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Iron in PDB 9erc: Hydrogenase-2 Ni-Li State

Enzymatic activity of Hydrogenase-2 Ni-Li State

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

Protein crystallography data

The structure of Hydrogenase-2 Ni-Li State, PDB code: 9erc 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) 86.07 / 1.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.877, 99.974, 168.071, 90, 90, 90
R / Rfree (%) 17.4 / 19.3

Other elements in 9erc:

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

Magnesium (Mg) 8 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-Li State (pdb code 9erc). 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-Li State, PDB code: 9erc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 9erc

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Iron binding site 1 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:13.9
occ:1.00
 FE1 S:SF4301 0.0 13.9 1.0
SG S:CYS220 2.3 14.2 1.0
S2 S:SF4301 2.3 12.8 1.0
S3 S:SF4301 2.3 12.9 1.0
S4 S:SF4301 2.3 13.3 1.0
FE4 S:SF4301 2.7 12.8 1.0
FE3 S:SF4301 2.7 14.3 1.0
FE2 S:SF4301 2.8 13.5 1.0
CB S:CYS220 3.4 14.8 1.0
N S:LEU221 3.9 13.0 1.0
CA S:CYS220 3.9 13.6 1.0
S1 S:SF4301 4.0 13.0 1.0
N S:TYR222 4.1 14.6 1.0
C S:CYS220 4.3 14.3 1.0
CB S:PHE201 4.3 14.4 1.0
CD2 S:PHE201 4.4 17.1 1.0
ND1 S:HIS192 4.5 14.2 1.0
CB S:ARG197 4.5 14.4 1.0
CB S:TYR222 4.5 15.0 1.0
O S:ARG197 4.7 14.5 1.0
CA S:TYR222 4.7 14.2 1.0
CG S:PHE201 4.8 15.9 1.0
C S:LEU221 4.8 14.7 1.0
C S:ARG197 4.8 13.7 1.0
CE1 S:HIS192 4.8 15.0 1.0
CA S:LEU221 4.8 13.0 1.0
SG S:CYS195 4.9 11.8 1.0
SG S:CYS226 4.9 12.3 1.0

Iron binding site 2 out of 24 in 9erc

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Iron binding site 2 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:13.5
occ:1.00
 FE2 S:SF4301 0.0 13.5 1.0
S1 S:SF4301 2.3 13.0 1.0
S3 S:SF4301 2.3 12.9 1.0
S4 S:SF4301 2.3 13.3 1.0
SG S:CYS226 2.3 12.3 1.0
FE4 S:SF4301 2.7 12.8 1.0
FE3 S:SF4301 2.7 14.3 1.0
FE1 S:SF4301 2.8 13.9 1.0
CB S:CYS226 3.2 13.4 1.0
S2 S:SF4301 3.9 12.8 1.0
CD S:PRO229 4.4 14.5 1.0
N S:GLY228 4.5 12.6 1.0
CA S:GLY228 4.5 13.5 1.0
CA S:CYS226 4.6 12.9 1.0
CG2 S:VAL249 4.7 13.2 1.0
SG S:CYS195 4.7 11.8 1.0
ND1 S:HIS192 4.7 14.2 1.0
SG S:CYS220 4.7 14.2 1.0
N S:TYR222 4.8 14.6 1.0
C S:CYS226 4.8 13.0 1.0
N S:LEU221 4.9 13.0 1.0

Iron binding site 3 out of 24 in 9erc

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Iron binding site 3 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:14.3
occ:1.00
 FE3 S:SF4301 0.0 14.3 1.0
ND1 S:HIS192 2.1 14.2 1.0
S1 S:SF4301 2.3 13.0 1.0
S4 S:SF4301 2.3 13.3 1.0
S2 S:SF4301 2.3 12.8 1.0
FE4 S:SF4301 2.7 12.8 1.0
FE2 S:SF4301 2.7 13.5 1.0
FE1 S:SF4301 2.7 13.9 1.0
CE1 S:HIS192 3.0 15.0 1.0
CG S:HIS192 3.1 14.3 1.0
CB S:HIS192 3.6 13.4 1.0
S3 S:SF4301 3.9 12.9 1.0
CA S:HIS192 3.9 13.2 1.0
NE2 S:HIS192 4.2 14.7 1.0
CG S:PRO229 4.2 15.1 1.0
CD S:PRO229 4.2 14.5 1.0
CD2 S:HIS192 4.2 16.9 1.0
CB S:CYS195 4.6 12.8 1.0
SG S:CYS195 4.6 11.8 1.0
SG S:CYS220 4.7 14.2 1.0
CD2 S:PHE201 4.7 17.1 1.0
O S:HIS192 4.7 14.6 1.0
N S:PRO229 4.8 13.8 1.0
SG S:CYS226 4.8 12.3 1.0
C S:HIS192 4.9 13.9 1.0
N S:HIS192 4.9 12.6 1.0

