Atomistry » Iron » PDB 8oz5-8py5 » 8pou
Atomistry »
  Iron »
    PDB 8oz5-8py5 »
      8pou »

Iron in PDB 8pou: Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.

Enzymatic activity of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.

All present enzymatic activity of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution., PDB code: 8pou 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 (°) 73.231, 95.74, 120.005, 90, 90, 90
R / Rfree (%) 13.2 / 16.1

Other elements in 8pou:

The structure of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms
Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. (pdb code 8pou). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution., PDB code: 8pou:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 1 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe701

b:17.2
occ:1.00
 FE L:NFV701 0.0 17.2 1.0
C1 L:NFV701 1.8 15.7 1.0
C3 L:NFV701 1.9 16.9 1.0
C2 L:NFV701 1.9 16.2 1.0
O4 L:NFV701 2.2 23.0 1.0
SG L:CYS78 2.3 18.8 1.0
SG L:CYS600 2.4 18.1 1.0
NI L:NFV701 2.9 19.5 1.0
O1 L:NFV701 3.0 18.7 1.0
N3 L:NFV701 3.0 17.6 1.0
N2 L:NFV701 3.0 15.4 1.0
CB L:CYS78 3.4 19.7 1.0
CB L:CYS600 3.4 16.7 1.0
CD L:ARG530 4.2 19.3 1.0
CG1 L:VAL551 4.3 15.5 0.5
NE2 L:HIS82 4.3 17.1 1.0
CB L:CYS597 4.3 20.6 1.0
NH1 L:ARG530 4.4 23.9 1.0
SG L:CYS597 4.4 22.2 1.0
SG L:CYS81 4.4 21.0 1.0
CD L:PRO552 4.7 15.9 1.0
CA L:CYS78 4.8 20.1 1.0
CA L:CYS600 4.8 17.0 1.0
SG L:CYS75 4.8 20.9 1.0
CB L:CYS75 4.9 18.2 1.0
NE L:ARG530 5.0 19.9 1.0

Iron binding site 2 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 2 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:24.4
occ:1.00
 FE1 S:SF41001 0.0 24.4 1.0
ND1 S:HIS187 2.1 22.5 1.0
S2 S:SF41001 2.3 25.9 1.0
S4 S:SF41001 2.3 23.5 1.0
S3 S:SF41001 2.3 23.8 1.0
FE4 S:SF41001 2.7 22.9 1.0
FE3 S:SF41001 2.8 23.4 1.0
FE2 S:SF41001 2.8 21.6 1.0
CE1 S:HIS187 2.9 24.3 1.0
CG S:HIS187 3.2 23.6 1.0
CB S:HIS187 3.6 23.6 1.0
CA S:HIS187 3.8 23.3 1.0
S1 S:SF41001 3.9 23.5 1.0
NE2 S:HIS187 4.1 22.7 1.0
CD S:PRO224 4.2 22.5 1.0
CD2 S:HIS187 4.2 24.0 1.0
CG S:PRO224 4.2 24.1 1.0
SG S:CYS215 4.6 23.4 1.0
CB S:CYS190 4.6 25.3 1.0
O S:HIS187 4.6 29.3 1.0
SG S:CYS190 4.7 25.2 1.0
CD2 S:PHE196 4.7 25.8 1.0
C S:HIS187 4.8 26.8 1.0
N S:HIS187 4.8 24.6 1.0
N S:PRO224 4.8 23.4 1.0
SG S:CYS221 4.9 20.8 1.0

Iron binding site 3 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 3 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:21.6
occ:1.00
 FE2 S:SF41001 0.0 21.6 1.0
S3 S:SF41001 2.3 23.8 1.0
S4 S:SF41001 2.3 23.5 1.0
SG S:CYS221 2.3 20.8 1.0
S1 S:SF41001 2.3 23.5 1.0
FE3 S:SF41001 2.7 23.4 1.0
FE4 S:SF41001 2.7 22.9 1.0
FE1 S:SF41001 2.8 24.4 1.0
CB S:CYS221 3.3 19.2 1.0
S2 S:SF41001 3.9 25.9 1.0
CD1 S:ILE243 3.9 20.6 1.0
CD S:PRO224 4.4 22.5 1.0
CG1 S:ILE243 4.5 20.6 1.0
CA S:GLY223 4.5 21.4 1.0
N S:GLY223 4.5 20.8 1.0
CA S:CYS221 4.6 18.5 1.0
SG S:CYS215 4.6 23.4 1.0
N S:TYR217 4.7 19.9 1.0
ND1 S:HIS187 4.7 22.5 1.0
SG S:CYS190 4.8 25.2 1.0
N S:LEU216 4.8 20.6 1.0
C S:CYS221 4.8 19.4 1.0
CB S:LEU216 4.9 20.3 1.0
O S:CYS221 5.0 20.1 1.0
C S:LEU216 5.0 19.9 1.0

