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Iron in PDB 3iiz: X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine

Protein crystallography data

The structure of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine, PDB code: 3iiz was solved by Y.Nicolet, P.Amara, J.M.Mouesca, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.16 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.628, 78.780, 85.943, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 18.4

Other elements in 3iiz:

The structure of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine (pdb code 3iiz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine, PDB code: 3iiz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3iiz

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Iron binding site 1 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2460

b:12.3
occ:1.00
 FE1 A:SF42460 0.0 12.3 1.0
S4 A:SF42460 2.3 12.2 1.0
S2 A:SF42460 2.3 12.6 1.0
S3 A:SF42460 2.3 11.8 1.0
SG A:CYS67 2.3 13.0 1.0
FE3 A:SF42460 2.7 11.6 1.0
FE4 A:SF42460 2.7 12.0 1.0
FE2 A:SF42460 2.8 12.7 1.0
CB A:CYS67 3.2 11.3 1.0
S1 A:SF42460 3.9 12.1 1.0
O A:HOH514 3.9 16.1 1.0
O A:SAM1501 4.2 12.6 1.0
N A:CYS67 4.3 11.2 1.0
CA A:CYS67 4.3 11.1 1.0
CB A:LYS65 4.4 11.2 1.0
CB A:CYS70 4.4 11.4 1.0
NH2 A:ARG172 4.5 13.7 1.0
SG A:CYS70 4.6 13.3 1.0
OH A:TYR69 4.7 12.0 1.0
SG A:CYS63 4.7 11.8 1.0
CE1 A:TYR69 4.8 10.3 1.0
O A:HOH466 4.8 12.9 1.0
N A:SAM1501 5.0 13.0 1.0
CZ A:TYR69 5.0 10.8 1.0

Iron binding site 2 out of 6 in 3iiz

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Iron binding site 2 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2460

b:12.7
occ:1.00
 FE2 A:SF42460 0.0 12.7 1.0
O A:SAM1501 2.3 12.6 1.0
S3 A:SF42460 2.3 11.8 1.0
S4 A:SF42460 2.3 12.2 1.0
N A:SAM1501 2.3 13.0 1.0
S1 A:SF42460 2.4 12.1 1.0
FE4 A:SF42460 2.8 12.0 1.0
FE1 A:SF42460 2.8 12.3 1.0
FE3 A:SF42460 2.8 11.6 1.0
C A:SAM1501 3.1 12.7 1.0
CA A:SAM1501 3.2 14.0 1.0
SD A:SAM1501 3.3 17.2 1.0
CG A:SAM1501 3.7 14.6 1.0
CB A:SAM1501 4.0 13.4 1.0
S2 A:SF42460 4.0 12.6 1.0
O A:HOH466 4.0 12.9 1.0
O A:HOH514 4.1 16.1 1.0
CE A:SAM1501 4.1 16.4 0.5
OXT A:SAM1501 4.2 12.4 1.0
SG A:CYS63 4.7 11.8 1.0
SG A:CYS70 4.9 13.3 1.0
C5' A:SAM1501 4.9 17.0 1.0
SG A:CYS67 5.0 13.0 1.0

Iron binding site 3 out of 6 in 3iiz

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Iron binding site 3 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2460

b:11.6
occ:1.00
 FE3 A:SF42460 0.0 11.6 1.0
S2 A:SF42460 2.2 12.6 1.0
SG A:CYS63 2.3 11.8 1.0
S1 A:SF42460 2.3 12.1 1.0
S4 A:SF42460 2.3 12.2 1.0
FE4 A:SF42460 2.7 12.0 1.0
FE1 A:SF42460 2.7 12.3 1.0
FE2 A:SF42460 2.8 12.7 1.0
CB A:CYS63 3.4 10.6 1.0
S3 A:SF42460 3.9 11.8 1.0
N A:SAM1501 4.1 13.0 1.0
CB A:LYS65 4.3 11.2 1.0
N A:GLU110 4.4 8.7 1.0
O A:LYS65 4.6 11.8 1.0
CA A:GLY109 4.6 9.6 1.0
CA A:CYS63 4.7 10.0 1.0
SG A:CYS70 4.7 13.3 1.0
SG A:CYS67 4.8 13.0 1.0
N A:LYS65 4.8 11.1 1.0
C A:LYS65 4.8 11.1 1.0
CA A:LYS65 4.9 10.5 1.0
O A:SAM1501 4.9 12.6 1.0
O A:LEU72 5.0 10.8 1.0
CB A:LEU72 5.0 11.4 1.0

