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

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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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

Go back to Sodium Binding Sites List in 1hbm
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: Tue Dec 15 05:25:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy