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Iron in PDB 1frf: Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans

Enzymatic activity of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans

All present enzymatic activity of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans:
1.18.99.1;

Protein crystallography data

The structure of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans, PDB code: 1frf was solved by Y.Montet, A.Volbeda, C.Piras, E.C.Hatchikian, M.Frey, J.C.Fontecilla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.610, 99.770, 184.510, 90.00, 90.88, 90.00
R / Rfree (%) 22 / 27.4

Other elements in 1frf:

The structure of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans (pdb code 1frf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans, PDB code: 1frf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1frf

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Iron binding site 1 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:16.5
occ:1.00
 FE1 S:SF4265 0.0 16.5 1.0
S3 S:SF4265 2.2 13.1 1.0
S4 S:SF4265 2.2 15.8 1.0
S2 S:SF4265 2.3 10.7 1.0
SG S:CYS218 2.3 12.6 1.0
FE3 S:SF4265 2.4 15.2 1.0
FE4 S:SF4265 2.5 16.0 1.0
FE2 S:SF4265 2.6 14.6 1.0
CB S:CYS218 3.2 8.6 1.0
S1 S:SF4265 3.7 10.4 1.0
CD S:PRO221 4.2 16.4 1.0
SG S:CYS212 4.3 12.1 1.0
ND1 S:HIS184 4.5 11.1 1.0
SG S:CYS187 4.5 15.0 1.0
CA S:CYS218 4.6 14.7 1.0
N S:LEU213 4.6 12.9 1.0
CG2 S:VAL239 4.7 6.3 1.0
CG S:PRO221 4.7 16.5 1.0
N S:TYR214 4.8 14.5 1.0
C S:LEU213 4.8 12.9 1.0
N S:GLY220 4.8 12.3 1.0
CA S:GLY220 4.9 13.3 1.0
CB S:LEU213 4.9 4.7 1.0
C S:CYS218 4.9 14.3 1.0
CG1 S:VAL239 4.9 6.1 1.0

Iron binding site 2 out of 12 in 1frf

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Iron binding site 2 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:14.6
occ:1.00
 FE2 S:SF4265 0.0 14.6 1.0
ND1 S:HIS184 2.0 11.1 1.0
S4 S:SF4265 2.3 15.8 1.0
S1 S:SF4265 2.3 10.4 1.0
S3 S:SF4265 2.3 13.1 1.0
FE4 S:SF4265 2.5 16.0 1.0
FE3 S:SF4265 2.5 15.2 1.0
FE1 S:SF4265 2.6 16.5 1.0
CE1 S:HIS184 2.8 9.5 1.0
CG S:HIS184 3.1 12.8 1.0
CB S:HIS184 3.6 12.4 1.0
S2 S:SF4265 3.8 10.7 1.0
CG S:PRO221 3.9 16.5 1.0
CA S:HIS184 4.0 13.3 1.0
NE2 S:HIS184 4.0 13.1 1.0
CD S:PRO221 4.0 16.4 1.0
CD2 S:HIS184 4.2 10.5 1.0
SG S:CYS212 4.4 12.1 1.0
SG S:CYS187 4.4 15.0 1.0
CB S:CYS187 4.5 15.8 1.0
O S:HIS184 4.5 15.7 1.0
SG S:CYS218 4.6 12.6 1.0
CD1 S:PHE193 4.6 16.3 1.0
C S:HIS184 4.7 14.7 1.0
CG S:PHE193 4.7 11.3 1.0
N S:PRO221 4.7 14.9 1.0
CB S:PHE193 4.7 11.1 1.0
CD1 S:LEU190 5.0 3.8 1.0

Iron binding site 3 out of 12 in 1frf

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Iron binding site 3 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:15.2
occ:1.00
 FE3 S:SF4265 0.0 15.2 1.0
S2 S:SF4265 2.2 10.7 1.0
S1 S:SF4265 2.2 10.4 1.0
SG S:CYS212 2.3 12.1 1.0
S4 S:SF4265 2.3 15.8 1.0
FE1 S:SF4265 2.4 16.5 1.0
FE4 S:SF4265 2.5 16.0 1.0
FE2 S:SF4265 2.5 14.6 1.0
CB S:CYS212 3.5 7.6 1.0
S3 S:SF4265 3.7 13.1 1.0
N S:LEU213 3.9 12.9 1.0
CA S:CYS212 4.0 12.8 1.0
CB S:PHE193 4.2 11.1 1.0
ND1 S:HIS184 4.2 11.1 1.0
CD1 S:PHE193 4.4 16.3 1.0
C S:CYS212 4.4 12.1 1.0
N S:TYR214 4.5 14.5 1.0
CB S:ARG189 4.5 10.1 1.0
CE1 S:HIS184 4.6 9.5 1.0
SG S:CYS187 4.6 15.0 1.0
SG S:CYS218 4.6 12.6 1.0
CG S:PHE193 4.7 11.3 1.0
O S:ARG189 4.7 13.1 1.0
C S:ARG189 4.8 14.6 1.0
CA S:LEU213 4.9 10.2 1.0
C S:LEU213 4.9 12.9 1.0
CB S:TYR214 5.0 13.3 1.0
CB S:CYS218 5.0 8.6 1.0

