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Iron in PDB 9ers: Hydrogenase-2 Ni-C State

Enzymatic activity of Hydrogenase-2 Ni-C State

All present enzymatic activity of Hydrogenase-2 Ni-C State:
1.12.99.6;

Protein crystallography data

The structure of Hydrogenase-2 Ni-C State, PDB code: 9ers was solved by K.L.Wong, S.B.Carr, P.A.Ash, K.A.Vincent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.73 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.864, 100.065, 168.359, 90, 90, 90
R / Rfree (%) 17.3 / 19.7

Other elements in 9ers:

The structure of Hydrogenase-2 Ni-C State also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Nickel (Ni) 2 atoms

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 Ni-C State (pdb code 9ers). 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 Ni-C State, PDB code: 9ers:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 9ers

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Iron binding site 1 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:19.8
occ:1.00
FE1 S:SF4301 0.0 19.8 1.0
S2 S:SF4301 2.3 20.0 1.0
SG S:CYS220 2.3 20.4 1.0
S3 S:SF4301 2.3 19.4 1.0
S4 S:SF4301 2.3 21.1 1.0
FE3 S:SF4301 2.7 21.4 1.0
FE4 S:SF4301 2.7 18.6 1.0
FE2 S:SF4301 2.8 19.1 1.0
CB S:CYS220 3.4 19.8 1.0
N S:LEU221 3.9 18.6 1.0
CA S:CYS220 3.9 18.9 1.0
S1 S:SF4301 3.9 18.9 1.0
N S:TYR222 4.1 19.4 1.0
C S:CYS220 4.3 20.2 1.0
CB S:PHE201 4.4 22.4 1.0
CD2 S:PHE201 4.4 23.7 1.0
ND1 S:HIS192 4.4 19.0 1.0
CB S:ARG197 4.5 18.7 1.0
CB S:TYR222 4.5 21.1 1.0
O S:ARG197 4.6 20.3 1.0
CA S:TYR222 4.7 20.0 1.0
CE1 S:HIS192 4.7 20.1 1.0
C S:ARG197 4.8 18.3 1.0
C S:LEU221 4.8 20.8 1.0
CG S:PHE201 4.8 23.1 1.0
SG S:CYS195 4.8 17.1 1.0
CA S:LEU221 4.9 19.2 1.0
SG S:CYS226 4.9 19.4 1.0

Iron binding site 2 out of 24 in 9ers

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Iron binding site 2 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:19.1
occ:1.00
FE2 S:SF4301 0.0 19.1 1.0
S1 S:SF4301 2.3 18.9 1.0
S3 S:SF4301 2.3 19.4 1.0
S4 S:SF4301 2.3 21.1 1.0
SG S:CYS226 2.3 19.4 1.0
FE4 S:SF4301 2.7 18.6 1.0
FE3 S:SF4301 2.7 21.4 1.0
FE1 S:SF4301 2.8 19.8 1.0
CB S:CYS226 3.2 19.4 1.0
S2 S:SF4301 3.9 20.0 1.0
N S:GLY228 4.5 20.0 1.0
CA S:GLY228 4.5 19.6 1.0
CD S:PRO229 4.5 19.9 1.0
CA S:CYS226 4.6 18.8 1.0
ND1 S:HIS192 4.6 19.0 1.0
CG2 S:VAL249 4.7 18.4 1.0
SG S:CYS195 4.7 17.1 1.0
SG S:CYS220 4.7 20.4 1.0
N S:TYR222 4.7 19.4 1.0
C S:CYS226 4.8 18.6 1.0
N S:LEU221 4.9 18.6 1.0
C S:LEU221 5.0 20.8 1.0

Iron binding site 3 out of 24 in 9ers

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Iron binding site 3 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:21.4
occ:1.00
FE3 S:SF4301 0.0 21.4 1.0
ND1 S:HIS192 2.0 19.0 1.0
S4 S:SF4301 2.3 21.1 1.0
S1 S:SF4301 2.3 18.9 1.0
S2 S:SF4301 2.3 20.0 1.0
FE4 S:SF4301 2.7 18.6 1.0
FE1 S:SF4301 2.7 19.8 1.0
FE2 S:SF4301 2.7 19.1 1.0
CE1 S:HIS192 2.9 20.1 1.0
CG S:HIS192 3.1 20.3 1.0
CB S:HIS192 3.6 18.6 1.0
S3 S:SF4301 3.8 19.4 1.0
CA S:HIS192 4.0 19.3 1.0
NE2 S:HIS192 4.1 20.4 1.0
CD2 S:HIS192 4.2 21.6 1.0
CG S:PRO229 4.3 21.2 1.0
CD S:PRO229 4.3 19.9 1.0
CB S:CYS195 4.6 18.2 1.0
SG S:CYS195 4.6 17.1 1.0
SG S:CYS220 4.7 20.4 1.0
CD2 S:PHE201 4.8 23.7 1.0
O S:HIS192 4.8 19.7 1.0
SG S:CYS226 4.8 19.4 1.0
N S:PRO229 4.8 20.4 1.0
C S:HIS192 4.9 19.6 1.0

