Atomistry » Sodium » PDB 1m90-1nji » 1mro
Atomistry »
  Sodium »
    PDB 1m90-1nji »
      1mro »

Sodium in PDB 1mro: Methyl-Coenzyme M Reductase

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase, PDB code: 1mro 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 (%) 19.7 / 20.7

Other elements in 1mro:

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

Nickel (Ni) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Methyl-Coenzyme M Reductase (pdb code 1mro). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Methyl-Coenzyme M Reductase, PDB code: 1mro:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1mro

Go back to Sodium Binding Sites List in 1mro
Sodium binding site 1 out of 2 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
C:Na803

b:19.2
occ:1.00
O C:HOH8195 2.0 23.3 1.0
O C:HOH8338 2.1 19.4 1.0
O C:HOH8044 2.1 21.7 1.0
O C:HOH8213 2.1 20.5 1.0
OE2 C:GLU30 2.2 19.0 1.0
CD C:GLU30 3.2 18.9 1.0
OE1 C:GLU30 3.6 19.0 1.0
O C:HOH8407 4.0 30.1 1.0
NZ C:LYS135 4.0 18.6 1.0
O C:HOH8557 4.1 37.6 1.0
O C:ILE31 4.2 19.2 1.0
OE2 C:GLU139 4.3 18.2 1.0
O C:HOH8558 4.3 36.9 1.0
O C:HOH8429 4.4 23.0 1.0
NZ C:LYS27 4.5 18.8 1.0
CG C:GLU30 4.6 18.6 1.0
CE C:LYS135 4.9 18.3 1.0
OD1 C:ASP33 5.0 22.3 1.0

Sodium binding site 2 out of 2 in 1mro

Go back to Sodium Binding Sites List in 1mro
Sodium binding site 2 out of 2 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
F:Na802

b:18.5
occ:1.00
O F:HOH8267 2.0 20.9 1.0
O F:HOH8217 2.1 19.3 1.0
O F:HOH8034 2.1 19.1 1.0
O F:HOH8122 2.1 19.8 1.0
O F:HOH8225 2.1 18.4 1.0
OE2 F:GLU30 2.7 20.3 1.0
CD F:GLU30 3.5 19.9 1.0
OE1 F:GLU30 3.5 19.9 1.0
O F:ILE31 4.0 19.3 1.0
O F:HOH8086 4.1 22.8 1.0
NZ F:LYS135 4.1 18.3 1.0
OE2 F:GLU139 4.3 18.6 1.0
O F:HOH8476 4.3 39.0 1.0
O F:HOH8427 4.3 24.8 1.0
NZ F:LYS27 4.5 19.1 1.0
CG F:GLU30 4.9 19.6 1.0
OD1 F:ASP33 4.9 22.9 1.0
C F:ILE31 5.0 19.4 1.0

Reference:

U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, R.K.Thauer. Crystal Structure of Methyl-Coenzyme M Reductase: the Key Enzyme of Biological Methane Formation. Science V. 278 1457 1997.
ISSN: ISSN 0036-8075
PubMed: 9367957
DOI: 10.1126/SCIENCE.278.5342.1457
Page generated: Tue Dec 15 05:30:40 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