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Iron in PDB 5a4m: Mechanism of Hydrogen Activation By Nife-Hydrogenases

Enzymatic activity of Mechanism of Hydrogen Activation By Nife-Hydrogenases

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

Protein crystallography data

The structure of Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4m was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sergent, S.B.Carr, S.E.V.Philips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.62 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.671, 97.162, 182.911, 90.00, 90.00, 90.00
R / Rfree (%) 13.425 / 16.235

Other elements in 5a4m:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5a4m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 5a4m

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Iron binding site 1 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe601

b:15.5
occ:1.00
 FE L:NFV601 0.0 15.5 1.0
C3 L:NFV601 1.8 15.9 1.0
C1 L:NFV601 1.8 14.4 1.0
O4 L:NFV601 1.9 19.4 1.0
C2 L:NFV601 1.9 16.9 1.0
SG L:CYS579 2.3 15.9 1.0
SG L:CYS79 2.3 18.6 1.0
NI L:NFV601 2.9 26.7 1.0
N3 L:NFV601 3.0 15.7 1.0
O1 L:NFV601 3.0 17.1 1.0
N2 L:NFV601 3.0 16.1 1.0
CB L:CYS579 3.4 15.5 1.0
CB L:CYS79 3.4 20.1 1.0
O L:HOH2106 3.9 28.6 1.0
CB L:CYS576 4.1 18.6 1.0
CD L:ARG509 4.3 17.5 1.0
NE2 L:HIS83 4.3 14.2 1.0
CG1 L:VAL530 4.3 17.7 1.0
SG L:CYS576 4.4 26.7 1.0
NH1 L:ARG509 4.4 18.4 1.0
CA L:CYS579 4.8 14.5 1.0
CA L:CYS79 4.8 21.0 1.0
CG L:PRO531 4.8 15.6 1.0
CG1 L:VAL82 4.8 15.6 1.0
CB L:CYS76 4.8 23.2 1.0
CB L:ALA507 4.9 15.2 1.0
CD L:PRO531 4.9 15.6 1.0
SG L:CYS76 5.0 28.3 1.0

Iron binding site 2 out of 24 in 5a4m

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Iron binding site 2 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe603

b:16.3
occ:1.00
 FE M:NFV603 0.0 16.3 1.0
C1 M:NFV603 1.7 17.7 1.0
C3 M:NFV603 1.8 15.9 1.0
O4 M:NFV603 1.9 19.9 1.0
C2 M:NFV603 1.9 17.8 1.0
SG M:CYS579 2.2 16.2 1.0
SG M:CYS79 2.3 18.5 1.0
NI M:NFV603 2.8 26.9 1.0
O1 M:NFV603 2.9 17.9 1.0
N3 M:NFV603 3.0 14.5 1.0
N2 M:NFV603 3.0 17.3 1.0
CB M:CYS79 3.4 19.7 1.0
CB M:CYS579 3.4 16.6 1.0
CB M:CYS576 4.1 19.6 1.0
CD M:ARG509 4.3 17.1 1.0
NE2 M:HIS83 4.3 16.4 1.0
CG1 M:VAL530 4.3 19.2 1.0
SG M:CYS576 4.4 26.8 1.0
NH1 M:ARG509 4.4 19.3 1.0
CA M:CYS579 4.8 15.3 1.0
CA M:CYS79 4.8 20.2 1.0
CG1 M:VAL82 4.8 14.9 1.0
CB M:CYS76 4.8 21.9 1.0
CG M:PRO531 4.8 14.9 1.0
CB M:ALA507 4.8 15.0 1.0
CD M:PRO531 4.9 14.5 1.0
SG M:CYS76 5.0 28.6 1.0

Iron binding site 3 out of 24 in 5a4m

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Iron binding site 3 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:18.3
occ:1.00
 FE1 S:SF4401 0.0 18.3 1.0
S3 S:SF4401 2.2 16.8 1.0
S4 S:SF4401 2.3 17.7 1.0
S2 S:SF4401 2.3 17.8 1.0
SG S:CYS190 2.3 17.4 1.0
FE4 S:SF4401 2.6 15.6 1.0
FE3 S:SF4401 2.7 20.1 1.0
FE2 S:SF4401 2.7 15.6 1.0
CB S:CYS190 3.2 16.5 1.0
S1 S:SF4401 3.7 18.2 1.0
CB S:ARG192 4.2 15.8 1.0
ND1 S:HIS187 4.3 19.4 1.0
CD1 S:ILE243 4.3 17.1 1.0
CG2 S:ILE243 4.4 15.3 1.0
CA S:CYS190 4.6 15.7 1.0
C S:ARG192 4.7 16.5 1.0
SG S:CYS221 4.7 15.8 1.0
N S:ARG192 4.8 15.9 1.0
N S:ARG193 4.8 16.4 1.0
CA S:ARG192 4.8 15.8 1.0
CG1 S:ILE243 4.9 16.3 1.0
SG S:CYS215 4.9 15.7 1.0

Iron binding site 4 out of 24 in 5a4m

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Iron binding site 4 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:15.6
occ:1.00
 FE2 S:SF4401 0.0 15.6 1.0
S4 S:SF4401 2.2 17.7 1.0
S3 S:SF4401 2.2 16.8 1.0
S1 S:SF4401 2.2 18.2 1.0
SG S:CYS215 2.3 15.7 1.0
FE1 S:SF4401 2.7 18.3 1.0
FE3 S:SF4401 2.7 20.1 1.0
FE4 S:SF4401 2.7 15.6 1.0
CB S:CYS215 3.4 15.2 1.0
N S:LEU216 3.8 15.4 1.0
S2 S:SF4401 3.8 17.8 1.0
CA S:CYS215 3.9 15.8 1.0
N S:TYR217 4.2 17.4 1.0
C S:CYS215 4.3 16.1 1.0
CB S:PHE196 4.4 19.5 1.0
ND1 S:HIS187 4.4 19.4 1.0
CD1 S:PHE196 4.4 20.3 1.0
CB S:TYR217 4.6 19.6 1.0
CE1 S:HIS187 4.6 20.9 1.0
CB S:ARG192 4.7 15.8 1.0
O S:ARG192 4.8 17.2 1.0
SG S:CYS190 4.8 17.4 1.0
CA S:TYR217 4.8 18.4 1.0
CA S:LEU216 4.8 16.2 1.0
CG S:PHE196 4.8 20.1 1.0
SG S:CYS221 4.8 15.8 1.0
C S:LEU216 4.9 16.9 1.0

Iron binding site 5 out of 24 in 5a4m

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Iron binding site 5 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:20.1
occ:1.00
 FE3 S:SF4401 0.0 20.1 1.0
ND1 S:HIS187 1.9 19.4 1.0
S1 S:SF4401 2.2 18.2 1.0
S2 S:SF4401 2.3 17.8 1.0
S4 S:SF4401 2.3 17.7 1.0
FE1 S:SF4401 2.7 18.3 1.0
FE2 S:SF4401 2.7 15.6 1.0
CE1 S:HIS187 2.7 20.9 1.0
FE4 S:SF4401 2.7 15.6 1.0
CG S:HIS187 3.1 19.0 1.0
CB S:HIS187 3.7 16.9 1.0
S3 S:SF4401 3.8 16.8 1.0
NE2 S:HIS187 3.9 20.6 1.0
CA S:HIS187 4.0 17.3 1.0
CD2 S:HIS187 4.1 20.8 1.0
CG S:PRO224 4.3 18.2 1.0
CD S:PRO224 4.3 18.2 1.0
CB S:CYS190 4.6 16.5 1.0
SG S:CYS190 4.6 17.4 1.0
SG S:CYS215 4.6 15.7 1.0
CD1 S:PHE196 4.7 20.3 1.0
O S:HIS187 4.8 18.8 1.0
SG S:CYS221 4.8 15.8 1.0
CD S:ARG193 4.8 24.4 1.0
N S:PRO224 4.9 17.3 1.0
C S:HIS187 5.0 17.3 1.0

Iron binding site 6 out of 24 in 5a4m

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Iron binding site 6 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:15.6
occ:1.00
 FE4 S:SF4401 0.0 15.6 1.0
S1 S:SF4401 2.2 18.2 1.0
S2 S:SF4401 2.2 17.8 1.0
S3 S:SF4401 2.2 16.8 1.0
SG S:CYS221 2.3 15.8 1.0
FE1 S:SF4401 2.6 18.3 1.0
FE2 S:SF4401 2.7 15.6 1.0
FE3 S:SF4401 2.7 20.1 1.0
CB S:CYS221 3.3 16.3 1.0
S4 S:SF4401 3.9 17.7 1.0
CD1 S:ILE243 4.0 17.1 1.0
CG1 S:ILE243 4.4 16.3 1.0
CA S:GLY223 4.5 15.6 1.0
N S:GLY223 4.5 15.9 1.0
ND1 S:HIS187 4.5 19.4 1.0
CD S:PRO224 4.6 18.2 1.0
CA S:CYS221 4.6 16.4 1.0
SG S:CYS215 4.7 15.7 1.0
SG S:CYS190 4.7 17.4 1.0
N S:TYR217 4.8 17.4 1.0
N S:LEU216 4.8 15.4 1.0
C S:CYS221 4.9 17.2 1.0
CB S:LEU216 5.0 15.8 1.0

