Atomistry » Sodium » PDB 8piw-8qaw » 8pox
Atomistry »
  Sodium »
    PDB 8piw-8qaw »
      8pox »

Sodium in PDB 8pox: Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution.

Enzymatic activity of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution.

All present enzymatic activity of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution.:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution., PDB code: 8pox was solved by J.Kalms, A.Schmidt, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.78 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.208, 95.688, 119.84, 90, 90, 90
R / Rfree (%) 12.7 / 15.6

Other elements in 8pox:

The structure of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms
Nickel (Ni) 1 atom
Iron (Fe) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution. (pdb code 8pox). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution., PDB code: 8pox:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8pox

Go back to Sodium Binding Sites List in 8pox
Sodium binding site 1 out of 3 in the Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na703

b:43.4
occ:1.00
O L:HOH1203 2.6 42.9 1.0
N L:LYS463 3.3 29.2 1.0
O L:HOH1095 3.5 41.2 1.0
CB L:LYS463 3.7 35.8 1.0
N L:LEU462 3.7 28.2 1.0
OH L:TYR421 3.9 47.5 1.0
CB L:THR461 3.9 31.4 1.0
CB L:LEU462 4.0 30.3 1.0
CA L:LYS463 4.0 32.5 1.0
OG1 L:THR461 4.1 31.5 1.0
CA L:LEU462 4.1 28.5 1.0
C L:LEU462 4.1 29.3 1.0
CE2 L:TYR421 4.4 36.6 1.0
CZ L:TYR421 4.5 37.2 1.0
C L:THR461 4.5 27.9 1.0
NH1 L:ARG425 4.6 53.4 0.3
CA L:THR461 4.7 29.6 1.0
O L:HOH822 4.8 52.0 1.0
CG2 L:THR461 4.8 33.8 1.0
CG L:LYS463 4.9 39.0 1.0
CZ3 L:TRP331 4.9 33.6 1.0

Sodium binding site 2 out of 3 in 8pox

Go back to Sodium Binding Sites List in 8pox
Sodium binding site 2 out of 3 in the Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na704

b:25.0
occ:1.00
O L:HOH1184 2.6 21.1 1.0
O L:HOH816 2.7 23.2 1.0
NE L:ARG88 3.1 17.1 1.0
NH1 L:ARG106 3.2 16.8 1.0
CD L:ARG106 3.5 15.8 1.0
NH2 L:ARG88 3.6 18.4 1.0
CD1 L:ILE98 3.7 21.2 1.0
CZ L:ARG88 3.8 18.2 1.0
CG L:ARG88 3.8 16.2 1.0
CD1 L:LEU84 3.9 16.1 1.0
CD L:ARG88 4.0 16.8 1.0
CZ L:ARG106 4.2 15.9 1.0
O L:HOH1022 4.2 26.3 1.0
NE L:ARG106 4.3 15.8 1.0
O L:HOH1208 4.3 41.6 1.0
CB L:ARG106 4.5 15.7 1.0
O L:HOH814 4.5 18.2 1.0
CG L:ARG106 4.6 15.4 1.0
O L:HOH1172 4.7 37.0 1.0
ND1 L:HIS103 4.7 23.1 1.0
OE2 L:GLU107 4.9 37.7 1.0
CG1 L:ILE98 4.9 19.9 1.0
OE1 L:GLU91 4.9 17.8 1.0

Sodium binding site 3 out of 3 in 8pox

Go back to Sodium Binding Sites List in 8pox
Sodium binding site 3 out of 3 in the Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the C19G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na1004

b:27.7
occ:1.00
O S:VAL202 2.6 20.9 1.0
O S:CYS215 2.7 21.2 1.0
N S:LYS218 2.9 18.9 1.0
C S:LEU216 3.2 17.6 1.0
CA S:LEU216 3.3 18.6 1.0
N S:TYR217 3.3 18.2 1.0
N S:VAL202 3.3 20.5 1.0
N S:MET219 3.4 19.0 1.0
CA S:LYS218 3.5 18.9 1.0
CB S:LYS218 3.5 18.9 1.0
C S:VAL202 3.5 20.4 1.0
C S:CYS215 3.5 19.6 1.0
O S:LEU216 3.6 18.3 1.0
CB S:PHE201 3.7 22.9 1.0
CA S:VAL202 3.8 20.4 1.0
C S:LYS218 3.8 18.6 1.0
N S:LEU216 3.8 19.0 1.0
CG S:MET219 3.8 19.9 1.0
C S:TYR217 3.8 18.1 1.0
CB S:VAL202 3.9 20.8 1.0
C S:PHE201 4.0 21.2 1.0
CA S:PHE201 4.0 22.1 1.0
CA S:TYR217 4.1 18.1 1.0
CD1 S:PHE201 4.1 23.2 1.0
CG S:LYS218 4.3 19.7 1.0
CG S:PHE201 4.4 24.0 1.0
CB S:MET219 4.4 20.2 1.0
CA S:MET219 4.5 19.0 1.0
CB S:LEU216 4.6 17.9 1.0
SD S:MET219 4.7 21.1 1.0
CG2 S:VAL202 4.7 21.0 1.0
CB S:TYR217 4.8 19.5 1.0
N S:GLU203 4.8 20.2 1.0
O S:LYS218 4.8 20.4 1.0
O S:TYR217 4.9 19.1 1.0
CA S:CYS215 4.9 19.8 1.0
CG1 S:VAL202 4.9 20.7 1.0
O S:PHE201 5.0 22.8 1.0

Reference:

A.Schmidt, J.Kalms, C.Lorent, S.Katz, S.Frielingsdorf, R.M.Evans, J.Fritsch, E.Siebert, C.Teutloff, F.A.Armstrong, I.Zebger, O.Lenz, P.Scheerer. Stepwise Conversion of the Cys 6 [4FE-3S] to A Cys 4 [4FE-4S] Cluster and Its Impact on the Oxygen Tolerance of [Nife]-Hydrogenase. Chem Sci V. 14 11105 2023.
ISSN: ISSN 2041-6520
PubMed: 37860641
DOI: 10.1039/D3SC03739H
Page generated: Wed Oct 9 13:01:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy