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Iron in PDB 6fpo: High Resolution Structure of Native Hydrogenase (Hyd-1)

Enzymatic activity of High Resolution Structure of Native Hydrogenase (Hyd-1)

All present enzymatic activity of High Resolution Structure of Native Hydrogenase (Hyd-1):
1.12.99.6;

Protein crystallography data

The structure of High Resolution Structure of Native Hydrogenase (Hyd-1), PDB code: 6fpo was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.55 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.786, 97.733, 183.102, 90.00, 90.00, 90.00
R / Rfree (%) 11.5 / 13.4

Other elements in 6fpo:

The structure of High Resolution Structure of Native Hydrogenase (Hyd-1) 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 High Resolution Structure of Native Hydrogenase (Hyd-1) (pdb code 6fpo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the High Resolution Structure of Native Hydrogenase (Hyd-1), PDB code: 6fpo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 6fpo

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Iron binding site 1 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.3
occ:1.00
 FE1 S:SF4401 0.0 7.3 1.0
S2 S:SF4401 2.3 7.8 1.0
SG S:CYS215 2.3 7.6 1.0
S3 S:SF4401 2.3 7.2 1.0
S4 S:SF4401 2.3 7.6 1.0
FE3 S:SF4401 2.7 7.7 1.0
FE4 S:SF4401 2.7 7.2 1.0
FE2 S:SF4401 2.8 7.1 1.0
CB S:CYS215 3.4 7.9 1.0
N S:LEU216 3.8 6.8 1.0
S1 S:SF4401 3.9 7.4 1.0
CA S:CYS215 3.9 7.3 1.0
N S:TYR217 4.2 7.0 1.0
C S:CYS215 4.3 6.9 1.0
CB S:PHE196 4.4 8.8 1.0
CD1 S:PHE196 4.5 10.0 1.0
ND1 S:HIS187 4.5 8.4 1.0
CB S:TYR217 4.6 8.1 1.0
CB S:ARG192 4.7 7.4 1.0
O S:ARG192 4.7 7.9 1.0
CE1 S:HIS187 4.8 9.1 1.0
CA S:LEU216 4.8 6.9 1.0
CG S:PHE196 4.8 9.2 1.0
C S:LEU216 4.8 7.4 1.0
CA S:TYR217 4.8 7.6 1.0
SG S:CYS190 4.8 7.4 1.0
SG S:CYS221 4.9 7.2 1.0
C S:ARG192 5.0 7.3 1.0

Iron binding site 2 out of 24 in 6fpo

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Iron binding site 2 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.1
occ:1.00
 FE2 S:SF4401 0.0 7.1 1.0
S4 S:SF4401 2.3 7.6 1.0
S1 S:SF4401 2.3 7.4 1.0
SG S:CYS221 2.3 7.2 1.0
S3 S:SF4401 2.3 7.2 1.0
FE4 S:SF4401 2.7 7.2 1.0
FE3 S:SF4401 2.7 7.7 1.0
FE1 S:SF4401 2.8 7.3 1.0
CB S:CYS221 3.2 7.4 1.0
S2 S:SF4401 3.9 7.8 1.0
CD1 S:ILE243 4.0 8.0 1.0
CG1 S:ILE243 4.4 7.3 1.0
CD S:PRO224 4.5 8.5 1.0
N S:GLY223 4.5 7.2 1.0
CA S:GLY223 4.6 7.3 1.0
CA S:CYS221 4.6 7.0 1.0
ND1 S:HIS187 4.6 8.4 1.0
SG S:CYS215 4.7 7.6 1.0
N S:TYR217 4.8 7.0 1.0
SG S:CYS190 4.8 7.4 1.0
N S:LEU216 4.9 6.8 1.0
C S:CYS221 4.9 7.3 1.0
CB S:LEU216 4.9 7.0 1.0
C S:LEU216 4.9 7.4 1.0
O S:CYS221 5.0 7.8 1.0

Iron binding site 3 out of 24 in 6fpo

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Iron binding site 3 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.7
occ:1.00
 FE3 S:SF4401 0.0 7.7 1.0
ND1 S:HIS187 2.1 8.4 1.0
S1 S:SF4401 2.3 7.4 1.0
S4 S:SF4401 2.3 7.6 1.0
S2 S:SF4401 2.3 7.8 1.0
FE4 S:SF4401 2.7 7.2 1.0
FE1 S:SF4401 2.7 7.3 1.0
FE2 S:SF4401 2.7 7.1 1.0
CE1 S:HIS187 2.9 9.1 1.0
CG S:HIS187 3.2 8.8 1.0
CB S:HIS187 3.6 8.5 1.0
CA S:HIS187 3.8 8.1 1.0
S3 S:SF4401 3.9 7.2 1.0
NE2 S:HIS187 4.1 10.7 1.0
CD2 S:HIS187 4.2 10.8 1.0
CD S:ARG193 4.3 10.8 0.5
CD S:PRO224 4.3 8.5 1.0
CG S:PRO224 4.3 9.2 1.0
CB S:CYS190 4.6 7.4 1.0
O S:HIS187 4.6 11.6 1.0
SG S:CYS215 4.7 7.6 1.0
SG S:CYS190 4.7 7.4 1.0
C S:HIS187 4.8 8.6 1.0
SG S:CYS221 4.8 7.2 1.0
CD1 S:PHE196 4.8 10.0 1.0
N S:HIS187 4.8 7.1 1.0
N S:PRO224 4.8 7.8 1.0
CG S:ARG193 4.9 10.6 0.5
CD S:ARG193 5.0 11.2 0.5