Iron binding site 7 out of 24 in 5a4m

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Iron binding site 7 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:16.5
occ:1.00
 FE1 S:F3S402 0.0 16.5 1.0
S2 S:F3S402 2.2 15.7 1.0
S1 S:F3S402 2.2 17.2 1.0
S3 S:F3S402 2.2 15.0 1.0
SG S:CYS252 2.3 17.1 1.0
FE4 S:F3S402 2.6 15.6 1.0
FE3 S:F3S402 2.6 15.7 1.0
CB S:CYS252 3.5 15.8 1.0
O L:HOH2105 3.7 17.8 1.0
N S:CYS252 3.8 14.8 1.0
S4 S:F3S402 3.9 16.6 1.0
O S:HOH2110 4.0 14.5 1.0
CA S:CYS252 4.0 15.3 1.0
O L:HOH2283 4.5 16.6 1.0
N S:ALA253 4.5 14.7 1.0
C S:CYS252 4.5 15.5 1.0
SG S:CYS230 4.7 15.1 1.0
ND2 S:ASN228 4.7 13.9 1.0
SG S:CYS249 4.7 16.9 1.0
C S:GLY251 5.0 15.4 1.0

Iron binding site 8 out of 24 in 5a4m

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Iron binding site 8 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:15.7
occ:1.00
 FE3 S:F3S402 0.0 15.7 1.0
S4 S:F3S402 2.2 16.6 1.0
S3 S:F3S402 2.3 15.0 1.0
S1 S:F3S402 2.3 17.2 1.0
SG S:CYS249 2.3 16.9 1.0
FE1 S:F3S402 2.6 16.5 1.0
FE4 S:F3S402 2.6 15.6 1.0
CB S:CYS249 3.3 16.0 1.0
CA S:CYS249 3.7 15.5 1.0
S2 S:F3S402 3.8 15.7 1.0
N S:LEU250 4.1 14.9 1.0
N S:GLY251 4.2 15.0 1.0
C S:CYS249 4.3 15.3 1.0
N S:CYS252 4.4 14.8 1.0
CG2 S:THR226 4.6 13.8 1.0
CG1 S:ILE186 4.7 18.2 1.0
SG S:CYS252 4.7 17.1 1.0
CA S:GLY251 4.8 15.7 1.0
SG S:CYS230 4.8 15.1 1.0
CG S:PRO242 4.9 14.1 1.0
N S:CYS249 5.0 15.1 1.0
O L:HOH2283 5.0 16.6 1.0

Iron binding site 9 out of 24 in 5a4m

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Iron binding site 9 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:15.6
occ:1.00
 FE4 S:F3S402 0.0 15.6 1.0
S4 S:F3S402 2.2 16.6 1.0
S3 S:F3S402 2.2 15.0 1.0
S2 S:F3S402 2.2 15.7 1.0
SG S:CYS230 2.3 15.1 1.0
FE1 S:F3S402 2.6 16.5 1.0
FE3 S:F3S402 2.6 15.7 1.0
CB S:CYS230 3.3 13.7 1.0
S1 S:F3S402 3.9 17.2 1.0
ND2 S:ASN228 4.0 13.9 1.0
O S:HOH2110 4.3 14.5 1.0
NE1 S:TRP235 4.3 15.2 1.0
CD1 S:ILE186 4.4 18.6 1.0
CD S:PRO242 4.5 13.6 1.0
CG S:PRO242 4.5 14.1 1.0
CG S:ASN228 4.6 14.2 1.0
CA S:CYS230 4.7 14.1 1.0
SG S:CYS252 4.7 17.1 1.0
CB S:ASN228 4.7 14.3 1.0
SG S:CYS249 4.8 16.9 1.0
CG1 S:ILE186 4.8 18.2 1.0

Iron binding site 10 out of 24 in 5a4m

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Iron binding site 10 out of 24 in 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 Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe404

b:24.7
occ:1.00
 FE1 S:SF3404 0.0 24.7 1.0
S3 S:SF3404 2.2 20.5 1.0
S1 S:SF3404 2.3 23.7 1.0
S2 S:SF3404 2.3 32.0 1.0
SG S:CYS115 2.3 20.5 1.0
FE7 S:SF3404 2.6 26.2 1.0
FE3 S:SF3404 2.8 19.0 1.0
O S:HOH2009 3.2 18.1 1.0
CB S:CYS115 3.3 18.8 1.0
FE4 S:SF3404 3.6 34.0 1.0
O L:HOH2282 3.8 29.1 1.0
O S:HOH2008 3.8 19.6 1.0
N S:CYS115 4.0 17.2 1.0
SG S:CYS19 4.1 17.6 1.0
CA S:CYS115 4.2 17.1 1.0
O L:HOH2070 4.3 18.5 1.0
SG S:CYS120 4.5 19.5 1.0
CB S:CYS120 4.5 17.9 1.0
SG S:CYS149 4.7 16.6 1.0
SG S:CYS20 4.7 16.4 1.0
N S:CYS17 4.8 18.8 1.0
SG S:CYS17 4.8 22.9 1.0
CA S:GLU16 5.0 19.4 1.0

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: ISSN 1552-4450
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976
Page generated: Mon Aug 5 18:47:21 2024

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