Iron binding site 4 out of 24 in 9ers

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Iron binding site 4 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:18.6
occ:1.00
FE4 S:SF4301 0.0 18.6 1.0
S3 S:SF4301 2.2 19.4 1.0
SG S:CYS195 2.3 17.1 1.0
S2 S:SF4301 2.3 20.0 1.0
S1 S:SF4301 2.4 18.9 1.0
FE2 S:SF4301 2.7 19.1 1.0
FE3 S:SF4301 2.7 21.4 1.0
FE1 S:SF4301 2.7 19.8 1.0
CB S:CYS195 3.2 18.2 1.0
S4 S:SF4301 3.9 21.1 1.0
CB S:ARG197 4.0 18.7 1.0
ND1 S:HIS192 4.5 19.0 1.0
C S:ARG197 4.5 18.3 1.0
N S:ARG197 4.6 20.0 1.0
CA S:ARG197 4.6 19.3 1.0
N S:ARG198 4.6 18.4 1.0
CA S:CYS195 4.6 17.7 1.0
CG1 S:VAL249 4.8 19.4 1.0
SG S:CYS226 4.8 19.4 1.0
CG S:ARG197 4.8 19.2 1.0
SG S:CYS220 4.9 20.4 1.0
C S:CYS195 4.9 18.6 1.0
CH2 S:TRP247 5.0 18.0 1.0

Iron binding site 5 out of 24 in 9ers

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Iron binding site 5 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:16.9
occ:1.00
FE1 S:F3S302 0.0 16.9 1.0
S1 S:F3S302 2.2 18.0 1.0
S2 S:F3S302 2.3 17.3 1.0
S3 S:F3S302 2.3 16.4 1.0
SG S:CYS258 2.3 16.8 1.0
FE4 S:F3S302 2.7 17.1 1.0
FE3 S:F3S302 2.7 16.6 1.0
CB S:CYS258 3.4 17.4 1.0
O L:HOH817 3.6 16.1 1.0
N S:CYS258 3.7 18.0 1.0
S4 S:F3S302 3.8 18.5 1.0
CA S:CYS258 3.9 18.0 1.0
N S:ASN259 4.2 18.6 1.0
OD1 S:ASN259 4.2 16.4 1.0
O S:HOH440 4.3 16.2 1.0
C S:CYS258 4.4 17.5 1.0
SG S:CYS235 4.7 18.4 1.0
C S:GLY257 4.8 18.9 1.0
CG S:ASN259 4.8 18.8 1.0
CE L:LYS211 4.9 15.7 1.0
O S:HOH414 4.9 16.2 1.0
SG S:CYS255 4.9 18.2 1.0
OE1 L:GLN216 4.9 17.7 1.0
N S:GLY257 5.0 17.5 1.0

Iron binding site 6 out of 24 in 9ers

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Iron binding site 6 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:16.6
occ:1.00
FE3 S:F3S302 0.0 16.6 1.0
S4 S:F3S302 2.2 18.5 1.0
SG S:CYS235 2.2 18.4 1.0
S3 S:F3S302 2.3 16.4 1.0
S1 S:F3S302 2.3 18.0 1.0
FE4 S:F3S302 2.7 17.1 1.0
FE1 S:F3S302 2.7 16.9 1.0
CB S:CYS235 3.3 18.2 1.0
O S:HOH440 4.0 16.2 1.0
S2 S:F3S302 4.0 17.3 1.0
CD1 S:ILE191 4.1 19.2 1.0
CZ S:PHE240 4.5 17.4 1.0
CE1 S:PHE240 4.5 16.4 1.0
OD1 S:ASN259 4.6 16.4 1.0
CA S:CYS235 4.7 17.1 1.0
SG S:CYS255 4.7 18.2 1.0
O S:HOH541 4.8 17.0 1.0
SG S:CYS258 4.8 16.8 1.0
CG S:ASN259 4.9 18.8 1.0
CD S:PRO248 4.9 17.7 1.0

Iron binding site 7 out of 24 in 9ers

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Iron binding site 7 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:17.1
occ:1.00
FE4 S:F3S302 0.0 17.1 1.0
S4 S:F3S302 2.2 18.5 1.0
S3 S:F3S302 2.2 16.4 1.0
S2 S:F3S302 2.3 17.3 1.0
SG S:CYS255 2.4 18.2 1.0
FE3 S:F3S302 2.7 16.6 1.0
FE1 S:F3S302 2.7 16.9 1.0
CB S:CYS255 3.3 17.4 1.0
CA S:CYS255 3.7 17.3 1.0
N S:TYR256 3.9 17.4 1.0
S1 S:F3S302 3.9 18.0 1.0
N S:GLY257 3.9 17.5 1.0
C S:CYS255 4.2 17.8 1.0
CD1 S:ILE191 4.2 19.2 1.0
N S:CYS258 4.3 18.0 1.0
CA S:GLY257 4.5 18.4 1.0
NE2 L:GLN216 4.7 19.0 1.0
SG S:CYS235 4.7 18.4 1.0
CG2 S:THR231 4.8 17.4 1.0
SG S:CYS258 4.9 16.8 1.0
C S:GLY257 4.9 18.9 1.0
C S:TYR256 4.9 18.5 1.0
CA S:TYR256 4.9 17.6 1.0