Iron binding site 4 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 4 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:23.4
occ:1.00
 FE3 S:SF41001 0.0 23.4 1.0
S1 S:SF41001 2.3 23.5 1.0
S2 S:SF41001 2.3 25.9 1.0
SG S:CYS190 2.3 25.2 1.0
S4 S:SF41001 2.3 23.5 1.0
FE2 S:SF41001 2.7 21.6 1.0
FE4 S:SF41001 2.7 22.9 1.0
FE1 S:SF41001 2.8 24.4 1.0
CB S:CYS190 3.1 25.3 1.0
S3 S:SF41001 3.9 23.8 1.0
CB S:ARG192 4.1 24.2 1.0
CD1 S:ILE243 4.2 20.6 1.0
CG2 S:ILE243 4.2 20.9 1.0
CA S:CYS190 4.6 26.9 1.0
ND1 S:HIS187 4.7 22.5 1.0
C S:ARG192 4.7 26.0 1.0
N S:ARG193 4.7 29.1 1.0
CA S:ARG192 4.7 25.2 1.0
N S:ARG192 4.8 26.4 1.0
SG S:CYS221 4.8 20.8 1.0
CG1 S:ILE243 4.8 20.6 1.0
CG S:ARG192 4.8 23.9 1.0
C S:CYS190 4.9 27.4 1.0
SG S:CYS215 4.9 23.4 1.0
CA S:HIS187 5.0 23.3 1.0

Iron binding site 5 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 5 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1001

b:22.9
occ:1.00
 FE4 S:SF41001 0.0 22.9 1.0
SG S:CYS215 2.3 23.4 1.0
S1 S:SF41001 2.3 23.5 1.0
S3 S:SF41001 2.3 23.8 1.0
S2 S:SF41001 2.3 25.9 1.0
FE1 S:SF41001 2.7 24.4 1.0
FE2 S:SF41001 2.7 21.6 1.0
FE3 S:SF41001 2.7 23.4 1.0
CB S:CYS215 3.4 22.9 1.0
N S:LEU216 3.8 20.6 1.0
S4 S:SF41001 3.9 23.5 1.0
CA S:CYS215 3.9 22.6 1.0
N S:TYR217 4.2 19.9 1.0
C S:CYS215 4.3 21.5 1.0
CB S:PHE196 4.3 26.4 1.0
CD2 S:PHE196 4.4 25.8 1.0
ND1 S:HIS187 4.5 22.5 1.0
CB S:ARG192 4.7 24.2 1.0
CB S:TYR217 4.7 22.4 1.0
CE1 S:HIS187 4.7 24.3 1.0
CA S:LEU216 4.8 20.7 1.0
CG S:PHE196 4.8 26.3 1.0
C S:LEU216 4.8 19.9 1.0
O S:ARG192 4.8 26.6 1.0
SG S:CYS221 4.8 20.8 1.0
CA S:TYR217 4.8 20.7 1.0
SG S:CYS190 4.9 25.2 1.0

Iron binding site 6 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 6 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:19.4
occ:1.00
 FE1 S:F3S1002 0.0 19.4 1.0
S3 S:F3S1002 2.3 21.4 1.0
S2 S:F3S1002 2.3 20.1 1.0
S1 S:F3S1002 2.3 20.1 1.0
SG S:CYS249 2.3 19.4 1.0
FE3 S:F3S1002 2.7 19.6 1.0
FE4 S:F3S1002 2.7 19.7 1.0
CB S:CYS249 3.1 18.0 1.0
CA S:CYS249 3.6 18.0 1.0
S4 S:F3S1002 3.9 18.3 1.0
N S:ILE250 4.1 17.6 1.0
N S:GLY251 4.2 18.7 1.0
C S:CYS249 4.3 17.8 1.0
N S:CYS252 4.4 18.3 1.0
CG2 S:THR226 4.5 22.6 1.0
O S:HOH1256 4.6 23.6 0.6
CG1 S:ILE186 4.7 28.9 1.0
CA S:GLY251 4.7 18.9 1.0
SG S:CYS252 4.8 20.0 1.0
CG S:PRO242 4.8 19.6 1.0
SG S:CYS230 4.8 21.7 1.0
N S:CYS249 4.9 18.6 1.0
CD1 S:ILE186 4.9 27.9 1.0

Iron binding site 7 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 7 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:19.6
occ:1.00
 FE3 S:F3S1002 0.0 19.6 1.0
S3 S:F3S1002 2.3 21.4 1.0
S4 S:F3S1002 2.3 18.3 1.0
S1 S:F3S1002 2.3 20.1 1.0
SG S:CYS230 2.3 21.7 1.0
FE1 S:F3S1002 2.7 19.4 1.0
FE4 S:F3S1002 2.7 19.7 1.0
CB S:CYS230 3.3 20.8 1.0
S2 S:F3S1002 3.9 20.1 1.0
ND2 S:ASN228 4.0 20.6 1.0
NE1 S:TRP235 4.3 20.2 1.0
CD1 S:ILE186 4.4 27.9 1.0
O S:HOH1179 4.4 20.4 1.0
CG S:PRO242 4.5 19.6 1.0
CG S:ASN228 4.5 21.3 1.0
CD S:PRO242 4.6 19.2 1.0
CB S:ASN228 4.6 20.9 1.0
SG S:CYS252 4.7 20.0 1.0
CA S:CYS230 4.7 20.9 1.0
SG S:CYS249 4.8 19.4 1.0
CG1 S:ILE186 4.9 28.9 1.0