Iron binding site 4 out of 12 in 1frf

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Iron binding site 4 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe265

b:16.0
occ:1.00
 FE4 S:SF4265 0.0 16.0 1.0
S2 S:SF4265 2.2 10.7 1.0
S3 S:SF4265 2.3 13.1 1.0
SG S:CYS187 2.3 15.0 1.0
S1 S:SF4265 2.3 10.4 1.0
FE1 S:SF4265 2.5 16.5 1.0
FE2 S:SF4265 2.5 14.6 1.0
FE3 S:SF4265 2.5 15.2 1.0
CB S:CYS187 3.1 15.8 1.0
S4 S:SF4265 3.8 15.8 1.0
CB S:ARG189 3.9 10.1 1.0
ND1 S:HIS184 4.1 11.1 1.0
CG1 S:VAL239 4.3 6.1 1.0
SG S:CYS218 4.5 12.6 1.0
CA S:CYS187 4.6 14.0 1.0
C S:ARG189 4.6 14.6 1.0
CA S:ARG189 4.6 13.2 1.0
N S:LEU190 4.7 14.1 1.0
N S:ARG189 4.7 14.3 1.0
SG S:CYS212 4.7 12.1 1.0
CA S:HIS184 4.8 13.3 1.0
CG2 S:VAL239 4.9 6.3 1.0
C S:CYS187 5.0 14.1 1.0
CE1 S:HIS184 5.0 9.5 1.0

Iron binding site 5 out of 12 in 1frf

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Iron binding site 5 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe266

b:8.1
occ:1.00
 FE1 S:F3S266 0.0 8.1 1.0
S1 S:F3S266 2.2 16.4 1.0
S2 S:F3S266 2.2 10.5 1.0
S3 S:F3S266 2.3 8.0 1.0
SG S:CYS248 2.3 9.2 1.0
FE4 S:F3S266 2.4 10.9 1.0
FE3 S:F3S266 2.6 14.0 1.0
CB S:CYS248 3.5 10.5 1.0
S4 S:F3S266 3.8 15.0 1.0
N S:CYS248 3.9 10.0 1.0
CA S:CYS248 4.1 9.5 1.0
SG S:CYS245 4.4 9.9 1.0
N S:SER249 4.6 10.4 1.0
C S:CYS248 4.6 9.1 1.0
NZ L:LYS225 4.6 11.3 1.0
SG S:CYS227 4.7 13.9 1.0
OD1 S:ASN225 4.7 21.9 1.0
N S:GLY247 4.8 9.2 1.0
C S:GLY247 4.9 7.4 1.0

Iron binding site 6 out of 12 in 1frf

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Iron binding site 6 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe266

b:14.0
occ:1.00
 FE3 S:F3S266 0.0 14.0 1.0
S1 S:F3S266 2.3 16.4 1.0
S4 S:F3S266 2.3 15.0 1.0
SG S:CYS227 2.3 13.9 1.0
S3 S:F3S266 2.3 8.0 1.0
FE4 S:F3S266 2.4 10.9 1.0
FE1 S:F3S266 2.6 8.1 1.0
CB S:CYS227 3.5 15.6 1.0
S2 S:F3S266 3.9 10.5 1.0
OD1 S:ASN225 4.1 21.9 1.0
SG S:CYS245 4.4 9.9 1.0
CE1 S:PHE232 4.6 2.0 1.0
CG S:ASN225 4.6 14.1 1.0
SG S:CYS248 4.7 9.2 1.0
CB S:ASN225 4.7 15.7 1.0
CG2 S:VAL183 4.7 2.0 1.0
CZ S:PHE232 4.7 2.0 1.0
CE3 S:TRP237 4.9 14.2 1.0
CG S:PRO238 4.9 3.8 1.0
CA S:CYS227 4.9 15.8 1.0
CD S:PRO238 5.0 2.0 1.0

Iron binding site 7 out of 12 in 1frf

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Iron binding site 7 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe266

b:10.9
occ:1.00
 FE4 S:F3S266 0.0 10.9 1.0
S4 S:F3S266 2.2 15.0 1.0
S3 S:F3S266 2.3 8.0 1.0
SG S:CYS245 2.3 9.9 1.0
S2 S:F3S266 2.3 10.5 1.0
FE3 S:F3S266 2.4 14.0 1.0
FE1 S:F3S266 2.4 8.1 1.0
CB S:CYS245 3.3 7.6 1.0
S1 S:F3S266 3.6 16.4 1.0
CA S:CYS245 3.7 8.0 1.0
N S:LEU246 4.0 9.9 1.0
N S:GLY247 4.3 9.2 1.0
C S:CYS245 4.3 10.0 1.0
OE1 L:GLN230 4.5 4.9 1.0
SG S:CYS227 4.6 13.9 1.0
SG S:CYS248 4.6 9.2 1.0
N S:CYS248 4.7 10.0 1.0
CG2 S:THR223 4.8 11.1 1.0
CA S:GLY247 4.8 7.7 1.0
CG S:PRO238 4.9 3.8 1.0

