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Iron in PDB 6ehs: E. Coli Hydrogenase-2 Chemically Reduced Structure

Enzymatic activity of E. Coli Hydrogenase-2 Chemically Reduced Structure

All present enzymatic activity of E. Coli Hydrogenase-2 Chemically Reduced Structure:
1.12.99.6;

Protein crystallography data

The structure of E. Coli Hydrogenase-2 Chemically Reduced Structure, PDB code: 6ehs was solved by S.B.Carr, R.M.Evans, S.E.Beaton, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.08 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.885, 100.065, 168.801, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 16.3

Other elements in 6ehs:

The structure of E. Coli Hydrogenase-2 Chemically Reduced Structure also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 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 E. Coli Hydrogenase-2 Chemically Reduced Structure (pdb code 6ehs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the E. Coli Hydrogenase-2 Chemically Reduced Structure, PDB code: 6ehs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 6ehs

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Iron binding site 1 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:15.5
occ:1.00
 FE1 S:SF4301 0.0 15.5 1.0
S2 S:SF4301 2.3 15.4 1.0
S3 S:SF4301 2.3 14.6 1.0
SG S:CYS220 2.3 16.1 1.0
S4 S:SF4301 2.3 15.6 1.0
FE3 S:SF4301 2.7 15.9 1.0
FE4 S:SF4301 2.7 14.9 1.0
FE2 S:SF4301 2.8 15.0 1.0
CB S:CYS220 3.4 16.9 1.0
N S:LEU221 3.9 14.0 1.0
S1 S:SF4301 3.9 14.9 1.0
CA S:CYS220 3.9 15.1 1.0
N S:TYR222 4.1 15.0 1.0
C S:CYS220 4.3 15.1 1.0
CB S:PHE201 4.4 16.1 1.0
CD2 S:PHE201 4.4 18.0 1.0
ND1 S:HIS192 4.5 15.1 1.0
CB S:ARG197 4.5 15.4 1.0
CB S:TYR222 4.5 15.7 1.0
O S:ARG197 4.7 16.0 1.0
CA S:TYR222 4.7 15.5 1.0
CE1 S:HIS192 4.7 16.6 1.0
C S:LEU221 4.8 14.9 1.0
CA S:LEU221 4.8 14.6 1.0
SG S:CYS195 4.8 14.6 1.0
C S:ARG197 4.8 14.5 1.0
CG S:PHE201 4.8 17.3 1.0
SG S:CYS226 4.9 14.6 1.0

Iron binding site 2 out of 24 in 6ehs

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Iron binding site 2 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:15.0
occ:1.00
 FE2 S:SF4301 0.0 15.0 1.0
S1 S:SF4301 2.3 14.9 1.0
SG S:CYS226 2.3 14.6 1.0
S3 S:SF4301 2.3 14.6 1.0
S4 S:SF4301 2.3 15.6 1.0
FE4 S:SF4301 2.7 14.9 1.0
FE3 S:SF4301 2.8 15.9 1.0
FE1 S:SF4301 2.8 15.5 1.0
CB S:CYS226 3.2 14.5 1.0
S2 S:SF4301 3.9 15.4 1.0
N S:GLY228 4.5 13.9 1.0
CA S:GLY228 4.5 14.7 1.0
CD S:PRO229 4.6 15.7 1.0
CA S:CYS226 4.6 14.3 1.0
CG2 S:VAL249 4.7 13.0 1.0
ND1 S:HIS192 4.7 15.1 1.0
SG S:CYS195 4.7 14.6 1.0
N S:TYR222 4.7 15.0 1.0
SG S:CYS220 4.7 16.1 1.0
C S:CYS226 4.9 14.2 1.0
N S:LEU221 4.9 14.0 1.0
C S:LEU221 5.0 14.9 1.0