Iron binding site 8 out of 24 in 9ers

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Iron binding site 8 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:18.4
occ:1.00
FE1 S:SF4303 0.0 18.4 1.0
S4 S:SF4303 2.2 18.1 1.0
SG S:CYS22 2.3 17.9 1.0
S3 S:SF4303 2.3 19.8 1.0
S2 S:SF4303 2.4 17.3 1.0
FE3 S:SF4303 2.7 16.7 1.0
FE2 S:SF4303 2.7 17.4 1.0
FE4 S:SF4303 2.7 19.2 1.0
CB S:CYS22 3.3 19.8 1.0
N S:CYS22 3.7 18.9 1.0
S1 S:SF4303 3.8 17.9 1.0
CA S:CYS22 4.0 17.8 1.0
NE2 L:HIS214 4.2 15.5 1.0
O S:HOH412 4.2 16.9 1.0
N S:GLY24 4.3 17.4 1.0
O S:HOH513 4.5 19.3 1.0
C S:CYS22 4.5 17.4 1.0
N S:THR23 4.5 18.0 1.0
CA S:GLY24 4.6 17.4 1.0
SG S:CYS154 4.6 17.3 1.0
SG S:CYS120 4.7 17.7 1.0
N S:CYS25 4.8 15.9 1.0
SG S:CYS25 4.8 18.2 1.0
CD2 L:HIS214 4.8 15.8 1.0
C S:GLU21 4.9 19.8 0.5
C S:GLU21 4.9 18.7 0.5

Iron binding site 9 out of 24 in 9ers

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Iron binding site 9 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:17.4
occ:1.00
FE2 S:SF4303 0.0 17.4 1.0
S4 S:SF4303 2.3 18.1 1.0
SG S:CYS120 2.3 17.7 1.0
S3 S:SF4303 2.3 19.8 1.0
S1 S:SF4303 2.4 17.9 1.0
FE3 S:SF4303 2.7 16.7 1.0
FE1 S:SF4303 2.7 18.4 1.0
FE4 S:SF4303 2.9 19.2 1.0
CB S:CYS120 3.2 16.5 1.0
O S:HOH513 3.8 19.3 1.0
O S:HOH543 3.8 16.6 1.0
O S:HOH441 3.9 15.0 1.0
S2 S:SF4303 3.9 17.3 1.0
N S:CYS120 4.0 17.6 1.0
CA S:CYS120 4.2 18.0 1.0
SG S:CYS154 4.4 17.3 1.0
SG S:CYS22 4.8 17.9 1.0
SG S:CYS25 4.9 18.2 1.0
CA S:GLY82 5.0 16.8 1.0
N S:CYS22 5.0 18.9 1.0

Iron binding site 10 out of 24 in 9ers

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Iron binding site 10 out of 24 in the Hydrogenase-2 Ni-C State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Hydrogenase-2 Ni-C State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:16.7
occ:1.00
FE3 S:SF4303 0.0 16.7 1.0
SG S:CYS154 2.2 17.3 1.0
S2 S:SF4303 2.3 17.3 1.0
S1 S:SF4303 2.3 17.9 1.0
S4 S:SF4303 2.3 18.1 1.0
FE1 S:SF4303 2.7 18.4 1.0
FE2 S:SF4303 2.7 17.4 1.0
FE4 S:SF4303 2.8 19.2 1.0
CB S:CYS154 3.4 17.2 1.0
CA S:CYS154 3.4 18.2 1.0
O S:HOH543 3.8 16.6 1.0
C S:CYS154 3.8 17.9 1.0
S3 S:SF4303 3.9 19.8 1.0
O S:CYS154 4.2 18.0 1.0
N S:PRO155 4.4 17.4 1.0
CG L:ARG59 4.4 17.3 1.0
CD2 L:HIS214 4.4 15.8 1.0
SG S:CYS120 4.4 17.7 1.0
NE2 L:HIS214 4.5 15.5 1.0
SG S:CYS22 4.5 17.9 1.0
O S:GLY153 4.6 16.5 1.0
N S:CYS154 4.7 17.9 1.0
CA S:PRO155 4.7 18.1 1.0
SG S:CYS25 4.8 18.2 1.0
NE L:ARG59 4.8 17.6 1.0

Reference:

S.B.Carr, W.Li, K.L.Wong, R.M.Evans, S.E.T.Kendall-Price, P.A.Ash, K.A.Vincent. Glutamate Flick Enables Proton Tunnelling During Fast Redox Biocatalysis To Be Published.
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