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Iron in PDB 3uqy: H2-Reduced Structure of E. Coli Hydrogenase-1

Enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1

All present enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1:
1.12.99.6;

Protein crystallography data

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.710, 97.400, 183.730, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 16

Other elements in 3uqy:

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 5 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 H2-Reduced Structure of E. Coli Hydrogenase-1 (pdb code 3uqy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 3uqy

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Iron binding site 1 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.1
occ:1.00
FE1 S:SF4401 0.0 7.1 1.0
S4 S:SF4401 2.3 7.2 1.0
SG S:CYS215 2.3 7.2 1.0
S3 S:SF4401 2.3 6.1 1.0
S2 S:SF4401 2.3 6.8 1.0
FE3 S:SF4401 2.7 7.2 1.0
FE2 S:SF4401 2.7 6.7 1.0
FE4 S:SF4401 2.8 6.6 1.0
CB S:CYS215 3.4 7.1 1.0
N S:LEU216 3.8 5.6 1.0
CA S:CYS215 3.9 6.8 1.0
S1 S:SF4401 3.9 6.6 1.0
N S:TYR217 4.2 6.7 1.0
CB S:PHE196 4.2 8.8 1.0
C S:CYS215 4.3 6.2 1.0
CD1 S:PHE196 4.3 8.1 1.0
ND1 S:HIS187 4.5 6.1 1.0
CB S:TYR217 4.6 7.1 1.0
CG S:PHE196 4.7 8.3 1.0
CB S:ARG192 4.7 6.9 1.0
O S:ARG192 4.7 7.7 1.0
CE1 S:HIS187 4.7 6.0 1.0
CA S:LEU216 4.8 5.5 1.0
CA S:TYR217 4.8 6.3 1.0
C S:LEU216 4.8 6.9 1.0
SG S:CYS190 4.9 6.6 1.0
SG S:CYS221 4.9 6.3 1.0
C S:ARG192 5.0 7.5 1.0

Iron binding site 2 out of 24 in 3uqy

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Iron binding site 2 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:6.7
occ:1.00
FE2 S:SF4401 0.0 6.7 1.0
S4 S:SF4401 2.3 7.2 1.0
SG S:CYS190 2.3 6.6 1.0
S3 S:SF4401 2.3 6.1 1.0
S1 S:SF4401 2.3 6.6 1.0
FE3 S:SF4401 2.7 7.2 1.0
FE4 S:SF4401 2.7 6.6 1.0
FE1 S:SF4401 2.7 7.1 1.0
CB S:CYS190 3.1 6.0 1.0
S2 S:SF4401 3.9 6.8 1.0
CB S:ARG192 4.2 6.9 1.0
CD1 S:ILE243 4.2 7.5 1.0
CG2 S:ILE243 4.3 6.2 1.0
ND1 S:HIS187 4.5 6.1 1.0
CA S:CYS190 4.5 6.0 1.0
C S:ARG192 4.7 7.5 1.0
N S:ARG192 4.7 6.6 1.0
CA S:ARG192 4.7 6.8 1.0
SG S:CYS221 4.8 6.3 1.0
N S:ARG193 4.8 7.0 1.0
CG1 S:ILE243 4.8 5.7 1.0
SG S:CYS215 4.9 7.2 1.0
C S:CYS190 5.0 6.9 1.0

Iron binding site 3 out of 24 in 3uqy

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Iron binding site 3 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.2
occ:1.00
FE3 S:SF4401 0.0 7.2 1.0
ND1 S:HIS187 2.1 6.1 1.0
S1 S:SF4401 2.3 6.6 1.0
S2 S:SF4401 2.3 6.8 1.0
S4 S:SF4401 2.3 7.2 1.0
FE2 S:SF4401 2.7 6.7 1.0
FE1 S:SF4401 2.7 7.1 1.0
FE4 S:SF4401 2.7 6.6 1.0
CE1 S:HIS187 2.9 6.0 1.0
CG S:HIS187 3.2 6.7 1.0
CB S:HIS187 3.7 6.7 1.0
S3 S:SF4401 3.9 6.1 1.0
CA S:HIS187 4.0 6.8 1.0
NE2 S:HIS187 4.1 8.6 1.0
CD2 S:HIS187 4.2 9.7 1.0
CG S:PRO224 4.3 7.5 1.0
CD S:PRO224 4.3 7.9 1.0
CD S:ARG193 4.4 13.0 1.0
CB S:CYS190 4.5 6.0 1.0
SG S:CYS190 4.7 6.6 1.0
SG S:CYS215 4.7 7.2 1.0
CD1 S:PHE196 4.7 8.1 1.0
SG S:CYS221 4.8 6.3 1.0
O S:HIS187 4.8 8.6 1.0
N S:PRO224 4.9 7.0 1.0
CG S:PHE196 4.9 8.3 1.0
CG S:ARG193 5.0 13.6 1.0
C S:HIS187 5.0 7.0 1.0

