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Iron in PDB 1piu: Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster

Enzymatic activity of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster

All present enzymatic activity of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster:
1.17.4.1;

Protein crystallography data

The structure of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster, PDB code: 1piu was solved by W.C.Voegtli, N.Khidekel, J.Baldwin, B.A.Ley, J.M.Bollinger Jr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.75 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.100, 84.600, 114.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.2

Other elements in 1piu:

The structure of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster also contains other interesting chemical elements:

Mercury (Hg) 10 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster (pdb code 1piu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster, PDB code: 1piu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1piu

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Iron binding site 1 out of 4 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:30.5
occ:1.00
 O A:O602 2.0 22.1 1.0
OE1 A:GLU115 2.1 23.2 1.0
OE1 A:GLU84 2.2 30.1 1.0
ND1 A:HIS118 2.4 10.9 1.0
O A:HOH676 2.4 16.8 1.0
CD A:GLU84 2.7 27.4 1.0
O A:HOH677 2.8 20.8 1.0
OE2 A:GLU84 2.9 27.6 1.0
CD A:GLU115 3.1 20.1 1.0
CE1 A:HIS118 3.2 10.3 1.0
FE A:FE402 3.3 18.7 1.0
OE2 A:GLU115 3.4 19.2 1.0
CG A:HIS118 3.5 13.2 1.0
OE1 A:GLU238 3.9 28.8 1.0
CB A:HIS118 4.0 13.5 1.0
CG A:GLU84 4.1 27.2 1.0
NE2 A:HIS118 4.4 10.7 1.0
CE1 A:HIS241 4.4 17.0 1.0
CG A:GLU115 4.4 17.4 1.0
CD A:GLU238 4.4 26.1 1.0
OE2 A:GLU238 4.5 19.9 1.0
CG2 A:ILE234 4.5 17.4 1.0
CZ A:PHE208 4.5 28.2 1.0
CA A:GLU115 4.5 16.7 1.0
ND1 A:HIS241 4.6 19.1 1.0
CD2 A:HIS118 4.6 15.1 1.0
CE2 A:PHE208 4.7 29.0 1.0
CB A:GLU115 4.7 14.3 1.0
CE1 A:PHE208 4.9 28.4 1.0

Iron binding site 2 out of 4 in 1piu

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Iron binding site 2 out of 4 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:18.7
occ:1.00
 OE2 A:GLU238 2.0 19.9 1.0
ND1 A:HIS241 2.1 19.1 1.0
OE2 A:GLU204 2.1 24.4 1.0
O A:HOH677 2.1 20.8 1.0
OE2 A:GLU115 2.2 19.2 1.0
O A:O602 2.2 22.1 1.0
CD A:GLU238 2.9 26.1 1.0
CE1 A:HIS241 3.0 17.0 1.0
CD A:GLU115 3.1 20.1 1.0
CD A:GLU204 3.1 24.4 1.0
OE1 A:GLU238 3.2 28.8 1.0
CG A:HIS241 3.2 17.9 1.0
FE A:FE401 3.3 30.5 1.0
OE1 A:GLU115 3.4 23.2 1.0
CB A:HIS241 3.7 14.8 1.0
CG A:GLU204 3.8 25.4 1.0
NE1 A:TRP111 3.9 14.9 1.0
OE1 A:GLU204 4.1 27.5 1.0
NE2 A:HIS241 4.1 16.3 1.0
O A:HOH676 4.2 16.8 1.0
CG A:GLU238 4.3 23.3 1.0
CD2 A:HIS241 4.3 16.2 1.0
CA A:GLU238 4.4 19.4 1.0
CG A:GLU115 4.5 17.4 1.0
CD1 A:TRP111 4.5 12.3 1.0
CB A:GLU204 4.5 19.7 1.0
CB A:GLU238 4.7 19.1 1.0
OE1 A:GLU84 4.8 30.1 1.0
NE2 A:GLN87 4.9 19.4 1.0
CE1 A:HIS118 5.0 10.3 1.0

