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Chlorine in PDB 8poz: Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.

Enzymatic activity of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.

All present enzymatic activity of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution., PDB code: 8poz was solved by A.Schmidt, J.Kalms, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.415, 95.751, 120.597, 90, 90, 90
R / Rfree (%) 14.1 / 17.2

Other elements in 8poz:

The structure of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution. also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution. (pdb code 8poz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution., PDB code: 8poz:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8poz

Go back to Chlorine Binding Sites List in 8poz
Chlorine binding site 1 out of 4 in the Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl703

b:18.5
occ:0.70
 ND1 L:HIS121 2.9 12.9 1.0
O L:HOH889 2.9 13.3 1.0
ND1 L:HIS126 3.0 14.3 1.0
NH1 L:ARG476 3.1 12.3 1.0
CE1 L:HIS121 3.1 13.1 1.0
CD L:ARG476 3.5 12.1 1.0
CD1 L:PHE122 3.7 13.9 1.0
CA L:PHE122 3.8 12.5 1.0
CG L:HIS126 3.8 13.5 1.0
CB L:PHE122 3.8 12.7 1.0
CG2 L:THR473 3.9 13.0 1.0
CE1 L:HIS126 3.9 14.7 1.0
CB L:HIS126 3.9 12.8 1.0
CZ L:ARG476 4.0 12.1 1.0
NE L:ARG476 4.1 11.9 1.0
CG L:HIS121 4.2 12.8 1.0
N L:PHE122 4.2 11.5 1.0
CG L:PHE122 4.2 13.4 1.0
NE2 L:HIS121 4.5 12.8 1.0
CG L:ARG476 4.5 12.0 1.0
CA L:THR473 4.6 12.1 1.0
CB L:THR473 4.6 12.5 1.0
OH L:TYR276 4.7 13.3 1.0
CB L:ARG476 4.7 11.8 1.0
C L:HIS121 4.7 12.4 1.0
CE1 L:PHE122 4.7 14.6 1.0
OG1 L:THR473 4.8 13.0 1.0
O L:THR473 4.8 11.8 1.0
O L:HIS592 4.9 11.4 1.0
CB L:HIS121 4.9 12.8 1.0
O L:HIS121 4.9 12.7 1.0
CD2 L:HIS121 5.0 13.1 1.0
CD2 L:HIS126 5.0 13.6 1.0

Chlorine binding site 2 out of 4 in 8poz

Go back to Chlorine Binding Sites List in 8poz
Chlorine binding site 2 out of 4 in the Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl704

b:35.6
occ:1.00
 NH1 L:ARG384 3.0 23.9 1.0
N L:LEU376 3.2 18.6 1.0
CA L:VAL375 3.8 18.2 1.0
CG L:ARG384 3.8 23.9 1.0
CD L:ARG384 3.8 24.9 1.0
C L:VAL375 4.0 17.8 1.0
CB L:LEU376 4.0 17.5 1.0
CG2 L:VAL375 4.1 20.4 1.0
CA L:LEU376 4.1 18.0 1.0
CZ L:ARG384 4.2 23.6 1.0
CG L:LEU376 4.2 17.4 1.0
O L:LEU376 4.3 20.7 1.0
NE L:ARG384 4.4 25.8 1.0
CB L:ARG384 4.4 22.8 1.0
CB L:VAL375 4.5 18.6 1.0
C L:LEU376 4.7 18.5 1.0
O L:TYR374 4.7 18.9 1.0
N L:VAL375 4.9 17.5 1.0
CD1 L:LEU376 4.9 17.9 1.0
CA L:ARG384 5.0 20.9 1.0

Chlorine binding site 3 out of 4 in 8poz

Go back to Chlorine Binding Sites List in 8poz
Chlorine binding site 3 out of 4 in the Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl1003

b:42.6
occ:0.40
 CL S:CL1003 0.0 42.6 0.4
CL S:CL1003 0.8 33.8 0.4
N S:GLY120 3.1 14.5 1.0
O S:HOH1167 3.2 28.4 1.0
O S:HOH1189 3.2 22.5 1.0
CA S:GLY120 3.4 14.7 1.0
CB S:TRP118 3.7 15.9 1.0
N S:GLY256 3.8 15.8 1.0
CD1 S:TRP258 4.0 14.1 1.0
C S:GLY120 4.1 13.3 1.0
O S:GLY120 4.1 13.1 1.0
O S:SER114 4.2 14.5 1.0
C S:TRP118 4.2 15.3 1.0
C S:GLY119 4.2 13.7 1.0
N S:GLY119 4.3 14.7 1.0
CA S:GLY256 4.3 16.0 1.0
CD1 S:PHE257 4.4 14.7 1.0
NE1 S:TRP258 4.4 13.9 1.0
O S:GLU254 4.4 15.4 1.0
O S:TRP118 4.4 17.9 1.0
CE1 S:PHE257 4.5 14.1 1.0
CB S:SER114 4.5 13.6 1.0
CA S:GLY119 4.6 14.1 1.0
CA S:TRP118 4.6 14.6 1.0
N S:PHE257 4.6 14.6 1.0
C S:SER114 4.7 13.1 1.0
C S:ASP255 4.7 15.5 1.0
CG S:TRP118 4.8 17.5 1.0
CA S:ASP255 4.9 15.2 1.0
C S:GLY256 4.9 14.5 1.0
O S:HOH1242 4.9 26.6 1.0
CD1 S:TRP118 5.0 17.9 1.0

Chlorine binding site 4 out of 4 in 8poz

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Chlorine binding site 4 out of 4 in the Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the C120G Variant of the Membrane-Bound [Nife]- Hydrogenase From Cupriavidus Necator in the H2-Reduced State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl1003

b:33.8
occ:0.40
 CL S:CL1003 0.0 33.8 0.4
CL S:CL1003 0.8 42.6 0.4
O S:HOH1189 3.0 22.5 1.0
N S:GLY256 3.1 15.8 1.0
O S:HOH1167 3.4 28.4 1.0
CB S:TRP118 3.5 15.9 1.0
N S:GLY120 3.5 14.5 1.0
CA S:GLY256 3.7 16.0 1.0
C S:TRP118 4.0 15.3 1.0
CA S:GLY120 4.0 14.7 1.0
O S:TRP118 4.1 17.9 1.0
C S:ASP255 4.2 15.5 1.0
N S:GLY119 4.3 14.7 1.0
O S:GLU254 4.3 15.4 1.0
OD1 S:ASP255 4.3 17.7 1.0
CA S:ASP255 4.4 15.2 1.0
N S:PHE257 4.4 14.6 1.0
CA S:TRP118 4.4 14.6 1.0
O S:GLY120 4.4 13.1 1.0
CD1 S:TRP258 4.4 14.1 1.0
C S:GLY119 4.5 13.7 1.0
C S:GLY256 4.5 14.5 1.0
CG S:TRP118 4.5 17.5 1.0
O S:SER114 4.5 14.5 1.0
C S:GLY120 4.6 13.3 1.0
CA S:GLY119 4.6 14.1 1.0
O S:HOH1242 4.6 26.6 1.0
CD1 S:PHE257 4.7 14.7 1.0
O S:HOH1295 4.8 39.2 1.0
CD1 S:TRP118 4.9 17.9 1.0
NE1 S:TRP258 5.0 13.9 1.0
CE1 S:PHE257 5.0 14.1 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: Sat Sep 28 19:26:28 2024

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