Iron binding site 3 out of 24 in 6ehs

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Iron binding site 3 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:15.9
occ:1.00
 FE3 S:SF4301 0.0 15.9 1.0
ND1 S:HIS192 2.1 15.1 1.0
S4 S:SF4301 2.3 15.6 1.0
S1 S:SF4301 2.3 14.9 1.0
S2 S:SF4301 2.3 15.4 1.0
FE4 S:SF4301 2.7 14.9 1.0
FE1 S:SF4301 2.7 15.5 1.0
FE2 S:SF4301 2.8 15.0 1.0
CE1 S:HIS192 2.9 16.6 1.0
CG S:HIS192 3.2 15.2 1.0
CB S:HIS192 3.6 14.1 1.0
S3 S:SF4301 3.9 14.6 1.0
CA S:HIS192 4.0 13.7 1.0
NE2 S:HIS192 4.1 16.8 1.0
CD2 S:HIS192 4.3 18.5 1.0
CG S:PRO229 4.3 16.4 1.0
CD S:PRO229 4.3 15.7 1.0
CB S:CYS195 4.6 13.9 1.0
SG S:CYS195 4.6 14.6 1.0
SG S:CYS220 4.7 16.1 1.0
CD2 S:PHE201 4.7 18.0 1.0
O S:HIS192 4.8 17.4 1.0
SG S:CYS226 4.8 14.6 1.0
N S:PRO229 4.9 15.2 1.0
N S:HIS192 4.9 14.0 1.0
C S:HIS192 4.9 14.4 1.0

Iron binding site 4 out of 24 in 6ehs

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Iron binding site 4 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe301

b:14.9
occ:1.00
 FE4 S:SF4301 0.0 14.9 1.0
SG S:CYS195 2.3 14.6 1.0
S3 S:SF4301 2.3 14.6 1.0
S2 S:SF4301 2.3 15.4 1.0
S1 S:SF4301 2.3 14.9 1.0
FE3 S:SF4301 2.7 15.9 1.0
FE2 S:SF4301 2.7 15.0 1.0
FE1 S:SF4301 2.7 15.5 1.0
CB S:CYS195 3.1 13.9 1.0
S4 S:SF4301 3.9 15.6 1.0
CB S:ARG197 4.1 15.4 1.0
ND1 S:HIS192 4.5 15.1 1.0
N S:ARG197 4.5 16.4 1.0
C S:ARG197 4.6 14.5 1.0
CA S:CYS195 4.6 14.5 1.0
CA S:ARG197 4.6 15.5 1.0
N S:ARG198 4.6 14.4 1.0
SG S:CYS226 4.8 14.6 1.0
CG1 S:VAL249 4.8 15.2 1.0
CG S:ARG197 4.9 16.2 1.0
C S:CYS195 4.9 14.1 1.0
SG S:CYS220 4.9 16.1 1.0
CH2 S:TRP247 5.0 14.2 1.0

Iron binding site 5 out of 24 in 6ehs

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Iron binding site 5 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:12.8
occ:1.00
 FE1 S:F3S302 0.0 12.8 1.0
S1 S:F3S302 2.2 13.3 1.0
S2 S:F3S302 2.3 13.0 1.0
S3 S:F3S302 2.3 13.8 1.0
SG S:CYS258 2.3 12.7 1.0
FE3 S:F3S302 2.7 13.3 1.0
FE4 S:F3S302 2.7 13.1 1.0
CB S:CYS258 3.4 13.4 1.0
N S:CYS258 3.7 12.6 1.0
O L:HOH823 3.7 14.8 1.0
S4 S:F3S302 3.8 13.8 1.0
CA S:CYS258 3.9 12.8 1.0
N S:ASN259 4.2 11.5 1.0
OD1 S:ASN259 4.2 12.1 1.0
O S:HOH479 4.2 14.2 1.0
C S:CYS258 4.4 13.8 1.0
SG S:CYS235 4.7 15.2 1.0
C S:GLY257 4.8 12.6 1.0
CG S:ASN259 4.8 12.0 1.0
O S:HOH410 4.9 16.4 1.0
SG S:CYS255 4.9 13.9 1.0
CE L:LYS211 4.9 14.3 1.0
N S:GLY257 4.9 13.4 1.0
OE1 L:GLN216 4.9 15.1 1.0