Iron binding site 4 out of 24 in 9erc

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Iron binding site 4 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:12.8
occ:1.00
 FE4 S:SF4301 0.0 12.8 1.0
S3 S:SF4301 2.3 12.9 1.0
SG S:CYS195 2.3 11.8 1.0
S2 S:SF4301 2.3 12.8 1.0
S1 S:SF4301 2.3 13.0 1.0
FE2 S:SF4301 2.7 13.5 1.0
FE3 S:SF4301 2.7 14.3 1.0
FE1 S:SF4301 2.7 13.9 1.0
CB S:CYS195 3.2 12.8 1.0
S4 S:SF4301 3.9 13.3 1.0
CB S:ARG197 4.0 14.4 1.0
ND1 S:HIS192 4.5 14.2 1.0
N S:ARG197 4.6 13.9 1.0
C S:ARG197 4.6 13.7 1.0
CA S:CYS195 4.6 12.3 1.0
CA S:ARG197 4.6 13.9 1.0
N S:ARG198 4.6 13.3 1.0
SG S:CYS226 4.8 12.3 1.0
CG1 S:VAL249 4.9 13.4 1.0
CG S:ARG197 4.9 15.2 1.0
SG S:CYS220 4.9 14.2 1.0
C S:CYS195 4.9 13.1 1.0

Iron binding site 5 out of 24 in 9erc

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Iron binding site 5 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:11.4
occ:1.00
 FE1 S:F3S302 0.0 11.4 1.0
S1 S:F3S302 2.2 10.9 1.0
S3 S:F3S302 2.3 11.7 1.0
S2 S:F3S302 2.3 11.5 1.0
SG S:CYS258 2.3 10.8 1.0
FE3 S:F3S302 2.6 11.7 1.0
FE4 S:F3S302 2.7 11.6 1.0
CB S:CYS258 3.4 11.1 1.0
O L:HOH864 3.6 10.2 1.0
N S:CYS258 3.7 11.2 1.0
S4 S:F3S302 3.8 11.5 1.0
CA S:CYS258 4.0 11.0 1.0
N S:ASN259 4.2 10.2 1.0
OD1 S:ASN259 4.2 12.0 1.0
O S:HOH499 4.2 11.5 1.0
C S:CYS258 4.4 11.0 1.0
SG S:CYS235 4.7 12.6 1.0
C S:GLY257 4.8 11.7 1.0
CG S:ASN259 4.8 12.4 1.0
O S:HOH415 4.9 12.3 1.0
CE L:LYS211 4.9 11.5 1.0
SG S:CYS255 4.9 11.7 1.0
N S:GLY257 5.0 10.8 1.0
OE1 L:GLN216 5.0 12.3 1.0

Iron binding site 6 out of 24 in 9erc

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Iron binding site 6 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:11.7
occ:1.00
 FE3 S:F3S302 0.0 11.7 1.0
S4 S:F3S302 2.2 11.5 1.0
S1 S:F3S302 2.2 10.9 1.0
S3 S:F3S302 2.3 11.7 1.0
SG S:CYS235 2.3 12.6 1.0
FE1 S:F3S302 2.6 11.4 1.0
FE4 S:F3S302 2.7 11.6 1.0
CB S:CYS235 3.3 11.9 1.0
O S:HOH499 4.0 11.5 1.0
S2 S:F3S302 4.0 11.5 1.0
CD1 S:ILE191 4.1 12.0 1.0
CZ S:PHE240 4.5 12.3 1.0
CE1 S:PHE240 4.5 11.8 1.0
OD1 S:ASN259 4.6 12.0 1.0
SG S:CYS255 4.7 11.7 1.0
CA S:CYS235 4.7 11.2 1.0
SG S:CYS258 4.7 10.8 1.0
O S:HOH546 4.9 12.2 1.0
CD S:PRO248 4.9 11.5 1.0
CG S:ASN259 4.9 12.4 1.0
CG S:PRO248 5.0 11.6 1.0
ND2 S:ASN259 5.0 12.4 1.0

Iron binding site 7 out of 24 in 9erc

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Iron binding site 7 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:11.6
occ:1.00
 FE4 S:F3S302 0.0 11.6 1.0
S4 S:F3S302 2.2 11.5 1.0
S3 S:F3S302 2.3 11.7 1.0
S2 S:F3S302 2.3 11.5 1.0
SG S:CYS255 2.4 11.7 1.0
FE3 S:F3S302 2.7 11.7 1.0
FE1 S:F3S302 2.7 11.4 1.0
CB S:CYS255 3.3 11.6 1.0
CA S:CYS255 3.7 11.6 1.0
N S:TYR256 3.9 10.5 1.0
S1 S:F3S302 3.9 10.9 1.0
N S:GLY257 3.9 10.8 1.0
CD1 S:ILE191 4.2 12.0 1.0
C S:CYS255 4.2 11.3 1.0
N S:CYS258 4.3 11.2 1.0
CA S:GLY257 4.5 11.1 1.0
NE2 L:GLN216 4.6 12.1 1.0
SG S:CYS235 4.7 12.6 1.0
CG2 S:THR231 4.8 12.6 1.0
SG S:CYS258 4.8 10.8 1.0
C S:TYR256 4.9 12.0 1.0
C S:GLY257 4.9 11.7 1.0
CA S:TYR256 4.9 11.4 1.0