Iron binding site 4 out of 24 in 6fpo

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Iron binding site 4 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.2
occ:1.00
 FE4 S:SF4401 0.0 7.2 1.0
SG S:CYS190 2.3 7.4 1.0
S2 S:SF4401 2.3 7.8 1.0
S3 S:SF4401 2.3 7.2 1.0
S1 S:SF4401 2.3 7.4 1.0
FE3 S:SF4401 2.7 7.7 1.0
FE1 S:SF4401 2.7 7.3 1.0
FE2 S:SF4401 2.7 7.1 1.0
CB S:CYS190 3.1 7.4 1.0
S4 S:SF4401 3.9 7.6 1.0
CB S:ARG192 4.2 7.4 1.0
CD1 S:ILE243 4.3 8.0 1.0
CG2 S:ILE243 4.3 7.5 1.0
ND1 S:HIS187 4.5 8.4 1.0
CA S:CYS190 4.6 6.6 1.0
C S:ARG192 4.7 7.3 1.0
N S:ARG192 4.7 7.1 1.0
CA S:ARG192 4.7 7.4 1.0
N S:ARG193 4.8 7.6 1.0
SG S:CYS221 4.8 7.2 1.0
CG1 S:ILE243 4.8 7.3 1.0
CA S:HIS187 4.9 8.1 1.0
SG S:CYS215 4.9 7.6 1.0
C S:CYS190 5.0 6.5 1.0

Iron binding site 5 out of 24 in 6fpo

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Iron binding site 5 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:7.9
occ:1.00
 FE1 S:F3S402 0.0 7.9 1.0
S1 S:F3S402 2.2 7.8 1.0
S2 S:F3S402 2.3 8.5 1.0
SG S:CYS252 2.3 8.4 1.0
S3 S:F3S402 2.3 8.0 1.0
FE3 S:F3S402 2.7 7.3 1.0
FE4 S:F3S402 2.7 7.8 1.0
CB S:CYS252 3.4 7.7 1.0
O L:HOH715 3.7 9.8 1.0
N S:CYS252 3.8 7.1 1.0
S4 S:F3S402 3.9 8.5 1.0
O S:HOH619 4.0 8.0 1.0
CA S:CYS252 4.0 7.7 1.0
NZ L:LYS226 4.2 13.5 0.5
N S:ALA253 4.5 7.7 1.0
C S:CYS252 4.5 7.4 1.0
O L:HOH1045 4.5 9.3 1.0
ND2 S:ASN228 4.7 7.2 1.0
SG S:CYS230 4.7 7.3 1.0
SG S:CYS249 4.7 7.6 1.0
C S:GLY251 4.9 7.1 1.0

Iron binding site 6 out of 24 in 6fpo

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Iron binding site 6 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:7.3
occ:1.00
 FE3 S:F3S402 0.0 7.3 1.0
S4 S:F3S402 2.2 8.5 1.0
S1 S:F3S402 2.2 7.8 1.0
S3 S:F3S402 2.3 8.0 1.0
SG S:CYS230 2.3 7.3 1.0
FE1 S:F3S402 2.7 7.9 1.0
FE4 S:F3S402 2.7 7.8 1.0
CB S:CYS230 3.2 7.3 1.0
S2 S:F3S402 4.0 8.5 1.0
ND2 S:ASN228 4.0 7.2 1.0
CD1 S:ILE186 4.3 10.7 1.0
O S:HOH619 4.3 8.0 1.0
NE1 S:TRP235 4.3 6.6 1.0
CG S:PRO242 4.5 7.0 1.0
CD S:PRO242 4.5 6.6 1.0
CG S:ASN228 4.7 7.1 1.0
CA S:CYS230 4.7 6.4 1.0
CB S:ASN228 4.7 6.8 1.0
SG S:CYS252 4.8 8.4 1.0
SG S:CYS249 4.8 7.6 1.0
CG1 S:ILE186 4.8 10.1 1.0

Iron binding site 7 out of 24 in 6fpo

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Iron binding site 7 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:7.8
occ:1.00
 FE4 S:F3S402 0.0 7.8 1.0
S4 S:F3S402 2.2 8.5 1.0
S2 S:F3S402 2.3 8.5 1.0
SG S:CYS249 2.3 7.6 1.0
S3 S:F3S402 2.3 8.0 1.0
FE1 S:F3S402 2.7 7.9 1.0
FE3 S:F3S402 2.7 7.3 1.0
CB S:CYS249 3.2 7.2 1.0
CA S:CYS249 3.7 6.7 1.0
S1 S:F3S402 3.9 7.8 1.0
N S:LEU250 4.0 7.1 1.0
N S:GLY251 4.2 7.5 1.0
C S:CYS249 4.3 6.8 1.0
N S:CYS252 4.4 7.1 1.0
CG2 S:THR226 4.6 7.7 1.0
CA S:GLY251 4.7 7.8 1.0
CG1 S:ILE186 4.8 10.1 1.0
SG S:CYS252 4.8 8.4 1.0
SG S:CYS230 4.8 7.3 1.0
CG S:PRO242 4.8 7.0 1.0
N S:CYS249 4.9 6.8 1.0
C S:GLY251 5.0 7.1 1.0

