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Iron in PDB 7nem: Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form

Enzymatic activity of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form

All present enzymatic activity of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form:
1.12.99.6;

Protein crystallography data

The structure of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form, PDB code: 7nem was solved by S.B.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.80 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.402, 100.252, 168.536, 90, 90, 90
R / Rfree (%) 15 / 16.7

Other elements in 7nem:

The structure of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Nickel (Ni) 2 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form (pdb code 7nem). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form, PDB code: 7nem:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 7nem

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Iron binding site 1 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:11.1
occ:1.00
 FE1 S:SF4401 0.0 11.1 1.0
S3 S:SF4401 2.2 11.0 1.0
S2 S:SF4401 2.3 11.2 1.0
SG S:CYS220 2.3 11.9 1.0
S4 S:SF4401 2.3 11.4 1.0
FE4 S:SF4401 2.7 11.1 1.0
FE3 S:SF4401 2.7 11.4 1.0
FE2 S:SF4401 2.8 11.2 1.0
CB S:CYS220 3.4 12.5 1.0
N S:LEU221 3.9 10.8 1.0
S1 S:SF4401 3.9 11.0 1.0
CA S:CYS220 4.0 11.6 1.0
N S:TYR222 4.1 11.5 1.0
C S:CYS220 4.3 11.9 1.0
CB S:PHE201 4.4 13.2 1.0
CD2 S:PHE201 4.5 14.5 1.0
ND1 S:HIS192 4.5 12.4 1.0
CB S:ARG197 4.5 11.1 1.0
CB S:TYR222 4.6 11.5 1.0
O S:ARG197 4.6 11.3 1.0
CA S:TYR222 4.7 11.7 1.0
CE1 S:HIS192 4.8 12.2 1.0
SG S:CYS226 4.8 10.8 1.0
C S:LEU221 4.8 11.3 1.0
SG S:CYS195 4.8 10.8 1.0
C S:ARG197 4.8 10.5 1.0
CG S:PHE201 4.9 13.3 1.0
CA S:LEU221 4.9 10.6 1.0

Iron binding site 2 out of 24 in 7nem

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Iron binding site 2 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:11.2
occ:1.00
 FE2 S:SF4401 0.0 11.2 1.0
S4 S:SF4401 2.3 11.4 1.0
SG S:CYS226 2.3 10.8 1.0
S1 S:SF4401 2.3 11.0 1.0
S3 S:SF4401 2.3 11.0 1.0
FE4 S:SF4401 2.7 11.1 1.0
FE3 S:SF4401 2.8 11.4 1.0
FE1 S:SF4401 2.8 11.1 1.0
CB S:CYS226 3.2 10.7 1.0
S2 S:SF4401 3.9 11.2 1.0
N S:GLY228 4.5 11.0 1.0
CD S:PRO229 4.5 11.2 1.0
CA S:CYS226 4.5 11.1 1.0
CA S:GLY228 4.5 11.5 1.0
ND1 S:HIS192 4.7 12.4 1.0
SG S:CYS220 4.7 11.9 1.0
SG S:CYS195 4.7 10.8 1.0
CG2 S:VAL249 4.7 11.6 1.0
N S:TYR222 4.8 11.5 1.0
C S:CYS226 4.8 10.7 1.0
N S:LEU221 4.9 10.8 1.0
O S:CYS226 4.9 11.6 1.0

Iron binding site 3 out of 24 in 7nem

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Iron binding site 3 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:11.4
occ:1.00
 FE3 S:SF4401 0.0 11.4 1.0
ND1 S:HIS192 2.0 12.4 1.0
S1 S:SF4401 2.3 11.0 1.0
S4 S:SF4401 2.3 11.4 1.0
S2 S:SF4401 2.3 11.2 1.0
FE4 S:SF4401 2.7 11.1 1.0
FE1 S:SF4401 2.7 11.1 1.0
FE2 S:SF4401 2.8 11.2 1.0
CE1 S:HIS192 3.0 12.2 1.0
CG S:HIS192 3.1 12.0 1.0
CB S:HIS192 3.6 12.0 1.0
S3 S:SF4401 3.9 11.0 1.0
CA S:HIS192 3.9 11.3 1.0
NE2 S:HIS192 4.1 12.3 1.0
CD2 S:HIS192 4.2 12.9 1.0
CD S:PRO229 4.3 11.2 1.0
CG S:PRO229 4.3 11.9 1.0
CB S:CYS195 4.6 10.7 1.0
SG S:CYS195 4.6 10.8 1.0
SG S:CYS220 4.7 11.9 1.0
O S:HIS192 4.7 12.0 1.0
CD2 S:PHE201 4.8 14.5 1.0
SG S:CYS226 4.8 10.8 1.0
N S:PRO229 4.9 10.7 1.0
C S:HIS192 4.9 11.4 1.0
N S:HIS192 5.0 11.3 1.0

