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Iron 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
Sodium (Na) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 16 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8pox

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Iron binding site 1 out of 16 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 Iron with other atoms in the Fe 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:Fe701

b:15.2
occ:1.00
 FE L:NFU701 0.0 15.2 1.0
C1 L:NFU701 1.8 15.0 1.0
C3 L:NFU701 1.8 15.4 1.0
C2 L:NFU701 1.8 15.0 1.0
SG L:CYS78 2.3 17.6 1.0
SG L:CYS600 2.3 16.5 1.0
NI L:NFU701 2.7 16.6 1.0
O3 L:NFU701 3.0 16.6 1.0
N1 L:NFU701 3.0 14.1 1.0
N2 L:NFU701 3.0 14.6 1.0
CB L:CYS78 3.4 16.7 1.0
CB L:CYS600 3.4 15.0 1.0
SG L:CYS597 4.2 19.1 1.0
CG1 L:VAL551 4.2 18.9 1.0
NE2 L:HIS82 4.2 15.8 1.0
CB L:CYS597 4.2 18.2 1.0
CD L:ARG530 4.3 16.7 1.0
NH1 L:ARG530 4.4 18.9 1.0
SG L:CYS81 4.4 18.3 1.0
CD L:PRO552 4.6 15.1 1.0
SG L:CYS75 4.7 16.5 1.0
CA L:CYS600 4.8 14.9 1.0
CA L:CYS78 4.8 17.4 1.0
CB L:CYS75 4.8 16.5 1.0
CG L:PRO552 5.0 15.1 1.0
CD2 L:HIS82 5.0 15.0 1.0

Iron binding site 2 out of 16 in 8pox

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Iron binding site 2 out of 16 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 Iron with other atoms in the Fe 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
S:Fe1001

b:19.3
occ:1.00
 FE1 S:SF41001 0.0 19.3 1.0
S3 S:SF41001 2.3 21.1 1.0
S2 S:SF41001 2.3 21.4 1.0
S4 S:SF41001 2.3 19.0 1.0
SG S:CYS221 2.3 18.9 1.0
FE3 S:SF41001 2.7 21.3 1.0
FE2 S:SF41001 2.7 21.1 1.0
FE4 S:SF41001 2.7 22.1 1.0
CB S:CYS221 3.3 17.9 1.0
CD1 S:ILE243 3.9 23.1 1.0
S1 S:SF41001 3.9 20.9 1.0
CG1 S:ILE243 4.4 21.1 1.0
CD S:PRO224 4.4 20.3 1.0
CA S:GLY223 4.5 19.2 1.0
N S:GLY223 4.6 18.8 1.0
CA S:CYS221 4.6 17.9 1.0
SG S:CYS215 4.7 20.6 1.0
ND1 S:HIS187 4.7 19.0 1.0
N S:TYR217 4.7 18.2 1.0
SG S:CYS190 4.8 22.2 1.0
N S:LEU216 4.8 19.0 1.0
C S:CYS221 4.9 17.5 1.0
CB S:LEU216 4.9 17.9 1.0
C S:LEU216 4.9 17.6 1.0

Iron binding site 3 out of 16 in 8pox

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Iron binding site 3 out of 16 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 Iron with other atoms in the Fe 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:Fe1001