Iron binding site 8 out of 24 in 6fpo

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Iron binding site 8 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:8.9
occ:0.85
 FE1 S:SF3403 0.0 8.9 0.8
S1 S:SF3403 2.2 7.9 0.8
S2 S:SF3403 2.3 9.7 0.8
SG S:CYS115 2.3 9.1 1.0
S3 S:SF3403 2.3 8.5 0.8
FE4 S:SF3403 2.6 10.9 0.8
FE3 S:SF3403 2.7 6.6 0.8
CB S:CYS115 3.4 9.1 1.0
O S:HOH516 3.4 16.0 1.0
O L:HOH732 3.8 9.7 1.0
O S:HOH532 3.8 13.2 1.0
FE7 S:SF3403 3.9 12.6 0.8
N S:CYS115 4.0 7.3 1.0
SG S:CYS19 4.0 30.0 1.0
CA S:CYS115 4.2 7.5 1.0
O S:HOH588 4.2 8.3 1.0
SG S:CYS120 4.4 8.9 1.0
CB S:CYS120 4.4 7.3 1.0
N S:CYS17 4.6 9.1 1.0
SG S:CYS149 4.7 8.1 1.0
SG S:CYS20 4.7 9.2 1.0
SG S:CYS17 4.7 10.4 1.0
CB S:GLU16 4.8 9.2 0.4
CA S:GLU16 4.8 8.2 0.4
CA S:GLU16 4.9 9.1 0.6

Iron binding site 9 out of 24 in 6fpo

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Iron binding site 9 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:6.6
occ:0.85
 FE3 S:SF3403 0.0 6.6 0.8
S1 S:SF3403 2.2 7.9 0.8
S3 S:SF3403 2.3 8.5 0.8
SG S:CYS149 2.3 8.1 1.0
SG S:CYS120 2.3 8.9 1.0
FE1 S:SF3403 2.7 8.9 0.8
CB S:CYS149 3.3 7.3 1.0
CB S:CYS120 3.4 7.3 1.0
FE4 S:SF3403 3.6 10.9 0.8
O L:HOH732 3.7 9.7 1.0
CA S:CYS149 3.9 6.6 1.0
SG S:CYS115 4.0 9.1 1.0
CG L:ARG74 4.4 7.0 1.0
SG S:CYS19 4.4 30.0 1.0
N S:CYS115 4.5 7.3 1.0
CB S:THR114 4.6 8.0 1.0
S2 S:SF3403 4.7 9.7 0.8
CA S:CYS120 4.8 7.7 1.0
C S:CYS149 4.9 6.2 1.0
N S:VAL121 4.9 7.1 1.0
O S:GLY148 4.9 7.5 1.0

Iron binding site 10 out of 24 in 6fpo

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Iron binding site 10 out of 24 in the High Resolution Structure of Native Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of High Resolution Structure of Native Hydrogenase (Hyd-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:10.9
occ:0.85
 FE4 S:SF3403 0.0 10.9 0.8
O L:HOH732 1.6 9.7 1.0
SG S:CYS19 2.3 30.0 1.0
SG S:CYS17 2.3 10.4 1.0
S3 S:SF3403 2.3 8.5 0.8
S2 S:SF3403 2.3 9.7 0.8
FE1 S:SF3403 2.6 8.9 0.8
FE7 S:SF3403 3.2 12.6 0.8
CB S:CYS17 3.4 9.5 1.0
CB S:CYS19 3.5 30.0 1.0
FE3 S:SF3403 3.6 6.6 0.8
N S:CYS19 3.7 9.0 1.0
N S:CYS17 3.8 9.1 1.0
S1 S:SF3403 3.8 7.9 0.8
CA S:CYS17 4.0 9.0 1.0
O S:HOH516 4.0 16.0 1.0
NE2 L:HIS229 4.1 11.0 1.0
CA S:CYS19 4.2 8.7 1.0
N S:THR18 4.2 9.1 1.0
C S:CYS17 4.3 9.1 1.0
SG S:CYS149 4.5 8.1 1.0
OE2 S:GLU76 4.5 12.8 0.5
O S:HOH588 4.6 8.3 1.0
SG S:CYS115 4.6 9.1 1.0
CD2 L:HIS229 4.8 8.9 1.0
N S:CYS20 4.8 7.9 1.0
C S:THR18 4.9 8.2 1.0
C S:GLU16 4.9 8.8 1.0
SG S:CYS20 5.0 9.2 1.0
C S:CYS19 5.0 8.2 1.0

Reference:

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Tue Aug 6 18:31:41 2024

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