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Sodium in PDB 1hbn: Methyl-Coenzyme M Reductase

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase, PDB code: 1hbn 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) 30.00 / 1.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.720, 116.883, 122.582, 90.00, 92.02, 90.00
R / Rfree (%) 12.4 / 19

Other elements in 1hbn:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 18 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 10 in 1hbn

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Sodium binding site 1 out of 10 in the Methyl-Coenzyme M Reductase


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

b:20.6
occ:1.00
 O A:LYS11 2.3 19.0 1.0
O A:PHE14 2.3 18.0 1.0
O A:HOH2050 2.3 19.8 1.0
O A:HOH2029 2.3 26.7 1.0
O A:HOH2028 2.3 28.6 1.0
O A:HOH2037 2.4 30.2 1.0
C A:LYS11 3.3 16.4 1.0
C A:PHE14 3.5 16.2 1.0
CA A:LYS11 3.8 16.2 1.0
O A:GLU15 3.9 18.5 1.0
O A:HOH2017 4.0 79.0 1.0
CA A:GLU15 4.0 17.7 1.0
C A:GLU15 4.1 17.6 1.0
N A:GLU15 4.1 16.9 1.0
CB A:LYS11 4.2 17.5 1.0
O A:GLU16 4.4 15.9 1.0
O A:HOH2026 4.4 26.3 1.0
O A:HOH2030 4.4 35.8 1.0
N A:LYS12 4.4 17.1 1.0
N A:PHE14 4.5 17.0 1.0
O A:HOH2038 4.6 56.7 1.0
CA A:PHE14 4.6 16.8 1.0
CA A:LYS12 4.8 18.6 1.0
C A:LYS12 4.9 17.6 1.0
N A:GLU16 4.9 16.6 1.0
O A:LEU10 4.9 15.8 1.0

Sodium binding site 2 out of 10 in 1hbn

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Sodium binding site 2 out of 10 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1560

b:22.4
occ:1.00
 O D:HOH2501 2.3 16.3 1.0
O A:HOH2487 2.4 24.7 1.0
O1 A:GOL1553 2.4 28.9 1.0
O D:HOH2314 2.4 20.9 1.0
O D:ARG270 2.4 14.4 1.0
O A:HOH2306 3.2 30.0 1.0
C D:ARG270 3.3 12.6 1.0
C1 A:GOL1553 3.5 28.4 1.0
CA D:ARG270 3.6 11.9 1.0
O E:HOH2090 3.6 49.8 1.0
CG D:ARG270 3.7 12.2 1.0
O2 A:GOL1553 3.9 29.7 1.0
NH1 A:ARG225 4.0 13.2 1.0
C2 A:GOL1553 4.1 28.1 1.0
O D:VAL269 4.2 12.4 1.0
CB D:ARG270 4.3 11.9 1.0
O D:TP71551 4.3 13.0 1.0
OE2 A:GLU275 4.4 23.4 1.0
CE1 A:MHS257 4.4 16.6 1.0
O2P D:TP71551 4.6 13.0 1.0
N D:AGM271 4.6 11.8 1.0
O E:HOH2103 4.6 31.1 1.0
N D:ARG270 4.7 11.6 1.0
C D:VAL269 4.9 11.5 1.0
CZ A:ARG225 5.0 11.4 1.0

Sodium binding site 3 out of 10 in 1hbn

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Sodium binding site 3 out of 10 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1561

b:19.9
occ:1.00
 O A:HOH2467 2.3 27.2 1.0
O A:HOH2472 2.3 27.8 1.0
O A:THR547 2.4 16.7 1.0
O A:ALA544 2.4 16.4 1.0
OG1 A:THR547 2.5 17.5 1.0
O A:PRO548 2.5 19.0 1.0
C A:THR547 3.1 16.0 1.0
C A:PRO548 3.2 19.8 1.0
C A:ALA544 3.4 15.8 1.0
CB A:THR547 3.6 16.0 1.0
CA A:ALA544 3.7 15.8 1.0
CA A:THR547 3.7 14.6 1.0
N A:PRO548 3.7 16.4 1.0
N A:THR547 3.9 13.9 1.0
O A:HOH2466 3.9 58.1 1.0
N A:ALA549 4.0 23.7 1.0
CA A:PRO548 4.0 18.1 1.0
O A:HOH2471 4.2 32.6 1.0
CB A:ALA544 4.2 19.4 1.0
CA A:ALA549 4.3 25.6 1.0
N A:LEU545 4.6 15.2 1.0
O D:HOH2485 4.6 44.1 1.0
CG2 A:THR547 4.8 17.6 1.0
O A:ARG543 4.8 14.3 1.0
O A:HOH2470 4.9 41.2 1.0
N A:ALA544 5.0 16.0 1.0
CD A:PRO548 5.0 17.4 1.0