b:21.1
occ:1.00
 FE2 S:SF41001 0.0 21.1 1.0
S1 S:SF41001 2.3 20.9 1.0
S4 S:SF41001 2.3 19.0 1.0
SG S:CYS215 2.3 20.6 1.0
S3 S:SF41001 2.3 21.1 1.0
FE4 S:SF41001 2.7 22.1 1.0
FE3 S:SF41001 2.7 21.3 1.0
FE1 S:SF41001 2.7 19.3 1.0
CB S:CYS215 3.5 20.9 1.0
N S:LEU216 3.7 19.0 1.0
S2 S:SF41001 3.9 21.4 1.0
CA S:CYS215 3.9 19.8 1.0
N S:TYR217 4.2 18.2 1.0
C S:CYS215 4.3 19.6 1.0
CB S:PHE196 4.3 23.2 1.0
ND1 S:HIS187 4.5 19.0 1.0
CD1 S:PHE196 4.5 23.7 1.0
CB S:ARG192 4.6 22.1 1.0
CE1 S:HIS187 4.7 22.2 1.0
CA S:LEU216 4.7 18.6 1.0
CB S:TYR217 4.7 19.5 1.0
CG S:PHE196 4.8 24.6 1.0
C S:LEU216 4.8 17.6 1.0
SG S:CYS221 4.9 18.9 1.0
O S:ARG192 4.9 23.9 1.0
SG S:CYS190 4.9 22.2 1.0
CA S:TYR217 4.9 18.1 1.0

Iron binding site 4 out of 16 in 8pox

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Iron binding site 4 out of 16 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 Iron with other atoms in the Fe binding site number 4 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:Fe1001

b:21.3
occ:1.00
 FE3 S:SF41001 0.0 21.3 1.0
S1 S:SF41001 2.3 20.9 1.0
S2 S:SF41001 2.3 21.4 1.0
S4 S:SF41001 2.3 19.0 1.0
SG S:CYS190 2.3 22.2 1.0
FE1 S:SF41001 2.7 19.3 1.0
FE4 S:SF41001 2.7 22.1 1.0
FE2 S:SF41001 2.7 21.1 1.0
CB S:CYS190 3.1 22.9 1.0
S3 S:SF41001 3.9 21.1 1.0
CB S:ARG192 4.1 22.1 1.0
CD1 S:ILE243 4.1 23.1 1.0
CG2 S:ILE243 4.2 20.2 1.0
CA S:CYS190 4.6 22.1 1.0
ND1 S:HIS187 4.6 19.0 1.0
CG1 S:ILE243 4.7 21.1 1.0
C S:ARG192 4.7 24.3 1.0
CA S:ARG192 4.7 24.4 1.0
SG S:CYS221 4.8 18.9 1.0
N S:ARG192 4.8 23.4 1.0
N S:ARG193 4.8 25.0 1.0
CG S:ARG192 4.9 22.3 1.0
SG S:CYS215 4.9 20.6 1.0
C S:CYS190 5.0 23.1 1.0

Iron binding site 5 out of 16 in 8pox

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Iron binding site 5 out of 16 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 Iron with other atoms in the Fe binding site number 5 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:Fe1001

b:22.1
occ:1.00
 FE4 S:SF41001 0.0 22.1 1.0
ND1 S:HIS187 2.1 19.0 1.0
S2 S:SF41001 2.3 21.4 1.0
S1 S:SF41001 2.3 20.9 1.0
S3 S:SF41001 2.3 21.1 1.0
FE2 S:SF41001 2.7 21.1 1.0
FE3 S:SF41001 2.7 21.3 1.0
FE1 S:SF41001 2.7 19.3 1.0
CE1 S:HIS187 2.9 22.2 1.0
CG S:HIS187 3.2 23.0 1.0
CB S:HIS187 3.7 23.5 1.0
CA S:HIS187 3.9 22.0 1.0
S4 S:SF41001 3.9 19.0 1.0
NE2 S:HIS187 4.1 23.2 1.0
CG S:PRO224 4.3 21.1 1.0
CD2 S:HIS187 4.3 24.0 1.0
CD S:PRO224 4.3 20.3 1.0
CD S:ARG193 4.4 30.8 1.0
CB S:CYS190 4.6 22.9 1.0
SG S:CYS215 4.6 20.6 1.0
SG S:CYS190 4.7 22.2 1.0
O S:HIS187 4.7 26.1 1.0
N S:PRO224 4.8 19.7 1.0
SG S:CYS221 4.8 18.9 1.0
CD1 S:PHE196 4.9 23.7 1.0
N S:HIS187 4.9 21.5 1.0
C S:HIS187 4.9 22.8 1.0
CG S:ARG193 5.0 31.9 1.0