Iron binding site 3 out of 4 in 1piu

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Iron binding site 3 out of 4 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:29.9
occ:1.00
 OE1 B:GLU84 2.1 28.0 1.0
OE1 B:GLU115 2.1 18.9 1.0
O B:O601 2.1 24.8 1.0
ND1 B:HIS118 2.4 14.3 1.0
O B:HOH661 2.4 23.1 1.0
OE2 B:GLU84 2.7 27.4 1.0
CD B:GLU84 2.7 27.0 1.0
O B:HOH662 2.9 14.2 1.0
CE1 B:HIS118 3.2 14.5 1.0
CD B:GLU115 3.2 15.2 1.0
FE B:FE404 3.4 20.5 1.0
CG B:HIS118 3.5 14.2 1.0
OE2 B:GLU115 3.6 19.5 1.0
CB B:HIS118 3.9 12.1 1.0
OE2 B:GLU238 4.0 30.6 1.0
CG B:GLU84 4.2 24.7 1.0
CZ B:PHE208 4.3 27.1 1.0
CE2 B:PHE208 4.3 29.7 1.0
NE2 B:HIS118 4.4 13.9 1.0
CG2 B:ILE234 4.4 16.7 1.0
CG B:GLU115 4.5 13.5 1.0
CD B:GLU238 4.6 22.9 1.0
CE1 B:HIS241 4.6 12.6 1.0
CD2 B:HIS118 4.6 13.2 1.0
OE1 B:GLU238 4.6 18.8 1.0
CA B:GLU115 4.6 15.5 1.0
ND1 B:HIS241 4.6 11.1 1.0
CB B:GLU115 4.8 12.6 1.0
CB B:GLU84 4.8 18.1 1.0
CE1 B:PHE208 4.9 26.1 1.0
CD2 B:PHE208 5.0 27.0 1.0

Iron binding site 4 out of 4 in 1piu

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Iron binding site 4 out of 4 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe404

b:20.5
occ:1.00
 OE1 B:GLU238 2.1 18.8 1.0
OE2 B:GLU115 2.1 19.5 1.0
O B:O601 2.1 24.8 1.0
OE2 B:GLU204 2.2 24.7 1.0
ND1 B:HIS241 2.2 11.1 1.0
O B:HOH662 2.3 14.2 1.0
CD B:GLU238 2.9 22.9 1.0
CD B:GLU115 3.0 15.2 1.0
CE1 B:HIS241 3.1 12.6 1.0
OE2 B:GLU238 3.1 30.6 1.0
CD B:GLU204 3.1 23.7 1.0
OE1 B:GLU115 3.3 18.9 1.0
CG B:HIS241 3.3 14.2 1.0
FE B:FE403 3.4 29.9 1.0
CG B:GLU204 3.6 25.3 1.0
CB B:HIS241 3.6 15.3 1.0
NE1 B:TRP111 3.9 17.9 1.0
OE1 B:GLU204 4.2 27.7 1.0
NE2 B:HIS241 4.2 11.8 1.0
O B:HOH661 4.3 23.1 1.0
CG B:GLU238 4.3 20.4 1.0
CD2 B:HIS241 4.4 12.4 1.0
CG B:GLU115 4.4 13.5 1.0
CB B:GLU204 4.5 21.5 1.0
CD1 B:TRP111 4.5 17.6 1.0
CA B:GLU238 4.6 17.5 1.0
NE2 B:GLN87 4.7 17.9 1.0
CB B:GLU238 4.8 15.0 1.0
OE1 B:GLU84 4.9 28.0 1.0
CE1 B:HIS118 4.9 14.5 1.0
ND1 B:HIS118 5.0 14.3 1.0
CG B:GLN87 5.0 18.4 1.0

Reference:

W.C.Voegtli, N.Khidekel, J.Baldwin, B.A.Ley, J.M.Bollinger Jr., A.C.Rosenzweig. Crystal Structure of the Ribonucleotide Reductase R2 Mutant That Accumulates A U-1,2-Peroxodiiron(III) Intermediate During Oxygen Activation J.Am.Chem.Soc. V. 122 3255 2000.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA991839L
Page generated: Sat Aug 3 13:08:51 2024

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