Iron binding site 4 out of 24 in 7nem

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Iron binding site 4 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:11.1
occ:1.00
 FE4 S:SF4401 0.0 11.1 1.0
SG S:CYS195 2.2 10.8 1.0
S2 S:SF4401 2.3 11.2 1.0
S3 S:SF4401 2.3 11.0 1.0
S1 S:SF4401 2.3 11.0 1.0
FE3 S:SF4401 2.7 11.4 1.0
FE1 S:SF4401 2.7 11.1 1.0
FE2 S:SF4401 2.7 11.2 1.0
CB S:CYS195 3.1 10.7 1.0
S4 S:SF4401 3.9 11.4 1.0
CB S:ARG197 4.1 11.1 1.0
ND1 S:HIS192 4.5 12.4 1.0
CA S:CYS195 4.5 9.7 1.0
C S:ARG197 4.5 10.5 1.0
N S:ARG197 4.6 10.5 1.0
N S:ARG198 4.6 10.8 1.0
CA S:ARG197 4.6 10.6 1.0
SG S:CYS226 4.8 10.8 1.0
CG1 S:VAL249 4.8 10.6 1.0
CG S:ARG197 4.9 12.4 1.0
C S:CYS195 4.9 9.4 1.0
SG S:CYS220 4.9 11.9 1.0

Iron binding site 5 out of 24 in 7nem

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Iron binding site 5 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:9.8
occ:1.00
 FE1 S:F3S402 0.0 9.8 1.0
S1 S:F3S402 2.2 9.7 1.0
S2 S:F3S402 2.3 10.1 1.0
SG S:CYS258 2.3 9.6 1.0
S3 S:F3S402 2.3 10.1 1.0
FE3 S:F3S402 2.7 9.9 1.0
FE4 S:F3S402 2.7 10.0 1.0
CB S:CYS258 3.4 10.3 1.0
O L:HOH847 3.7 9.6 1.0
N S:CYS258 3.7 9.4 1.0
S4 S:F3S402 3.8 10.0 1.0
CA S:CYS258 4.0 9.6 1.0
N S:ASN259 4.2 9.7 1.0
OD1 S:ASN259 4.2 10.2 1.0
O S:HOH603 4.3 12.0 1.0
C S:CYS258 4.4 9.8 1.0
SG S:CYS235 4.7 10.8 1.0
O S:HOH516 4.8 17.7 1.0
C S:GLY257 4.8 9.6 1.0
CG S:ASN259 4.8 10.5 1.0
SG S:CYS255 4.9 10.5 1.0
OE1 L:GLN216 4.9 10.6 1.0
CE L:LYS211 4.9 11.3 1.0
N S:GLY257 4.9 9.2 1.0

Iron binding site 6 out of 24 in 7nem

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Iron binding site 6 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:9.9
occ:1.00
 FE3 S:F3S402 0.0 9.9 1.0
S4 S:F3S402 2.2 10.0 1.0
S1 S:F3S402 2.2 9.7 1.0
SG S:CYS235 2.3 10.8 1.0
S3 S:F3S402 2.3 10.1 1.0
FE4 S:F3S402 2.7 10.0 1.0
FE1 S:F3S402 2.7 9.8 1.0
CB S:CYS235 3.3 10.0 1.0
S2 S:F3S402 4.0 10.1 1.0
O S:HOH603 4.1 12.0 1.0
CD1 S:ILE191 4.1 12.4 1.0
CZ S:PHE240 4.5 10.3 1.0
CE1 S:PHE240 4.5 11.3 1.0
CA S:CYS235 4.6 10.0 1.0
SG S:CYS255 4.7 10.5 1.0
OD1 S:ASN259 4.7 10.2 1.0
SG S:CYS258 4.7 9.6 1.0
O S:HOH656 4.9 12.0 1.0
ND2 S:ASN259 4.9 11.1 1.0
CG S:ASN259 4.9 10.5 1.0
CD S:PRO248 5.0 10.2 1.0

Iron binding site 7 out of 24 in 7nem

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Iron binding site 7 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:10.0
occ:1.00
 FE4 S:F3S402 0.0 10.0 1.0
S4 S:F3S402 2.2 10.0 1.0
S3 S:F3S402 2.3 10.1 1.0
SG S:CYS255 2.3 10.5 1.0
S2 S:F3S402 2.3 10.1 1.0
FE3 S:F3S402 2.7 9.9 1.0
FE1 S:F3S402 2.7 9.8 1.0
CB S:CYS255 3.3 11.0 1.0
CA S:CYS255 3.7 10.2 1.0
N S:TYR256 3.9 8.6 1.0
S1 S:F3S402 3.9 9.7 1.0
N S:GLY257 3.9 9.2 1.0
C S:CYS255 4.2 9.9 1.0
CD1 S:ILE191 4.2 12.4 1.0
N S:CYS258 4.3 9.4 1.0
CA S:GLY257 4.5 9.8 1.0
NE2 L:GLN216 4.6 10.5 1.0
SG S:CYS235 4.7 10.8 1.0
CG2 S:THR231 4.8 10.0 1.0
SG S:CYS258 4.9 9.6 1.0
C S:TYR256 4.9 9.5 1.0
C S:GLY257 4.9 9.6 1.0
CA S:TYR256 4.9 9.1 1.0
N S:CYS255 5.0 10.0 1.0