Iron binding site 6 out of 24 in 6ehs

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Iron binding site 6 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:13.3
occ:1.00
 FE3 S:F3S302 0.0 13.3 1.0
S4 S:F3S302 2.2 13.8 1.0
S1 S:F3S302 2.2 13.3 1.0
SG S:CYS235 2.3 15.2 1.0
S3 S:F3S302 2.3 13.8 1.0
FE4 S:F3S302 2.7 13.1 1.0
FE1 S:F3S302 2.7 12.8 1.0
CB S:CYS235 3.3 13.1 1.0
S2 S:F3S302 4.0 13.0 1.0
O S:HOH479 4.0 14.2 1.0
CD1 S:ILE191 4.1 17.1 1.0
CZ S:PHE240 4.5 13.8 1.0
CE2 S:PHE240 4.5 12.2 1.0
OD1 S:ASN259 4.7 12.1 1.0
CA S:CYS235 4.7 13.0 1.0
SG S:CYS255 4.7 13.9 1.0
SG S:CYS258 4.8 12.7 1.0
O S:HOH508 4.9 14.6 1.0
CD S:PRO248 4.9 12.5 1.0
ND2 S:ASN259 5.0 13.4 1.0
CG S:ASN259 5.0 12.0 1.0

Iron binding site 7 out of 24 in 6ehs

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Iron binding site 7 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe302

b:13.1
occ:1.00
 FE4 S:F3S302 0.0 13.1 1.0
S4 S:F3S302 2.2 13.8 1.0
S3 S:F3S302 2.3 13.8 1.0
S2 S:F3S302 2.3 13.0 1.0
SG S:CYS255 2.3 13.9 1.0
FE3 S:F3S302 2.7 13.3 1.0
FE1 S:F3S302 2.7 12.8 1.0
CB S:CYS255 3.3 14.2 1.0
CA S:CYS255 3.7 13.7 1.0
S1 S:F3S302 3.9 13.3 1.0
N S:TYR256 3.9 12.0 1.0
N S:GLY257 3.9 13.4 1.0
CD1 S:ILE191 4.2 17.1 1.0
C S:CYS255 4.2 11.9 1.0
N S:CYS258 4.3 12.6 1.0
CA S:GLY257 4.5 12.8 1.0
NE2 L:GLN216 4.6 13.5 1.0
SG S:CYS235 4.7 15.2 1.0
CG2 S:THR231 4.8 13.6 1.0
SG S:CYS258 4.9 12.7 1.0
C S:TYR256 4.9 13.9 1.0
C S:GLY257 4.9 12.6 1.0
CA S:TYR256 4.9 13.1 1.0
N S:CYS255 5.0 13.2 1.0

Iron binding site 8 out of 24 in 6ehs

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Iron binding site 8 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:14.8
occ:1.00
 FE1 S:SF4303 0.0 14.8 1.0
S4 S:SF4303 2.2 14.0 1.0
SG S:CYS22 2.3 13.7 1.0
S3 S:SF4303 2.3 17.6 1.0
S2 S:SF4303 2.3 13.4 1.0
FE3 S:SF4303 2.6 13.2 1.0
FE4 S:SF4303 2.7 16.8 1.0
FE2 S:SF4303 2.7 15.6 1.0
CB S:CYS22 3.3 14.0 1.0
N S:CYS22 3.7 14.0 1.0
S1 S:SF4303 3.8 14.0 1.0
CA S:CYS22 4.0 13.7 1.0
O S:HOH404 4.2 17.5 1.0
N S:GLY24 4.2 12.9 1.0
NE2 L:HIS214 4.2 12.2 1.0
C S:CYS22 4.5 14.2 1.0
O S:HOH524 4.5 17.4 1.0
CA S:GLY24 4.5 11.2 1.0
N S:THR23 4.6 13.3 1.0
SG S:CYS154 4.7 12.8 1.0
N S:CYS25 4.8 12.5 1.0
SG S:CYS120 4.8 15.0 1.0
SG S:CYS25 4.8 16.2 1.0
CD2 L:HIS214 4.9 13.0 1.0
C S:GLU21 4.9 16.6 1.0