Iron binding site 8 out of 12 in 1frf

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Iron binding site 8 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe267

b:9.0
occ:1.00
 FE1 S:SF4267 0.0 9.0 1.0
S4 S:SF4267 2.2 7.9 1.0
S3 S:SF4267 2.2 5.8 1.0
SG S:CYS17 2.3 6.9 1.0
S2 S:SF4267 2.3 12.6 1.0
FE3 S:SF4267 2.5 8.2 1.0
FE2 S:SF4267 2.5 8.2 1.0
FE4 S:SF4267 2.7 10.4 1.0
CB S:CYS17 3.5 5.2 1.0
S1 S:SF4267 3.8 6.7 1.0
N S:CYS17 3.9 7.0 1.0
N S:GLY19 4.2 7.9 1.0
CA S:CYS17 4.2 4.0 1.0
CE1 L:HIS228 4.2 4.5 1.0
CA S:GLY19 4.4 7.8 1.0
SG S:CYS147 4.4 9.4 1.0
O S:HOH270 4.6 8.4 1.0
SG S:CYS114 4.6 8.2 1.0
C S:CYS17 4.6 5.1 1.0
N S:THR18 4.7 4.8 1.0
SG S:CYS20 4.8 5.0 1.0
N S:CYS20 4.8 9.1 1.0
CG L:ARG70 4.9 7.0 1.0
C S:GLY19 5.0 6.0 1.0

Iron binding site 9 out of 12 in 1frf

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Iron binding site 9 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe267

b:8.2
occ:1.00
 FE2 S:SF4267 0.0 8.2 1.0
S4 S:SF4267 2.2 7.9 1.0
S1 S:SF4267 2.3 6.7 1.0
S3 S:SF4267 2.3 5.8 1.0
SG S:CYS114 2.3 8.2 1.0
FE3 S:SF4267 2.5 8.2 1.0
FE1 S:SF4267 2.5 9.0 1.0
FE4 S:SF4267 2.6 10.4 1.0
CB S:CYS114 3.3 2.4 1.0
S2 S:SF4267 3.7 12.6 1.0
O S:HOH270 4.1 8.4 1.0
N S:CYS114 4.2 2.0 1.0
SG S:CYS147 4.3 9.4 1.0
CA S:CYS114 4.4 3.9 1.0
SG S:CYS17 4.6 6.9 1.0
SG S:CYS20 4.7 5.0 1.0
N S:CYS17 4.9 7.0 1.0

Iron binding site 10 out of 12 in 1frf

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Iron binding site 10 out of 12 in the Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe267

b:8.2
occ:1.00
 FE3 S:SF4267 0.0 8.2 1.0
S4 S:SF4267 2.2 7.9 1.0
S2 S:SF4267 2.2 12.6 1.0
SG S:CYS147 2.3 9.4 1.0
S1 S:SF4267 2.3 6.7 1.0
FE2 S:SF4267 2.5 8.2 1.0
FE1 S:SF4267 2.5 9.0 1.0
FE4 S:SF4267 2.6 10.4 1.0
CA S:CYS147 3.4 6.8 1.0
CB S:CYS147 3.4 7.6 1.0
S3 S:SF4267 3.8 5.8 1.0
C S:CYS147 3.9 6.8 1.0
SG S:CYS114 4.2 8.2 1.0
O S:GLY146 4.3 10.8 1.0
O S:CYS147 4.3 3.9 1.0
N S:PRO148 4.4 7.1 1.0
CE1 L:HIS228 4.5 4.5 1.0
SG S:CYS17 4.5 6.9 1.0
CG L:ARG70 4.6 7.0 1.0
N S:CYS147 4.6 8.0 1.0
CA S:PRO148 4.6 7.6 1.0
SG S:CYS20 4.7 5.0 1.0
NE L:ARG70 4.7 2.4 1.0
ND1 L:HIS228 4.8 9.6 1.0
C S:GLY146 4.9 8.9 1.0

Reference:

M.Rousset, Y.Montet, B.Guigliarelli, N.Forget, M.Asso, P.Bertrand, J.C.Fontecilla-Camps, E.C.Hatchikian. 3FE-4S] to [4FE-4S] Cluster Conversion in Desulfovibrio Fructosovorans [Nife] Hydrogenase By Site-Directed Mutagenesis Proc.Natl.Acad.Sci.Usa V. 95 11625 1998.
ISSN: ISSN 0027-8424
PubMed: 9751716
DOI: 10.1073/PNAS.95.20.11625
Page generated: Sat Aug 3 05:13:41 2024

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