Iron binding site 6 out of 16 in 8pox

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Iron binding site 6 out of 16 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 Iron with other atoms in the Fe binding site number 6 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:Fe1002

b:17.5
occ:1.00
 FE1 S:F3S1002 0.0 17.5 1.0
S1 S:F3S1002 2.2 17.0 1.0
S2 S:F3S1002 2.3 17.2 1.0
SG S:CYS249 2.3 17.4 1.0
S3 S:F3S1002 2.3 18.3 1.0
FE4 S:F3S1002 2.7 17.1 1.0
FE3 S:F3S1002 2.7 17.9 1.0
CB S:CYS249 3.2 15.6 1.0
CA S:CYS249 3.6 16.1 1.0
S4 S:F3S1002 3.9 17.6 1.0
N S:ILE250 4.1 16.0 1.0
N S:GLY251 4.2 15.8 1.0
C S:CYS249 4.3 16.2 1.0
N S:CYS252 4.5 16.6 1.0
CG1 S:ILE186 4.5 23.9 1.0
CG2 S:THR226 4.5 19.6 1.0
CD1 S:ILE186 4.6 22.6 1.0
O S:HOH1249 4.7 25.1 1.0
CA S:GLY251 4.8 16.2 1.0
SG S:CYS252 4.8 17.2 1.0
SG S:CYS230 4.8 19.1 1.0
CG S:PRO242 4.8 16.2 1.0
N S:CYS249 4.9 16.4 1.0

Iron binding site 7 out of 16 in 8pox

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Iron binding site 7 out of 16 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 Iron with other atoms in the Fe binding site number 7 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:Fe1002

b:17.9
occ:1.00
 FE3 S:F3S1002 0.0 17.9 1.0
S1 S:F3S1002 2.2 17.0 1.0
SG S:CYS230 2.3 19.1 1.0
S4 S:F3S1002 2.3 17.6 1.0
S3 S:F3S1002 2.3 18.3 1.0
FE1 S:F3S1002 2.7 17.5 1.0
FE4 S:F3S1002 2.7 17.1 1.0
CB S:CYS230 3.3 19.0 1.0
S2 S:F3S1002 4.0 17.2 1.0
ND2 S:ASN228 4.0 18.3 1.0
CD1 S:ILE186 4.2 22.6 1.0
NE1 S:TRP235 4.3 17.3 1.0
O S:HOH1176 4.4 18.7 1.0
CD S:PRO242 4.5 16.4 1.0
CG S:ASN228 4.5 19.4 1.0
CG S:PRO242 4.6 16.2 1.0
CB S:ASN228 4.6 19.1 1.0
CA S:CYS230 4.7 18.3 1.0
SG S:CYS252 4.8 17.2 1.0
SG S:CYS249 4.8 17.4 1.0
CG1 S:ILE186 4.9 23.9 1.0

Iron binding site 8 out of 16 in 8pox

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Iron binding site 8 out of 16 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 Iron with other atoms in the Fe binding site number 8 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:Fe1002

b:17.1
occ:1.00
 FE4 S:F3S1002 0.0 17.1 1.0
S4 S:F3S1002 2.3 17.6 1.0
SG S:CYS252 2.3 17.2 1.0
S2 S:F3S1002 2.3 17.2 1.0
S3 S:F3S1002 2.3 18.3 1.0
FE1 S:F3S1002 2.7 17.5 1.0
FE3 S:F3S1002 2.7 17.9 1.0
CB S:CYS252 3.4 16.1 1.0
N S:CYS252 3.8 16.6 1.0
O L:HOH1040 3.9 15.7 1.0
S1 S:F3S1002 3.9 17.0 1.0
O S:HOH1176 4.0 18.7 1.0
NZ L:LYS226 4.1 17.3 1.0
CA S:CYS252 4.1 16.3 1.0
ND2 S:ASN228 4.5 18.3 1.0
N S:SER253 4.6 16.9 1.0
C S:CYS252 4.6 17.4 1.0
SG S:CYS230 4.7 19.1 1.0
SG S:CYS249 4.7 17.4 1.0
C S:GLY251 5.0 15.5 1.0