Iron binding site 8 out of 24 in 9erc

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Iron binding site 8 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:11.4
occ:1.00
 FE1 S:SF4303 0.0 11.4 1.0
S4 S:SF4303 2.2 11.5 1.0
S3 S:SF4303 2.3 11.7 1.0
SG S:CYS22 2.3 11.9 1.0
S2 S:SF4303 2.3 10.2 1.0
FE3 S:SF4303 2.6 11.0 1.0
FE2 S:SF4303 2.7 11.5 1.0
FE4 S:SF4303 2.7 12.0 1.0
CB S:CYS22 3.4 12.2 1.0
N S:CYS22 3.7 11.8 1.0
S1 S:SF4303 3.8 11.7 1.0
CA S:CYS22 4.0 11.4 1.0
NE2 L:HIS214 4.2 11.4 1.0
N S:GLY24 4.2 11.7 1.0
O S:HOH412 4.3 11.2 1.0
O S:HOH536 4.5 13.6 1.0
CA S:GLY24 4.5 11.1 1.0
C S:CYS22 4.6 10.9 1.0
N S:THR23 4.6 10.9 1.0
SG S:CYS154 4.6 11.8 1.0
SG S:CYS120 4.8 11.3 1.0
N S:CYS25 4.8 11.3 1.0
CD2 L:HIS214 4.8 12.0 1.0
SG S:CYS25 4.9 12.3 1.0
CG L:ARG59 4.9 11.2 1.0
C S:GLU21 4.9 13.4 1.0

Iron binding site 9 out of 24 in 9erc

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Iron binding site 9 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:11.5
occ:1.00
 FE2 S:SF4303 0.0 11.5 1.0
S4 S:SF4303 2.3 11.5 1.0
S3 S:SF4303 2.3 11.7 1.0
SG S:CYS120 2.3 11.3 1.0
S1 S:SF4303 2.3 11.7 1.0
FE3 S:SF4303 2.6 11.0 1.0
FE1 S:SF4303 2.7 11.4 1.0
FE4 S:SF4303 2.8 12.0 1.0
CB S:CYS120 3.2 10.7 1.0
O S:HOH549 3.8 12.1 1.0
O S:HOH453 3.9 11.3 1.0
O S:HOH536 3.9 13.6 1.0
S2 S:SF4303 3.9 10.2 1.0
N S:CYS120 4.0 11.7 1.0
CA S:CYS120 4.2 11.4 1.0
SG S:CYS154 4.4 11.8 1.0
SG S:CYS25 4.9 12.3 1.0
SG S:CYS22 4.9 11.9 1.0
CA S:GLY82 5.0 12.0 1.0
N S:CYS22 5.0 11.8 1.0

Iron binding site 10 out of 24 in 9erc

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Iron binding site 10 out of 24 in the Hydrogenase-2 Ni-Li 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-Li State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:11.0
occ:1.00
 FE3 S:SF4303 0.0 11.0 1.0
S2 S:SF4303 2.3 10.2 1.0
SG S:CYS154 2.3 11.8 1.0
S4 S:SF4303 2.3 11.5 1.0
S1 S:SF4303 2.3 11.7 1.0
FE1 S:SF4303 2.6 11.4 1.0
FE2 S:SF4303 2.6 11.5 1.0
FE4 S:SF4303 2.8 12.0 1.0
CB S:CYS154 3.4 10.1 1.0
CA S:CYS154 3.4 10.7 1.0
C S:CYS154 3.8 10.2 1.0
S3 S:SF4303 3.8 11.7 1.0
O S:HOH549 3.8 12.1 1.0
O S:CYS154 4.2 11.2 1.0
CG L:ARG59 4.3 11.2 1.0
N S:PRO155 4.3 10.6 1.0
SG S:CYS120 4.4 11.3 1.0
CD2 L:HIS214 4.5 12.0 1.0
SG S:CYS22 4.5 11.9 1.0
NE2 L:HIS214 4.5 11.4 1.0
O S:GLY153 4.6 10.7 1.0
CA S:PRO155 4.7 10.6 1.0
N S:CYS154 4.7 11.1 1.0
SG S:CYS25 4.8 12.3 1.0
NE L:ARG59 4.9 11.0 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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