Iron binding site 8 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 8 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1002

b:19.7
occ:1.00
 FE4 S:F3S1002 0.0 19.7 1.0
SG S:CYS252 2.3 20.0 1.0
S4 S:F3S1002 2.3 18.3 1.0
S2 S:F3S1002 2.3 20.1 1.0
S3 S:F3S1002 2.3 21.4 1.0
FE1 S:F3S1002 2.7 19.4 1.0
FE3 S:F3S1002 2.7 19.6 1.0
CB S:CYS252 3.3 18.9 1.0
N S:CYS252 3.8 18.3 1.0
O L:HOH990 3.9 19.7 1.0
S1 S:F3S1002 4.0 20.1 1.0
CA S:CYS252 4.0 18.4 1.0
O S:HOH1179 4.0 20.4 1.0
NZ L:LYS226 4.1 23.1 1.0
N S:SER253 4.5 18.3 1.0
C S:CYS252 4.5 18.6 1.0
ND2 S:ASN228 4.6 20.6 1.0
O S:HOH1256 4.7 22.7 0.4
SG S:CYS230 4.7 21.7 1.0
SG S:CYS249 4.7 19.4 1.0
C S:GLY251 4.9 18.5 1.0

Iron binding site 9 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 9 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:23.3
occ:1.00
 FE1 S:SF41003 0.0 23.3 1.0
SG S:CYS17 2.2 21.1 1.0
S4 S:SF41003 2.3 20.9 1.0
S2 S:SF41003 2.3 22.4 1.0
S3 S:SF41003 2.3 23.0 0.5
FE3 S:SF41003 2.6 16.2 0.7
FE2 S:SF41003 2.7 24.0 1.0
S3 S:SF41003 2.7 27.5 0.5
FE4 S:SF41003 2.7 26.5 1.0
FE3 S:SF41003 3.3 29.7 0.3
CB S:CYS17 3.3 19.9 1.0
N S:CYS17 3.7 21.6 1.0
S1 S:SF41003 3.7 15.9 0.5
N S:GLY19 3.9 20.4 1.0
CA S:CYS17 4.0 20.8 1.0
NE2 L:HIS229 4.1 17.4 1.0
S1 S:SF41003 4.1 31.2 0.5
CA S:GLY19 4.2 18.9 1.0
N S:THR18 4.3 20.4 1.0
C S:CYS17 4.3 19.0 1.0
O S:HOH1152 4.6 18.4 1.0
SG S:CYS149 4.7 20.4 1.0
N S:CYS20 4.7 20.2 1.0
SG S:CYS115 4.7 24.5 1.0
CD2 L:HIS229 4.9 19.5 1.0
SG S:CYS20 4.9 23.4 1.0
C S:GLY19 4.9 20.1 1.0
C S:GLU16 4.9 22.5 1.0
CG L:ARG73 4.9 17.9 1.0

Iron binding site 10 out of 13 in 8pou

Go back to Iron Binding Sites List in 8pou
Iron binding site 10 out of 13 in the Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the C19G/C120G Variant of the Membrane-Bound [Nife]-Hydrogenase From Cupriavidus Necator in the Air-Oxidized State at 1.65 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe1003

b:24.0
occ:1.00
 FE2 S:SF41003 0.0 24.0 1.0
S1 S:SF41003 2.1 31.2 0.5
S3 S:SF41003 2.2 23.0 0.5
S4 S:SF41003 2.3 20.9 1.0
SG S:CYS115 2.3 24.5 1.0
S1 S:SF41003 2.3 15.9 0.5
FE3 S:SF41003 2.5 29.7 0.3
FE3 S:SF41003 2.7 16.2 0.7
FE1 S:SF41003 2.7 23.3 1.0
FE4 S:SF41003 2.8 26.5 1.0
S3 S:SF41003 3.0 27.5 0.5
CB S:CYS115 3.3 21.9 1.0
S2 S:SF41003 3.8 22.4 1.0
O S:HOH1111 3.9 25.3 1.0
N S:CYS115 4.0 19.6 1.0
O S:HOH1287 4.0 23.9 1.0
O S:HOH1152 4.1 18.4 1.0
CA S:CYS115 4.3 20.9 1.0
SG S:CYS149 4.6 20.4 1.0
SG S:CYS20 4.7 23.4 1.0
N S:CYS17 4.7 21.6 1.0
SG S:CYS17 4.8 21.1 1.0
CA S:GLU16 5.0 21.9 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 Aug 10 13:08:49 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