Atomistry » Iron » PDB 5adf-5az3 » 5adu
Atomistry »
  Iron »
    PDB 5adf-5az3 »
      5adu »

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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Go back to Iron Binding Sites List in 5adu
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy