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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

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