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Iron in PDB 5adu: The Mechanism of Hydrogen Activation By Nife-Hydrogenases

Enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases

All present enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases:
1.12.99.6;

Protein crystallography data

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5adu was solved by R.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.V.Phillips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.78 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.855, 98.979, 185.207, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.2

Other elements in 5adu:

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases also contains other interesting chemical elements:

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

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iron atom in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5adu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 26 binding sites of Iron where determined in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5adu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 26 in 5adu

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Iron binding site 1 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe601

b:6.1
occ:1.00
 FE L:FCO601 0.0 6.1 1.0
C3 L:FCO601 1.8 6.4 1.0
C2 L:FCO601 1.9 5.9 1.0
C1 L:FCO601 1.9 6.3 1.0
SG L:CSO79 2.3 8.6 1.0
SG L:CYS579 2.3 6.5 1.0
O L:HOH2073 2.5 12.8 1.0
NI L:NI602 2.7 14.5 1.0
O3 L:FCO601 2.9 7.0 1.0
N2 L:FCO601 3.0 6.7 1.0
N1 L:FCO601 3.1 7.0 1.0
OD L:CSO79 3.4 17.0 1.0
CB L:CYS579 3.4 5.9 1.0
CB L:CSO79 3.5 6.4 1.0
SG L:CYS576 4.1 15.9 1.0
CB L:CYS576 4.3 9.7 1.0
NE2 L:HIS83 4.4 6.0 1.0
CD L:ARG509 4.4 8.9 1.0
CG1 L:VAL530 4.4 7.8 1.0
CG L:PRO531 4.8 7.4 1.0
SG L:CYS76 4.8 8.5 1.0
CA L:CSO79 4.8 5.8 1.0
NH1 L:ARG509 4.9 10.7 1.0
CB L:ALA507 4.9 6.2 1.0
CA L:CYS579 4.9 5.6 1.0
CG1 L:VAL82 4.9 7.1 1.0
CB L:CYS76 4.9 8.3 1.0

Iron binding site 2 out of 26 in 5adu

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Iron binding site 2 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe601

b:6.2
occ:1.00
 FE M:FCO601 0.0 6.2 1.0
C3 M:FCO601 1.8 6.4 1.0
C2 M:FCO601 1.9 6.0 1.0
C1 M:FCO601 1.9 6.8 1.0
SG M:CSO79 2.3 8.7 1.0
SG M:CYS579 2.3 6.6 1.0
O M:HOH2077 2.5 13.8 1.0
NI M:NI602 2.7 14.8 1.0
O3 M:FCO601 2.9 7.4 1.0
N2 M:FCO601 3.0 6.2 1.0
N1 M:FCO601 3.1 7.2 1.0
CB M:CSO79 3.4 6.7 1.0
OD M:CSO79 3.4 17.8 1.0
CB M:CYS579 3.5 6.2 1.0
SG M:CYS576 4.1 15.1 1.0
CB M:CYS576 4.3 9.6 1.0
CD M:ARG509 4.4 9.0 1.0
NE2 M:HIS83 4.4 6.2 1.0
CG1 M:VAL530 4.4 7.0 1.0
SG M:CYS76 4.8 7.2 0.8
CG M:PRO531 4.8 8.0 1.0
NH1 M:ARG509 4.8 10.8 1.0
CA M:CSO79 4.8 6.1 1.0
CA M:CYS579 4.9 5.2 1.0
CB M:ALA507 4.9 6.2 1.0
CB M:CYS76 4.9 7.7 1.0
CG1 M:VAL82 4.9 8.2 1.0

Iron binding site 3 out of 26 in 5adu

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Iron binding site 3 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:5.7
occ:1.00
 FE1 S:SF4401 0.0 5.7 1.0
SG S:CYS215 2.3 6.0 1.0
S2 S:SF4401 2.3 6.0 1.0
S3 S:SF4401 2.3 5.4 1.0
S4 S:SF4401 2.4 5.8 1.0
FE3 S:SF4401 2.7 5.8 1.0
FE4 S:SF4401 2.8 5.5 1.0
FE2 S:SF4401 2.8 5.5 1.0
CB S:CYS215 3.4 5.9 1.0
N S:LEU216 3.9 5.6 1.0
S1 S:SF4401 4.0 5.9 1.0
CA S:CYS215 4.0 5.8 1.0
N S:TYR217 4.2 5.4 1.0
CB S:PHE196 4.3 8.0 1.0
C S:CYS215 4.4 5.3 1.0
CD2 S:PHE196 4.5 8.4 1.0
ND1 S:HIS187 4.6 6.2 1.0
CB S:TYR217 4.7 7.5 1.0
O S:ARG192 4.8 6.7 1.0
CG S:PHE196 4.8 8.2 1.0
CB S:ARG192 4.8 6.0 1.0
CA S:LEU216 4.8 5.5 1.0
C S:LEU216 4.9 5.5 1.0
CE1 S:HIS187 4.9 6.5 1.0
CA S:TYR217 4.9 5.9 1.0
SG S:CYS221 4.9 5.4 1.0
SG S:CYS190 4.9 5.5 1.0