Iron binding site 4 out of 24 in 3uqy

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Iron binding site 4 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:6.6
occ:1.00
FE4 S:SF4401 0.0 6.6 1.0
S2 S:SF4401 2.3 6.8 1.0
S1 S:SF4401 2.3 6.6 1.0
S3 S:SF4401 2.3 6.1 1.0
SG S:CYS221 2.3 6.3 1.0
FE2 S:SF4401 2.7 6.7 1.0
FE3 S:SF4401 2.7 7.2 1.0
FE1 S:SF4401 2.8 7.1 1.0
CB S:CYS221 3.2 6.0 1.0
S4 S:SF4401 3.9 7.2 1.0
CD1 S:ILE243 4.0 7.5 1.0
CG1 S:ILE243 4.4 5.7 1.0
CD S:PRO224 4.5 7.9 1.0
CA S:GLY223 4.5 7.2 1.0
N S:GLY223 4.5 6.9 1.0
ND1 S:HIS187 4.6 6.1 1.0
CA S:CYS221 4.6 5.6 1.0
SG S:CYS215 4.7 7.2 1.0
SG S:CYS190 4.8 6.6 1.0
N S:TYR217 4.8 6.7 1.0
N S:LEU216 4.8 5.6 1.0
C S:CYS221 4.9 6.8 1.0
CB S:LEU216 5.0 6.0 1.0
C S:LEU216 5.0 6.9 1.0

Iron binding site 5 out of 24 in 3uqy

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Iron binding site 5 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:6.7
occ:1.00
FE1 S:F3S402 0.0 6.7 1.0
S1 S:F3S402 2.2 6.1 1.0
S2 S:F3S402 2.2 6.6 1.0
S3 S:F3S402 2.3 6.2 1.0
SG S:CYS252 2.3 6.3 1.0
FE3 S:F3S402 2.6 6.3 1.0
FE4 S:F3S402 2.7 6.4 1.0
CB S:CYS252 3.4 4.9 1.0
O L:HOH754 3.8 7.6 1.0
N S:CYS252 3.8 5.2 1.0
S4 S:F3S402 3.9 6.6 1.0
O S:HOH509 3.9 7.0 1.0
CA S:CYS252 4.0 4.3 1.0
N S:ALA253 4.5 6.0 1.0
C S:CYS252 4.5 5.7 1.0
O L:HOH738 4.5 7.4 1.0
ND2 S:ASN228 4.6 7.1 1.0
SG S:CYS230 4.7 6.2 1.0
SG S:CYS249 4.7 6.0 1.0
C S:GLY251 5.0 5.9 1.0
CG S:PRO242 5.0 5.1 1.0

Iron binding site 6 out of 24 in 3uqy

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Iron binding site 6 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:6.3
occ:1.00
FE3 S:F3S402 0.0 6.3 1.0
S1 S:F3S402 2.2 6.1 1.0
S4 S:F3S402 2.2 6.6 1.0
S3 S:F3S402 2.2 6.2 1.0
SG S:CYS230 2.3 6.2 1.0
FE1 S:F3S402 2.6 6.7 1.0
FE4 S:F3S402 2.7 6.4 1.0
CB S:CYS230 3.3 6.1 1.0
S2 S:F3S402 3.9 6.6 1.0
ND2 S:ASN228 4.0 7.1 1.0
CD1 S:ILE186 4.2 9.9 1.0
O S:HOH509 4.3 7.0 1.0
NE1 S:TRP235 4.3 6.7 1.0
CD S:PRO242 4.5 6.0 1.0
CG S:PRO242 4.5 5.1 1.0
CG S:ASN228 4.6 5.9 1.0
CA S:CYS230 4.7 5.8 1.0
CB S:ASN228 4.7 6.0 1.0
CG1 S:ILE186 4.7 8.2 1.0
SG S:CYS252 4.7 6.3 1.0
SG S:CYS249 4.8 6.0 1.0

Iron binding site 7 out of 24 in 3uqy

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Iron binding site 7 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:6.4
occ:1.00
FE4 S:F3S402 0.0 6.4 1.0
S4 S:F3S402 2.2 6.6 1.0
S2 S:F3S402 2.3 6.6 1.0
S3 S:F3S402 2.3 6.2 1.0
SG S:CYS249 2.3 6.0 1.0
FE1 S:F3S402 2.7 6.7 1.0
FE3 S:F3S402 2.7 6.3 1.0
CB S:CYS249 3.3 5.6 1.0
CA S:CYS249 3.7 6.5 1.0
S1 S:F3S402 3.8 6.1 1.0
N S:LEU250 4.0 4.8 1.0
N S:GLY251 4.2 5.8 1.0
C S:CYS249 4.3 5.6 1.0
N S:CYS252 4.4 5.2 1.0
CG1 S:ILE186 4.6 8.2 1.0
CG2 S:THR226 4.6 8.0 1.0
CG S:PRO242 4.7 5.1 1.0
SG S:CYS252 4.8 6.3 1.0
CA S:GLY251 4.8 5.6 1.0
SG S:CYS230 4.8 6.2 1.0
CD1 S:ILE186 5.0 9.9 1.0
N S:CYS249 5.0 5.0 1.0

