1 21.8 1.0
N D:GLU15 4.2 22.3 1.0
CB D:LYS11 4.3 23.3 1.0
O D:GLU16 4.5 21.6 1.0
N D:PHE14 4.6 20.0 1.0
N D:LYS12 4.6 22.8 1.0
CA D:PHE14 4.6 20.9 1.0
O D:HOH2004 4.8 38.0 1.0
O D:HOH2012 4.9 26.6 1.0
O D:HOH2008 4.9 50.7 1.0
CA D:LYS12 5.0 22.6 1.0
N D:GLU16 5.0 20.3 1.0

Sodium binding site 8 out of 9 in 1hbm

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Sodium binding site 8 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1558

b:24.1
occ:1.00
 O D:HOH2139 2.3 27.1 1.0
O D:HOH2432 2.4 13.4 1.0
O D:HOH2266 2.4 20.4 1.0
O D:ARG270 2.4 11.4 1.0
O1 A:GOL1552 2.4 31.5 1.0
O A:HOH2424 3.2 15.3 1.0
C1 A:GOL1552 3.3 32.1 1.0
C D:ARG270 3.3 8.5 1.0
O E:HOH2076 3.5 28.4 1.0
CA D:ARG270 3.5 8.2 1.0
CG D:ARG270 3.7 9.1 1.0
O2 A:GOL1552 4.0 29.9 1.0
NH1 A:ARG225 4.1 9.9 1.0
O D:VAL269 4.1 8.5 1.0
C2 A:GOL1552 4.1 32.3 1.0
CB D:ARG270 4.3 8.7 1.0
CE1 A:MHS257 4.4 16.0 1.0
O D:SHT1551 4.5 11.8 1.0
OE2 A:GLU275 4.5 15.3 1.0
O E:HOH2087 4.5 29.0 1.0
N D:AGM271 4.6 9.6 1.0
O2P D:SHT1551 4.6 12.5 1.0
N D:ARG270 4.7 9.2 1.0
C D:VAL269 4.8 9.5 1.0

Sodium binding site 9 out of 9 in 1hbm

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Sodium binding site 9 out of 9 in the Methyl-Coenzyme M Reductase Enzyme Product Complex


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1559

b:18.2
occ:1.00
 O A:HOH2174 2.3 14.8 1.0
O D:ILE60 2.4 16.3 1.0
O D:HOH2098 2.4 23.4 1.0
O D:THR62 2.4 17.0 1.0
O D:PRO58 2.4 19.8 1.0
O D:HOH2103 2.8 22.3 1.0
O D:HOH2099 3.3 18.1 1.0
C D:THR62 3.4 17.6 1.0
C D:ILE60 3.5 15.2 1.0
C D:PRO58 3.6 17.9 1.0
N D:THR62 3.8 15.4 1.0
C D:GLY61 3.9 17.2 1.0
O A:HOH2177 4.1 11.9 1.0
O D:GLY61 4.1 18.7 1.0
N D:ILE60 4.1 17.2 1.0
CA D:THR62 4.2 15.7 1.0
N D:PRO63 4.2 17.0 1.0
CA D:PRO63 4.3 16.7 1.0
C D:ASP59 4.3 18.2 1.0
CA D:PRO58 4.4 16.7 1.0
N D:GLY61 4.4 14.9 1.0
N D:ASP59 4.4 16.8 1.0
CA D:ILE60 4.4 15.7 1.0
CA D:GLY61 4.4 16.4 1.0
O A:ALA144 4.5 11.7 1.0
CA D:ASP59 4.5 18.2 1.0
O D:HOH2104 4.5 15.5 1.0
N D:LEU64 4.7 14.9 1.0
O D:HOH2093 4.7 18.7 1.0
O D:ASN57 4.8 13.7 1.0
O D:ASP59 4.9 16.6 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 18:41:04 2024

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