Iron binding site 9 out of 24 in 6ehs

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Iron binding site 9 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:15.6
occ:1.00
 FE2 S:SF4303 0.0 15.6 1.0
S4 S:SF4303 2.2 14.0 1.0
S1 S:SF4303 2.3 14.0 1.0
SG S:CYS120 2.3 15.0 1.0
S3 S:SF4303 2.3 17.6 1.0
FE3 S:SF4303 2.6 13.2 1.0
FE1 S:SF4303 2.7 14.8 1.0
FE4 S:SF4303 2.9 16.8 1.0
CB S:CYS120 3.3 13.8 1.0
O S:HOH520 3.8 15.3 1.0
O S:HOH524 3.9 17.4 1.0
O S:HOH430 3.9 13.8 1.0
S2 S:SF4303 3.9 13.4 1.0
N S:CYS120 4.0 12.6 1.0
CA S:CYS120 4.2 12.6 1.0
SG S:CYS154 4.4 12.8 1.0
SG S:CYS22 4.9 13.7 1.0
SG S:CYS25 4.9 16.2 1.0
CG1 S:VAL126 5.0 15.7 1.0
N S:CYS22 5.0 14.0 1.0

Iron binding site 10 out of 24 in 6ehs

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Iron binding site 10 out of 24 in the E. Coli Hydrogenase-2 Chemically Reduced Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of E. Coli Hydrogenase-2 Chemically Reduced Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe303

b:13.2
occ:1.00
 FE3 S:SF4303 0.0 13.2 1.0
S1 S:SF4303 2.3 14.0 1.0
S2 S:SF4303 2.3 13.4 1.0
S4 S:SF4303 2.3 14.0 1.0
SG S:CYS154 2.3 12.8 1.0
FE2 S:SF4303 2.6 15.6 1.0
FE1 S:SF4303 2.6 14.8 1.0
FE4 S:SF4303 2.7 16.8 1.0
CB S:CYS154 3.4 11.9 1.0
CA S:CYS154 3.4 12.0 1.0
S3 S:SF4303 3.8 17.6 1.0
O S:HOH520 3.9 15.3 1.0
C S:CYS154 3.9 11.4 1.0
O S:CYS154 4.3 12.2 1.0
N S:PRO155 4.4 10.9 1.0
CG L:ARG59 4.4 13.8 1.0
SG S:CYS120 4.4 15.0 1.0
CD2 L:HIS214 4.5 13.0 1.0
SG S:CYS22 4.5 13.7 1.0
O S:GLY153 4.5 11.6 1.0
NE2 L:HIS214 4.6 12.2 1.0
N S:CYS154 4.8 11.9 1.0
CA S:PRO155 4.8 12.2 1.0
SG S:CYS25 4.8 16.2 1.0
NE L:ARG59 4.9 14.2 1.0

Reference:

S.E.Beaton, R.M.Evans, A.J.Finney, C.M.Lamont, F.A.Armstrong, F.Sargent, S.B.Carr. The Structure of Hydrogenase-2 Fromescherichia Coli: Implications For H2-Driven Proton Pumping. Biochem. J. V. 475 1353 2018.
ISSN: ESSN 1470-8728
PubMed: 29555844
DOI: 10.1042/BCJ20180053
Page generated: Tue Aug 6 17:24:42 2024

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