Iron binding site 4 out of 6 in 3iiz

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Iron binding site 4 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2460

b:12.0
occ:1.00
 FE4 A:SF42460 0.0 12.0 1.0
S1 A:SF42460 2.2 12.1 1.0
SG A:CYS70 2.3 13.3 1.0
S3 A:SF42460 2.3 11.8 1.0
S2 A:SF42460 2.3 12.6 1.0
FE3 A:SF42460 2.7 11.6 1.0
FE1 A:SF42460 2.7 12.3 1.0
FE2 A:SF42460 2.8 12.7 1.0
CB A:CYS70 3.0 11.4 1.0
S4 A:SF42460 3.9 12.2 1.0
CE A:SAM1501 4.1 16.4 0.5
CB A:LEU72 4.3 11.4 1.0
SD A:SAM1501 4.4 17.2 1.0
CA A:CYS70 4.5 11.7 1.0
N A:ARG73 4.8 10.3 1.0
SG A:CYS67 4.8 13.0 1.0
CB A:CYS67 4.8 11.3 1.0
SG A:CYS63 4.8 11.8 1.0
N A:SAM1501 4.8 13.0 1.0
O A:SAM1501 4.8 12.6 1.0
C A:LEU72 4.8 10.3 1.0
N A:LEU72 4.9 11.1 1.0
CG A:LEU72 4.9 13.0 1.0
CD2 A:LEU305 4.9 23.1 1.0
CA A:LEU72 4.9 10.7 1.0
C A:CYS70 5.0 11.6 1.0

Iron binding site 5 out of 6 in 3iiz

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Iron binding site 5 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2648

b:19.7
occ:0.60
 FE1 A:FES2648 0.0 19.7 0.6
SG A:CYS311 2.1 24.7 0.7
S A:H2S2649 2.1 15.4 0.9
S2 A:FES2648 2.2 21.3 0.6
S1 A:FES2648 2.2 18.4 0.6
FE2 A:FES2648 2.8 21.9 0.6
SG A:CYS319 3.2 14.8 1.0
CB A:CYS311 3.3 21.0 1.0
O A:HOH569 3.3 24.3 1.0
CB A:CYS319 3.7 11.0 1.0
CA A:CYS311 3.8 21.4 1.0
CA A:CYS319 4.3 10.9 1.0
N A:CYS311 4.3 21.6 1.0
NH1 A:ARG279 4.4 18.6 1.0
NH2 A:ARG279 4.5 16.9 1.0
S A:H2S2650 4.6 20.3 0.7
CZ A:ARG279 4.9 16.3 1.0
SG A:CYS322 5.0 15.1 0.7

Iron binding site 6 out of 6 in 3iiz

Go back to Iron Binding Sites List in 3iiz
Iron binding site 6 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2648

b:21.9
occ:0.60
 FE2 A:FES2648 0.0 21.9 0.6
S1 A:FES2648 2.2 18.4 0.6
S2 A:FES2648 2.2 21.3 0.6
NH2 A:ARG279 2.2 16.9 1.0
S A:H2S2650 2.3 20.3 0.7
FE1 A:FES2648 2.8 19.7 0.6
NH1 A:ARG279 2.9 18.6 1.0
CZ A:ARG279 2.9 16.3 1.0
SG A:CYS322 3.6 15.1 0.7
NE A:ARG279 4.2 15.2 1.0
CG1 A:VAL323 4.2 11.3 1.0
SG A:CYS311 4.2 24.7 0.7
O A:HOH569 4.4 24.3 1.0
CE A:MET326 4.4 11.1 1.0
CB A:CYS322 4.4 12.8 0.7
CB A:CYS322 4.4 13.2 0.3
S A:H2S2649 4.4 15.4 0.9
CD1 A:ILE310 4.6 22.6 0.7
O A:HOH585 4.8 25.1 1.0

Reference:

Y.Nicolet, P.Amara, J.-M.Mouesca, J.C.Fontecilla-Camps. Unexpected Electron Transfer Mechanism Upon Adomet Cleavage in Radical Sam Proteins Proc.Natl.Acad.Sci.Usa 2009.
ISSN: ESSN 1091-6490
PubMed: 19706452
DOI: 10.1073/PNAS.0904385106
Page generated: Sun Dec 13 15:08:53 2020

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