Iron binding site 4 out of 26 in 5adu

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Iron binding site 4 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:5.5
occ:1.00
 FE2 S:SF4401 0.0 5.5 1.0
S4 S:SF4401 2.3 5.8 1.0
S1 S:SF4401 2.3 5.9 1.0
SG S:CYS221 2.3 5.4 1.0
S3 S:SF4401 2.4 5.4 1.0
FE3 S:SF4401 2.8 5.8 1.0
FE4 S:SF4401 2.8 5.5 1.0
FE1 S:SF4401 2.8 5.7 1.0
CB S:CYS221 3.3 5.7 1.0
S2 S:SF4401 4.0 6.0 1.0
CD1 S:ILE243 4.0 6.2 1.0
CG1 S:ILE243 4.5 5.7 1.0
CD S:PRO224 4.6 6.8 1.0
N S:GLY223 4.6 5.5 1.0
CA S:GLY223 4.6 5.6 1.0
CA S:CYS221 4.7 5.4 1.0
ND1 S:HIS187 4.7 6.2 1.0
SG S:CYS215 4.8 6.0 1.0
N S:TYR217 4.8 5.4 1.0
SG S:CYS190 4.8 5.5 1.0
N S:LEU216 4.9 5.6 1.0
C S:CYS221 4.9 5.6 1.0
CB S:LEU216 5.0 6.0 1.0

Iron binding site 5 out of 26 in 5adu

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Iron binding site 5 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:5.8
occ:1.00
 FE3 S:SF4401 0.0 5.8 1.0
ND1 S:HIS187 2.1 6.2 1.0
S1 S:SF4401 2.3 5.9 1.0
S4 S:SF4401 2.3 5.8 1.0
S2 S:SF4401 2.3 6.0 1.0
FE4 S:SF4401 2.7 5.5 1.0
FE1 S:SF4401 2.7 5.7 1.0
FE2 S:SF4401 2.8 5.5 1.0
CE1 S:HIS187 3.0 6.5 1.0
CG S:HIS187 3.2 6.3 1.0
CB S:HIS187 3.7 6.5 1.0
S3 S:SF4401 3.9 5.4 1.0
CA S:HIS187 4.1 6.3 1.0
NE2 S:HIS187 4.2 7.3 1.0
CD2 S:HIS187 4.3 7.0 1.0
CG S:PRO224 4.4 7.2 1.0
CD S:PRO224 4.4 6.8 1.0
CB S:CYS190 4.6 5.7 1.0
SG S:CYS215 4.7 6.0 1.0
SG S:CYS190 4.7 5.5 1.0
CD2 S:PHE196 4.8 8.4 1.0
O S:HIS187 4.8 8.2 1.0
SG S:CYS221 4.8 5.4 1.0
N S:PRO224 4.9 6.3 1.0
CD S:ARG193 4.9 10.9 1.0

Iron binding site 6 out of 26 in 5adu

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Iron binding site 6 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:5.5
occ:1.00
 FE4 S:SF4401 0.0 5.5 1.0
S2 S:SF4401 2.3 6.0 1.0
SG S:CYS190 2.3 5.5 1.0
S3 S:SF4401 2.3 5.4 1.0
S1 S:SF4401 2.4 5.9 1.0
FE3 S:SF4401 2.7 5.8 1.0
FE1 S:SF4401 2.8 5.7 1.0
FE2 S:SF4401 2.8 5.5 1.0
CB S:CYS190 3.2 5.7 1.0
S4 S:SF4401 3.9 5.8 1.0
CB S:ARG192 4.3 6.0 1.0
CD1 S:ILE243 4.3 6.2 1.0
CG2 S:ILE243 4.4 5.8 1.0
ND1 S:HIS187 4.6 6.2 1.0
CA S:CYS190 4.6 5.3 1.0
C S:ARG192 4.7 6.0 1.0
N S:ARG192 4.8 5.4 1.0
CA S:ARG192 4.8 5.9 1.0
N S:ARG193 4.8 5.9 1.0
SG S:CYS221 4.8 5.4 1.0
CG1 S:ILE243 4.9 5.7 1.0
SG S:CYS215 5.0 6.0 1.0