Sodium binding site 4 out of 10 in 1hbn

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Sodium binding site 4 out of 10 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1562

b:19.1
occ:1.00
 O A:HOH2126 2.3 20.6 1.0
O A:THR62 2.3 16.2 1.0
O A:ILE60 2.4 18.5 1.0
O D:HOH2200 2.4 17.1 1.0
O A:PRO58 3.0 19.8 1.0
O A:HOH2129 3.0 22.7 1.0
O A:HOH2128 3.2 25.9 1.0
C A:THR62 3.4 14.8 1.0
C A:ILE60 3.6 15.4 1.0
N A:THR62 3.8 14.3 1.0
C A:PRO58 3.8 16.1 1.0
C A:GLY61 3.9 15.5 1.0
O D:HOH2202 4.0 17.1 1.0
O A:GLY61 4.1 17.1 1.0
CA A:THR62 4.2 14.0 1.0
N A:PRO63 4.3 15.5 1.0
N A:ILE60 4.3 14.9 1.0
CA A:PRO63 4.3 15.7 1.0
O D:ALA144 4.3 11.9 1.0
O A:HOH2137 4.4 17.6 1.0
CA A:PRO58 4.4 15.6 1.0
CA A:GLY61 4.4 16.1 1.0
N A:GLY61 4.4 15.7 1.0
O A:HOH2120 4.5 24.0 1.0
CA A:ILE60 4.5 15.3 1.0
N A:LEU64 4.6 15.2 1.0
C A:ASP59 4.7 16.2 1.0
N A:ASP59 4.7 15.3 1.0
O A:ASN57 4.7 14.3 1.0
CA A:ASP59 5.0 16.8 1.0
C A:PRO63 5.0 14.9 1.0

Sodium binding site 5 out of 10 in 1hbn

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Sodium binding site 5 out of 10 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1567

b:20.1
occ:1.00
 O A:HOH2027 2.4 33.1 1.0
O A:HOH2380 2.6 30.4 1.0
O A:HOH2061 2.7 39.8 1.0
O A:HOH2201 2.8 50.7 1.0
OE1 A:GLU387 4.3 33.0 1.0
O A:HOH2378 4.3 27.0 0.5
O A:GLU387 4.3 14.8 1.0
CB A:GLU19 4.3 14.7 1.0
O A:GLU19 4.5 14.3 1.0
CG A:GLU19 4.8 16.8 1.0

Sodium binding site 6 out of 10 in 1hbn

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Sodium binding site 6 out of 10 in the Methyl-Coenzyme M Reductase


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

b:17.2
occ:1.00
 O B:ASN441 2.3 18.1 1.0
O B:HOH2419 2.4 27.7 1.0
C B:ASN441 3.5 17.2 1.0
CB B:ASN441 3.9 17.5 1.0
CA B:ASN441 4.0 16.6 1.0
O B:HOH2420 4.5 21.1 1.0
N B:GLU442 4.6 17.9 1.0
ND2 B:ASN441 4.6 17.8 1.0
CG B:ASN441 4.8 18.6 1.0
CA B:GLU442 5.0 20.7 1.0

Sodium binding site 7 out of 10 in 1hbn

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Sodium binding site 7 out of 10 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1448

b:29.0
occ:1.00
 O B:HOH2139 2.3 30.0 1.0
O B:HOH2164 2.4 33.4 1.0
O B:HOH2162 2.4 34.8 1.0
O B:HOH2154 2.4 36.0 1.0
O B:ASP99 2.4 24.6 1.0
O B:THR101 2.4 21.4 1.0
C B:THR101 3.5 18.4 1.0
C B:ASP99 3.6 22.7 1.0
N B:THR101 3.7 16.3 1.0
OD1 B:ASN102 3.8 27.3 1.0
C B:ASP100 3.9 17.2 1.0
CA B:ASP100 4.0 18.1 1.0
O B:HOH2157 4.0 24.4 1.0
CA B:THR101 4.1 16.6 1.0
N B:ASP100 4.2 19.6 1.0
NZ B:LYS90 4.2 23.1 1.0
N B:ASP99 4.5 27.5 1.0
O B:ASP100 4.5 17.4 1.0
C B:ASP98 4.6 29.6 1.0
N B:ASN102 4.6 17.1 1.0
OD2 B:ASP98 4.6 24.1 0.0
CE B:LYS90 4.6 23.0 1.0
CB B:THR101 4.7 16.3 1.0
CG B:ASN102 4.7 24.3 1.0
OD2 B:ASP99 4.7 19.0 1.0
CA B:ASP99 4.7 24.6 1.0
O B:ASP98 4.8 31.6 1.0
CA B:ASP98 4.8 29.1 1.0
CA B:ASN102 4.9 17.8 1.0