Iron binding site 8 out of 24 in 3uqy

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Iron binding site 8 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:6.7
occ:1.00
FE1 S:F4S403 0.0 6.7 1.0
SG S:CYS17 2.3 6.3 1.0
S2 S:F4S403 2.3 6.4 1.0
S1 S:F4S403 2.3 6.2 1.0
SG S:CYS19 2.3 5.8 1.0
FE2 S:F4S403 2.6 6.5 1.0
FE4 S:F4S403 2.8 6.9 1.0
CB S:CYS17 3.4 6.0 1.0
CB S:CYS19 3.4 5.2 1.0
FE3 S:F4S403 3.6 6.3 1.0
N S:CYS17 3.6 5.9 1.0
N S:CYS19 3.6 5.1 1.0
S3 S:F4S403 3.7 6.0 1.0
CA S:CYS17 3.9 4.7 1.0
CA S:CYS19 4.1 5.1 1.0
N S:THR18 4.1 6.0 1.0
NE2 L:HIS229 4.2 5.9 1.0
C S:CYS17 4.2 6.6 1.0
SG S:CYS149 4.5 5.9 1.0
O S:HOH502 4.5 7.0 1.0
SG S:CYS115 4.6 7.0 1.0
N S:CYS20 4.8 5.9 1.0
C S:THR18 4.8 5.9 1.0
CD2 L:HIS229 4.8 5.5 1.0
C S:GLU16 4.8 6.9 1.0
C S:CYS19 4.9 5.8 1.0
CG L:ARG74 5.0 6.7 1.0

Iron binding site 9 out of 24 in 3uqy

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Iron binding site 9 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:6.5
occ:1.00
FE2 S:F4S403 0.0 6.5 1.0
S3 S:F4S403 2.3 6.0 1.0
SG S:CYS115 2.3 7.0 1.0
S2 S:F4S403 2.3 6.4 1.0
S1 S:F4S403 2.3 6.2 1.0
FE1 S:F4S403 2.6 6.7 1.0
FE3 S:F4S403 2.8 6.3 1.0
FE4 S:F4S403 2.8 6.9 1.0
CB S:CYS115 3.3 6.2 1.0
O S:HOH520 4.0 7.2 1.0
SG S:CYS19 4.0 5.8 1.0
N S:CYS115 4.1 5.4 1.0
O S:HOH502 4.2 7.0 1.0
CA S:CYS115 4.2 6.5 1.0
SG S:CYS120 4.4 6.6 1.0
CB S:CYS120 4.5 6.5 1.0
N S:CYS17 4.5 5.9 1.0
SG S:CYS20 4.6 6.2 1.0
SG S:CYS17 4.7 6.3 1.0
SG S:CYS149 4.8 5.9 1.0
CA S:GLU16 4.8 7.0 1.0

Iron binding site 10 out of 24 in 3uqy

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Iron binding site 10 out of 24 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:6.3
occ:1.00
FE3 S:F4S403 0.0 6.3 1.0
SG S:CYS149 2.3 5.9 1.0
S2 S:F4S403 2.3 6.4 1.0
S3 S:F4S403 2.3 6.0 1.0
SG S:CYS120 2.4 6.6 1.0
FE2 S:F4S403 2.8 6.5 1.0
CB S:CYS149 3.3 6.2 1.0
CB S:CYS120 3.5 6.5 1.0
FE1 S:F4S403 3.6 6.7 1.0
CA S:CYS149 4.0 4.5 1.0
FE4 S:F4S403 4.0 6.9 1.0
SG S:CYS115 4.1 7.0 1.0
SG S:CYS19 4.1 5.8 1.0
CG L:ARG74 4.4 6.7 1.0
N S:CYS115 4.5 5.4 1.0
CB S:THR114 4.7 5.7 1.0
S1 S:F4S403 4.7 6.2 1.0
C S:CYS149 4.8 5.0 1.0
O S:GLY148 4.9 5.0 1.0
CA S:CYS120 4.9 5.3 1.0
N S:VAL121 5.0 5.0 1.0

Reference:

A.Volbeda, P.Amara, C.Darnault, J.M.Mouesca, A.Parkin, M.M.Roessler, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Crystallographic and Computational Studies of the O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli. Proc.Natl.Acad.Sci.Usa V. 109 5305 2012.
ISSN: ISSN 0027-8424
PubMed: 22431599
DOI: 10.1073/PNAS.1119806109
Page generated: Sun Aug 4 21:16:19 2024

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