Iron binding site 8 out of 24 in 7nem

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Iron binding site 8 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:9.7
occ:1.00
 FE1 S:SF4403 0.0 9.7 1.0
S4 S:SF4403 2.2 9.8 1.0
SG S:CYS22 2.3 9.3 1.0
S2 S:SF4403 2.3 9.7 1.0
S3 S:SF4403 2.3 10.1 1.0
FE3 S:SF4403 2.7 9.7 1.0
FE2 S:SF4403 2.7 10.0 1.0
FE4 S:SF4403 2.7 10.1 1.0
CB S:CYS22 3.3 9.0 1.0
N S:CYS22 3.8 9.1 1.0
S1 S:SF4403 3.8 10.1 1.0
CA S:CYS22 4.0 9.2 1.0
NE2 L:HIS214 4.2 9.3 1.0
O S:HOH509 4.2 11.2 1.0
N S:GLY24 4.3 9.5 1.0
O S:HOH604 4.5 11.6 1.0
C S:CYS22 4.5 9.4 1.0
CA S:GLY24 4.6 9.2 1.0
N S:THR23 4.6 10.0 1.0
SG S:CYS154 4.7 9.6 1.0
SG S:CYS120 4.7 9.9 1.0
N S:CYS25 4.8 9.7 1.0
CD2 L:HIS214 4.8 9.0 1.0
SG S:CYS25 4.9 9.9 1.0
C S:GLU21 4.9 10.4 1.0
CG L:ARG59 5.0 9.8 1.0

Iron binding site 9 out of 24 in 7nem

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Iron binding site 9 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:10.0
occ:1.00
 FE2 S:SF4403 0.0 10.0 1.0
S3 S:SF4403 2.3 10.1 1.0
SG S:CYS120 2.3 9.9 1.0
S4 S:SF4403 2.3 9.8 1.0
S1 S:SF4403 2.3 10.1 1.0
FE3 S:SF4403 2.6 9.7 1.0
FE1 S:SF4403 2.7 9.7 1.0
FE4 S:SF4403 2.8 10.1 1.0
CB S:CYS120 3.2 10.0 1.0
O S:HOH667 3.9 11.2 1.0
O S:HOH541 3.9 9.6 1.0
S2 S:SF4403 3.9 9.7 1.0
O S:HOH604 4.0 11.6 1.0
N S:CYS120 4.0 9.7 1.0
CA S:CYS120 4.2 9.8 1.0
SG S:CYS154 4.4 9.6 1.0
SG S:CYS22 4.8 9.3 1.0
SG S:CYS25 4.9 9.9 1.0
N S:CYS22 5.0 9.1 1.0
CA S:GLY82 5.0 10.8 1.0

Iron binding site 10 out of 24 in 7nem

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Iron binding site 10 out of 24 in the Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Hydrogenase-2 Variant R479K - Anaerobically Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:9.7
occ:1.00
 FE3 S:SF4403 0.0 9.7 1.0
S2 S:SF4403 2.2 9.7 1.0
SG S:CYS154 2.3 9.6 1.0
S1 S:SF4403 2.3 10.1 1.0
S4 S:SF4403 2.3 9.8 1.0
FE2 S:SF4403 2.6 10.0 1.0
FE1 S:SF4403 2.7 9.7 1.0
FE4 S:SF4403 2.7 10.1 1.0
CB S:CYS154 3.4 9.2 1.0
CA S:CYS154 3.4 9.2 1.0
C S:CYS154 3.8 9.7 1.0
S3 S:SF4403 3.9 10.1 1.0
O S:HOH667 3.9 11.2 1.0
O S:CYS154 4.2 9.8 1.0
N S:PRO155 4.3 9.0 1.0
CG L:ARG59 4.4 9.8 1.0
SG S:CYS120 4.4 9.9 1.0
CD2 L:HIS214 4.4 9.0 1.0
O S:GLY153 4.5 9.9 1.0
SG S:CYS22 4.5 9.3 1.0
NE2 L:HIS214 4.6 9.3 1.0
CA S:PRO155 4.7 9.3 1.0
N S:CYS154 4.7 9.4 1.0
SG S:CYS25 4.8 9.9 1.0
NE L:ARG59 4.9 9.4 1.0

Reference:

R.M.Evans, S.E.Beaton, L.Kertiss, W.K.Myers, S.B.Carr, F.A.Armstrong. A Comprehensive Structural and Kinetic Investigation of the Role of the Active-Site Argininein Bidirectional Hydrogen Activation By the [Nife]-Hydrogenase "Hyd-2) From Escherichia Coli To Be Published.
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