Atomistry » Sodium » PDB 1ghy-1hn1 » 1hbn
Atomistry »
  Sodium »
    PDB 1ghy-1hn1 »
      1hbn »

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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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

Go back to Sodium Binding Sites List in 1hbn
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 Aug 17 05:10:20 2025

Last articles

Na in 7DDK
Na in 7DDI
Na in 7DCS
Na in 7DDH
Na in 7DDF
Na in 7DCU
Na in 7DCT
Na in 7DCJ
Na in 7D93
Na in 7D94
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy