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Iron in PDB 1piz: Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH

Enzymatic activity of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH

All present enzymatic activity of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1piz was solved by W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, 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) 23.85 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.000, 84.200, 114.200, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.2

Other elements in 1piz:

The structure of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH also contains other interesting chemical elements:

Mercury (Hg) 11 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH (pdb code 1piz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1piz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1piz

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Iron binding site 1 out of 4 in the Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe376

b:13.9
occ:1.00
 OE2 A:GLU238 2.0 11.1 1.0
ND1 A:HIS118 2.1 7.7 1.0
OE1 A:GLU115 2.1 10.4 1.0
OE1 A:GLU84 2.2 11.6 1.0
OE2 A:GLU84 2.3 11.9 1.0
CD A:GLU84 2.6 10.4 1.0
CE1 A:HIS118 2.9 6.3 1.0
CD A:GLU238 3.1 10.5 1.0
CD A:GLU115 3.2 10.9 1.0
CG A:HIS118 3.2 8.0 1.0
CB A:HIS118 3.7 9.1 1.0
OE1 A:GLU238 3.7 11.4 1.0
OE2 A:GLU115 3.7 12.6 1.0
CZ A:PHE208 3.8 17.2 1.0
FE A:FE377 3.9 9.3 1.0
NE2 A:HIS118 4.1 7.5 1.0
CG A:GLU84 4.1 10.2 1.0
CE2 A:PHE208 4.2 17.0 1.0
CG2 A:ILE234 4.2 7.2 1.0
CD2 A:HIS118 4.2 7.3 1.0
CA A:GLU115 4.2 10.2 1.0
CG A:GLU238 4.3 9.8 1.0
CE1 A:PHE208 4.3 17.0 1.0
CG A:GLU115 4.4 10.8 1.0
CB A:GLU115 4.5 9.9 1.0
CE1 A:HIS241 4.7 10.5 1.0
O A:HOH407 4.8 17.9 1.0
ND1 A:HIS241 4.8 10.9 1.0
CB A:GLU84 4.9 10.1 1.0
O A:GLU115 4.9 10.1 1.0
CD2 A:PHE208 4.9 17.0 1.0

Iron binding site 2 out of 4 in 1piz

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Iron binding site 2 out of 4 in the Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe377

b:9.3
occ:1.00
 OE1 A:GLU238 1.9 11.4 1.0
OE1 A:GLU204 2.0 15.8 1.0
OE2 A:GLU115 2.0 12.6 1.0
ND1 A:HIS241 2.1 10.9 1.0
CD A:GLU204 2.8 15.0 1.0
CD A:GLU115 2.8 10.9 1.0
OE2 A:GLU204 2.9 16.7 1.0
CD A:GLU238 3.0 10.5 1.0
CE1 A:HIS241 3.0 10.5 1.0
CG A:HIS241 3.1 10.3 1.0
OE1 A:GLU115 3.1 10.4 1.0
OE2 A:GLU238 3.3 11.1 1.0
CB A:HIS241 3.4 9.7 1.0
NE1 A:TRP111 3.6 9.5 1.0
CE2 A:PHE208 3.8 17.0 1.0
FE A:FE376 3.9 13.9 1.0
CD1 A:TRP111 4.1 9.4 1.0
NE2 A:HIS241 4.1 10.8 1.0
CG A:GLU115 4.2 10.8 1.0
CD2 A:HIS241 4.2 10.9 1.0
CG A:GLU204 4.2 14.8 1.0
CG A:GLU238 4.3 9.8 1.0
CA A:GLU238 4.3 10.4 1.0
CD2 A:PHE208 4.4 17.0 1.0
CB A:GLU238 4.6 9.7 1.0
CZ A:PHE208 4.7 17.2 1.0
CB A:GLU204 4.8 13.5 1.0
CE2 A:TRP111 4.8 9.3 1.0
CA A:HIS241 5.0 9.4 1.0

Iron binding site 3 out of 4 in 1piz

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Iron binding site 3 out of 4 in the Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe376

b:15.8
occ:1.00
 OE2 B:GLU238 2.0 14.1 1.0
ND1 B:HIS118 2.0 8.9 1.0
OE1 B:GLU115 2.1 11.9 1.0
OE1 B:GLU84 2.2 13.4 1.0
OE2 B:GLU84 2.2 13.2 1.0
CD B:GLU84 2.5 13.1 1.0
CE1 B:HIS118 2.9 9.4 1.0
CD B:GLU115 3.1 11.0 1.0
CD B:GLU238 3.1 10.9 1.0
CG B:HIS118 3.2 9.2 1.0
OE2 B:GLU115 3.6 11.8 1.0
CB B:HIS118 3.6 9.6 1.0
OE1 B:GLU238 3.7 12.2 1.0
CZ B:PHE208 3.8 18.0 1.0
FE B:FE377 3.9 10.0 1.0
CG B:GLU84 4.0 12.9 1.0
NE2 B:HIS118 4.1 9.2 1.0
CE2 B:PHE208 4.1 17.9 1.0
CG2 B:ILE234 4.2 9.6 1.0
CD2 B:HIS118 4.2 8.7 1.0
CA B:GLU115 4.3 9.6 1.0
CG B:GLU238 4.4 10.8 1.0
CE1 B:PHE208 4.4 17.5 1.0
CG B:GLU115 4.4 10.2 1.0
CB B:GLU115 4.5 9.5 1.0
CE1 B:HIS241 4.7 6.8 1.0
O B:HOH408 4.8 16.5 1.0
ND1 B:HIS241 4.8 5.9 1.0
CB B:GLU84 4.8 11.3 1.0
O B:GLU115 4.9 8.8 1.0
CD2 B:PHE208 4.9 17.1 1.0

Iron binding site 4 out of 4 in 1piz

Go back to Iron Binding Sites List in 1piz
Iron binding site 4 out of 4 in the Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ribonucleotide Reductase R2 D84E Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe377

b:10.0
occ:1.00
 OE1 B:GLU238 1.9 12.2 1.0
OE1 B:GLU204 2.0 17.4 1.0
OE2 B:GLU115 2.0 11.8 1.0
ND1 B:HIS241 2.1 5.9 1.0
CD B:GLU204 2.8 15.5 1.0
CD B:GLU115 2.8 11.0 1.0
CD B:GLU238 2.9 10.9 1.0
OE2 B:GLU204 2.9 19.3 1.0
CE1 B:HIS241 3.0 6.8 1.0
OE1 B:GLU115 3.1 11.9 1.0
CG B:HIS241 3.1 5.6 1.0
OE2 B:GLU238 3.3 14.1 1.0
CB B:HIS241 3.4 7.1 1.0
NE1 B:TRP111 3.7 10.8 1.0
CE2 B:PHE208 3.8 17.9 1.0
FE B:FE376 3.9 15.8 1.0
CG B:GLU115 4.2 10.2 1.0
NE2 B:HIS241 4.2 5.9 1.0
CD1 B:TRP111 4.2 9.8 1.0
CD2 B:HIS241 4.2 6.2 1.0
CG B:GLU238 4.2 10.8 1.0
CG B:GLU204 4.2 16.0 1.0
CA B:GLU238 4.3 9.3 1.0
CD2 B:PHE208 4.4 17.1 1.0
CB B:GLU238 4.5 9.9 1.0
CZ B:PHE208 4.7 18.0 1.0
CB B:GLU204 4.8 14.5 1.0
CE2 B:TRP111 4.8 11.3 1.0
CA B:HIS241 5.0 7.7 1.0

Reference:

W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollinger Jr., A.C.Rosenzweig. Variable Coordination Geometries at the Diiron(II) Active Site of Ribonucleotide Reductase R2. J.Am.Chem.Soc. V. 125 15822 2003.
ISSN: ISSN 0002-7863
PubMed: 14677973
DOI: 10.1021/JA0370387
Page generated: Sat Aug 3 13:08:58 2024

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