Sodium binding site 8 out of 10 in 1hbn

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Sodium binding site 8 out of 10 in the Methyl-Coenzyme M Reductase


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

b:24.5
occ:1.00
 O D:LYS11 2.3 22.2 1.0
O D:PHE14 2.3 20.8 1.0
O D:HOH2028 2.3 24.9 1.0
O D:HOH2014 2.4 31.4 1.0
O D:HOH2013 2.4 31.7 1.0
O D:HOH2023 2.4 29.5 1.0
C D:LYS11 3.4 19.8 1.0
C D:PHE14 3.5 20.2 1.0
CA D:LYS11 3.8 19.1 1.0
CA D:GLU15 3.9 22.6 1.0
O D:GLU15 3.9 23.2 1.0
C D:GLU15 4.1 20.8 1.0
N D:GLU15 4.2 20.9 1.0
CB D:LYS11 4.2 19.8 1.0
O D:GLU16 4.5 19.3 1.0
N D:LYS12 4.5 19.3 1.0
O D:HOH2015 4.5 41.5 1.0
N D:PHE14 4.6 18.6 1.0
CA D:PHE14 4.6 19.1 1.0
O D:HOH2007 4.8 58.9 1.0
O D:HOH2010 4.9 29.4 1.0
CA D:LYS12 4.9 20.4 1.0
O D:LEU10 5.0 17.5 1.0
N D:GLU16 5.0 19.3 1.0
O D:HOH2017 5.0 60.1 1.0

Sodium binding site 9 out of 10 in 1hbn

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Sodium binding site 9 out of 10 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1560

b:20.9
occ:1.00
 O A:HOH2481 2.3 15.4 1.0
O3 D:GOL1554 2.4 27.5 1.0
O A:HOH2302 2.4 19.9 1.0
O D:HOH2507 2.4 22.9 1.0
O A:ARG270 2.4 14.3 1.0
O D:HOH2319 3.2 23.7 1.0
C A:ARG270 3.4 12.2 1.0
C3 D:GOL1554 3.5 27.2 1.0
CA A:ARG270 3.6 11.8 1.0
O D:HOH2490 3.7 40.2 1.0
CG A:ARG270 3.8 12.3 1.0
O1 D:GOL1554 3.9 24.4 1.0
C1 D:GOL1554 3.9 24.9 1.0
NH1 D:ARG225 4.0 12.2 1.0
C2 D:GOL1554 4.2 25.8 1.0
O A:VAL269 4.2 11.5 1.0
CB A:ARG270 4.3 11.6 1.0
OXT A:TP71551 4.4 13.1 1.0
CE1 D:MHS257 4.4 15.6 1.0
OE2 D:GLU275 4.4 23.2 1.0
O1P A:TP71551 4.6 12.8 1.0
N A:AGM271 4.6 11.2 1.0
O D:HOH2489 4.7 34.3 1.0
N A:ARG270 4.8 11.3 1.0
C A:VAL269 4.9 11.1 1.0
CZ D:ARG225 5.0 11.6 1.0

Sodium binding site 10 out of 10 in 1hbn

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Sodium binding site 10 out of 10 in the Methyl-Coenzyme M Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Methyl-Coenzyme M Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1561

b:19.4
occ:1.00
 O D:THR62 2.3 16.8 1.0
O D:HOH2113 2.3 26.1 1.0
O D:ILE60 2.4 17.9 1.0
O A:HOH2206 2.4 18.6 1.0
O D:PRO58 2.5 22.0 1.0
O D:HOH2115 2.9 30.6 1.0
O D:HOH2112 3.3 24.6 1.0
C D:THR62 3.4 14.7 1.0
C D:ILE60 3.5 16.1 1.0
C D:PRO58 3.5 20.0 1.0
N D:THR62 3.8 15.1 1.0
C D:GLY61 3.9 16.8 1.0
N D:ILE60 4.1 16.5 1.0
O A:HOH2209 4.1 18.7 1.0
O D:GLY61 4.1 18.6 1.0
CA D:THR62 4.2 14.4 1.0
N D:PRO63 4.2 15.8 1.0
C D:ASP59 4.2 17.3 1.0
CA D:PRO63 4.2 15.9 1.0
CA D:GLY61 4.3 16.7 1.0
N D:ASP59 4.4 17.2 1.0
N D:GLY61 4.4 15.8 1.0
CA D:ILE60 4.4 16.4 1.0
CA D:PRO58 4.4 18.4 1.0
O D:HOH2119 4.4 17.7 1.0
CA D:ASP59 4.4 19.1 1.0
O A:ALA144 4.4 12.8 1.0
N D:LEU64 4.6 15.9 1.0
O D:ASP59 4.7 20.6 1.0
O D:ASN57 4.8 14.7 1.0
O D:HOH2107 4.8 25.9 1.0
C D:PRO63 5.0 15.6 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 18:41:14 2024

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