Iron binding site 7 out of 26 in 5adu

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Iron binding site 7 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:5.7
occ:1.00
 FE1 S:F3S402 0.0 5.7 1.0
S1 S:F3S402 2.2 5.6 1.0
S2 S:F3S402 2.3 6.2 1.0
SG S:CYS252 2.3 6.0 1.0
S3 S:F3S402 2.3 5.6 1.0
FE3 S:F3S402 2.7 5.4 1.0
FE4 S:F3S402 2.7 5.7 1.0
CB S:CYS252 3.4 5.6 1.0
O L:HOH2071 3.8 8.3 1.0
N S:CYS252 3.8 5.0 1.0
S4 S:F3S402 3.9 6.4 1.0
O S:HOH2077 4.1 6.7 1.0
CA S:CYS252 4.1 5.6 1.0
N S:ALA253 4.5 5.7 1.0
C S:CYS252 4.6 5.4 1.0
O L:HOH2196 4.6 7.9 1.0
ND2 S:ASN228 4.7 5.2 1.0
SG S:CYS230 4.7 5.5 1.0
SG S:CYS249 4.8 5.6 1.0
C S:GLY251 5.0 5.3 1.0

Iron binding site 8 out of 26 in 5adu

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Iron binding site 8 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:5.4
occ:1.00
 FE3 S:F3S402 0.0 5.4 1.0
S4 S:F3S402 2.2 6.4 1.0
S1 S:F3S402 2.3 5.6 1.0
S3 S:F3S402 2.3 5.6 1.0
SG S:CYS230 2.3 5.5 1.0
FE1 S:F3S402 2.7 5.7 1.0
FE4 S:F3S402 2.7 5.7 1.0
CB S:CYS230 3.3 5.4 1.0
S2 S:F3S402 4.0 6.2 1.0
ND2 S:ASN228 4.0 5.2 1.0
CD1 S:ILE186 4.3 9.5 1.0
NE1 S:TRP235 4.4 5.1 1.0
O S:HOH2077 4.4 6.7 1.0
CD S:PRO242 4.6 5.0 1.0
CG S:PRO242 4.6 5.1 1.0
CG S:ASN228 4.7 5.0 1.0
CA S:CYS230 4.7 5.3 1.0
CB S:ASN228 4.8 5.5 1.0
SG S:CYS252 4.8 6.0 1.0
SG S:CYS249 4.8 5.6 1.0
CG1 S:ILE186 4.9 8.0 1.0

Iron binding site 9 out of 26 in 5adu

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Iron binding site 9 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:5.7
occ:1.00
 FE4 S:F3S402 0.0 5.7 1.0
S4 S:F3S402 2.3 6.4 1.0
S2 S:F3S402 2.3 6.2 1.0
SG S:CYS249 2.3 5.6 1.0
S3 S:F3S402 2.4 5.6 1.0
FE1 S:F3S402 2.7 5.7 1.0
FE3 S:F3S402 2.7 5.4 1.0
CB S:CYS249 3.3 5.1 1.0
CA S:CYS249 3.7 4.8 1.0
S1 S:F3S402 3.9 5.6 1.0
N S:LEU250 4.1 5.1 1.0
N S:GLY251 4.2 5.1 1.0
C S:CYS249 4.4 5.0 1.0
N S:CYS252 4.4 5.0 1.0
CG2 S:THR226 4.6 6.4 1.0
CG1 S:ILE186 4.8 8.0 1.0
CA S:GLY251 4.8 5.4 1.0
SG S:CYS252 4.8 6.0 1.0
SG S:CYS230 4.9 5.5 1.0
CG S:PRO242 4.9 5.1 1.0

Iron binding site 10 out of 26 in 5adu

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Iron binding site 10 out of 26 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:6.1
occ:1.00
 FE1 S:SF3403 0.0 6.1 1.0
S1 S:SF3403 2.3 6.1 1.0
SG S:CYS115 2.3 6.0 1.0
S2 S:SF3403 2.3 6.3 1.0
S3 S:SF3403 2.3 5.8 1.0
FE4 S:SF3403 2.6 6.3 1.0
FE3 S:SF3403 2.8 5.4 1.0
CB S:CYS115 3.4 5.9 1.0
FE7 S:SF3403 3.5 17.0 0.7
FE7 S:SF3403 3.9 6.2 0.3
O S:HOH2005 3.9 8.5 1.0
N S:CYS115 4.1 5.1 1.0
SG S:CYS19 4.1 6.7 1.0
CA S:CYS115 4.2 5.2 1.0
O L:HOH2047 4.3 6.1 1.0
SG S:CYS120 4.4 5.6 1.0
CB S:CYS120 4.5 5.4 1.0
N S:CYS17 4.6 5.6 1.0
SG S:CYS20 4.7 6.3 1.0
SG S:CYS149 4.8 5.4 1.0
SG S:CYS17 4.8 5.7 1.0
CA S:GLU16 4.9 6.5 0.5
CA S:GLU16 4.9 6.0 0.5
CB S:GLU16 5.0 9.4 0.5

Reference:

R.M.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.Phillips, F.A.Armstrong. Mechanism of Hydrogen Activation By [Nife] Hydrogenases. Nat. Chem. Biol. V. 12 46 2016.
ISSN: ESSN 1552-4469
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976
Page generated: Mon Aug 5 19:32:30 2024

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