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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

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