Iron binding site 9 out of 16 in 8pox

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Iron binding site 9 out of 16 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 Iron with other atoms in the Fe binding site number 9 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:Fe1003

b:17.1
occ:0.82
 FE1 S:SF41003 0.0 17.1 0.8
FE1 S:ER21006 0.0 17.1 0.2
S2 S:SF41003 2.3 16.9 0.8
S4 S:ER21006 2.3 16.9 0.2
S3 S:SF41003 2.3 17.4 0.8
S1 S:ER21006 2.3 17.4 0.2
S4 S:SF41003 2.3 17.5 0.8
S2 S:ER21006 2.3 17.5 0.2
SG S:CYS17 2.3 16.3 1.0
FE3 S:SF41003 2.6 15.1 0.8
FE2 S:SF41003 2.7 18.3 0.8
FE2 S:ER21006 2.7 18.3 0.2
FE4 S:SF41003 2.7 17.5 0.8
FE4 S:ER21006 2.7 17.5 0.2
CB S:CYS17 3.4 14.1 1.0
FE3 S:ER21006 3.5 30.4 0.2
N S:CYS17 3.7 16.2 1.0
S1 S:SF41003 3.8 18.0 0.8
S3 S:ER21006 3.8 18.0 0.2
N S:GLY19 3.9 17.5 1.0
CA S:CYS17 4.0 15.9 1.0
NE2 L:HIS229 4.1 14.9 1.0
CA S:GLY19 4.2 16.8 1.0
N S:THR18 4.3 16.2 1.0
C S:CYS17 4.3 16.2 1.0
SG S:CYS149 4.6 17.3 1.0
N S:CYS20 4.6 17.9 1.0
O S:HOH1159 4.6 17.8 1.0
SG S:CYS115 4.7 19.6 1.0
CD2 L:HIS229 4.8 15.1 1.0
C S:GLY19 4.8 17.1 1.0
C S:GLU16 4.9 18.6 1.0
SG S:CYS20 4.9 18.6 1.0
CG L:ARG73 5.0 16.4 1.0

Iron binding site 10 out of 16 in 8pox

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Iron binding site 10 out of 16 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 Iron with other atoms in the Fe binding site number 10 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:Fe1003

b:18.3
occ:0.82
 FE2 S:SF41003 0.0 18.3 0.8
FE2 S:ER21006 0.0 18.3 0.2
SG S:CYS115 2.3 19.6 1.0
S4 S:SF41003 2.3 17.5 0.8
S2 S:ER21006 2.3 17.5 0.2
S3 S:SF41003 2.3 17.4 0.8
S1 S:ER21006 2.3 17.4 0.2
S1 S:SF41003 2.3 18.0 0.8
S3 S:ER21006 2.3 18.0 0.2
FE3 S:ER21006 2.6 30.4 0.2
FE1 S:SF41003 2.7 17.1 0.8
FE1 S:ER21006 2.7 17.1 0.2
FE3 S:SF41003 2.7 15.1 0.8
FE4 S:SF41003 2.8 17.5 0.8
FE4 S:ER21006 2.8 17.5 0.2
CB S:CYS115 3.3 19.3 1.0
O S:HOH1137 3.9 21.3 1.0
S2 S:SF41003 3.9 16.9 0.8
S4 S:ER21006 3.9 16.9 0.2
N S:CYS115 4.1 17.7 1.0
O S:HOH1159 4.1 17.8 1.0
CA S:CYS115 4.2 17.7 1.0
SG S:CYS120 4.4 18.0 1.0
N S:CYS17 4.6 16.2 1.0
CB S:CYS120 4.6 17.9 1.0
SG S:CYS20 4.6 18.6 1.0
SG S:CYS149 4.7 17.3 1.0
SG S:CYS17 4.8 16.3 1.0
CA S:GLU16 4.8 19.5 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 21:35:29 2024

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