Magnesium in PDB 5odc: Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution

Enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution

All present enzymatic activity of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution:
1.12.99.6; 1.8.98.1;

Protein crystallography data

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution, PDB code: 5odc was solved by T.Wagner, J.Koch, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 378.047, 98.446, 137.884, 90.00, 110.70, 90.00
R / Rfree (%) 17.8 / 20

Other elements in 5odc:

The structure of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 110 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution (pdb code 5odc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution, PDB code: 5odc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5odc

Go back to Magnesium Binding Sites List in 5odc
Magnesium binding site 1 out of 2 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:39.8
occ:1.00
 OH F:TYR56 2.7 31.4 1.0
OD2 E:ASP279 2.7 36.2 1.0
OD2 F:ASP52 2.8 43.8 1.0
CE2 F:TYR56 3.2 29.6 1.0
N F:TYR49 3.2 31.4 1.0
CZ F:TYR56 3.3 33.4 1.0
CB F:ASP52 3.4 34.3 1.0
CB F:ARG48 3.4 26.4 1.0
CG F:ASP52 3.5 42.0 1.0
CD F:ARG48 3.7 28.5 1.0
CA F:ARG48 3.7 31.1 1.0
CA E:GLY282 3.9 28.2 1.0
CG E:ASP279 3.9 33.8 1.0
O E:GLY282 3.9 29.5 1.0
C F:ARG48 3.9 35.4 1.0
NE F:ARG48 4.0 30.6 1.0
C E:GLY282 4.0 30.0 1.0
CB F:TYR49 4.0 34.9 1.0
CG F:ARG48 4.1 27.5 1.0
CA F:TYR49 4.2 33.1 1.0
O F:TYR49 4.2 36.6 1.0
CD2 F:TYR49 4.4 38.9 1.0
CD2 F:TYR56 4.5 29.2 1.0
NZ E:LYS286 4.5 39.4 1.0
CG F:TYR49 4.6 38.5 1.0
CE E:LYS286 4.6 15.9 1.0
C F:TYR49 4.7 37.6 1.0
CE1 F:TYR56 4.7 29.1 1.0
OD1 E:ASP279 4.7 32.2 1.0
CB E:ASP279 4.8 33.8 1.0
OD1 F:ASP52 4.8 45.2 1.0
N E:SER283 4.8 28.4 1.0
CA F:ASP52 4.9 32.9 1.0

Magnesium binding site 2 out of 2 in 5odc

Go back to Magnesium Binding Sites List in 5odc
Magnesium binding site 2 out of 2 in the Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Heterodisulfide Reductase / [Nife]-Hydrogenase Complex From Methanothermococcus Thermolithotrophicus at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg201

b:44.8
occ:1.00
 O I:HOH321 2.8 49.5 1.0
OD2 I:ASP73 3.1 69.4 1.0
N I:ARG53 3.4 35.3 1.0
O I:ARG53 3.7 38.0 1.0
CG I:ASP73 3.9 65.0 1.0
CB I:ASP73 3.9 52.6 1.0
CD1 I:TYR52 4.0 46.2 1.0
CA I:TYR52 4.1 42.0 1.0
O I:SER51 4.1 47.7 1.0
C I:TYR52 4.3 41.3 1.0
CA I:ARG53 4.3 33.8 1.0
CB I:LYS56 4.3 39.6 1.0
C I:ARG53 4.3 38.1 1.0
O I:HOH315 4.4 45.1 1.0
CB I:ARG53 4.5 33.0 1.0
CG2 I:VAL57 4.5 42.5 1.0
CE1 I:TYR52 4.6 46.3 1.0
C I:SER51 4.9 47.4 1.0
CG I:TYR52 4.9 44.7 1.0
N I:TYR52 4.9 42.9 1.0

Reference:

T.Wagner, J.Koch, U.Ermler, S.Shima. Methanogenic Heterodisulfide Reductase (Hdrabc-Mvhagd) Uses Two Noncubane [4FE-4S] Clusters For Reduction. Science V. 357 699 2017.
ISSN: ESSN 1095-9203
PubMed: 28818947
DOI: 10.1126/SCIENCE.AAN0425
Page generated: Mon Dec 14 20:59:33 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