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Iron in PDB 1pj0: Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH

Enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH

All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0 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) 19.32 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.000, 84.400, 114.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.6

Other elements in 1pj0:

The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH also contains other interesting chemical elements:

Mercury (Hg) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH (pdb code 1pj0). 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/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1pj0

Go back to Iron Binding Sites List in 1pj0
Iron binding site 1 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F 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/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe376

b:20.6
occ:1.00
 OE2 A:GLU238 2.0 19.8 1.0
ND1 A:HIS118 2.1 12.8 1.0
OE1 A:GLU115 2.1 16.0 1.0
OE1 A:GLU84 2.2 14.3 1.0
OE2 A:GLU84 2.3 14.9 1.0
CD A:GLU84 2.5 13.9 1.0
CE1 A:HIS118 3.0 13.0 1.0
CD A:GLU238 3.2 18.8 1.0
CG A:HIS118 3.2 13.1 1.0
CD A:GLU115 3.2 15.3 1.0
CB A:HIS118 3.6 13.7 1.0
OE2 A:GLU115 3.7 16.5 1.0
OE1 A:GLU238 3.8 19.2 1.0
CZ A:PHE208 3.8 19.2 1.0
FE A:FE377 4.0 14.1 1.0
CG A:GLU84 4.0 13.6 1.0
NE2 A:HIS118 4.1 13.0 1.0
CE2 A:PHE208 4.2 19.0 1.0
CA A:GLU115 4.2 14.2 1.0
CG2 A:ILE234 4.2 13.8 1.0
CD2 A:HIS118 4.3 12.8 1.0
CG A:GLU238 4.3 17.2 1.0
CE1 A:PHE208 4.3 18.8 1.0
CG A:GLU115 4.4 14.4 1.0
CB A:GLU115 4.4 14.1 1.0
O A:HOH437 4.6 23.5 1.0
CE1 A:HIS241 4.8 14.0 1.0
O A:GLU115 4.8 14.2 1.0
CB A:GLU84 4.9 13.5 1.0
ND1 A:HIS241 4.9 14.0 1.0
CD2 A:PHE208 4.9 19.1 1.0

Iron binding site 2 out of 4 in 1pj0

Go back to Iron Binding Sites List in 1pj0
Iron binding site 2 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F 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/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe377

b:14.1
occ:1.00
 OE1 A:GLU238 1.9 19.2 1.0
OE2 A:GLU115 2.0 16.5 1.0
OE1 A:GLU204 2.0 20.8 1.0
ND1 A:HIS241 2.1 14.0 1.0
CD A:GLU204 2.8 19.9 1.0
CD A:GLU115 2.8 15.3 1.0
OE2 A:GLU204 2.8 21.8 1.0
CD A:GLU238 2.9 18.8 1.0
OE1 A:GLU115 3.1 16.0 1.0
CE1 A:HIS241 3.1 14.0 1.0
CG A:HIS241 3.1 14.2 1.0
OE2 A:GLU238 3.2 19.8 1.0
CB A:HIS241 3.4 14.5 1.0
NE1 A:TRP111 3.6 15.3 1.0
CE2 A:PHE208 3.9 19.0 1.0
FE A:FE376 4.0 20.6 1.0
CD1 A:TRP111 4.1 14.6 1.0
CG A:GLU115 4.1 14.4 1.0
NE2 A:HIS241 4.2 13.7 1.0
CG A:GLU204 4.2 19.4 1.0
CD2 A:HIS241 4.2 13.9 1.0
CG A:GLU238 4.3 17.2 1.0
CA A:GLU238 4.3 16.2 1.0
CD2 A:PHE208 4.4 19.1 1.0
CB A:GLU238 4.6 16.4 1.0
CZ A:PHE208 4.7 19.2 1.0
CE2 A:TRP111 4.8 15.0 1.0
CB A:GLU204 4.8 17.8 1.0
CA A:HIS241 4.9 14.6 1.0
N A:GLU238 5.0 16.1 1.0

Iron binding site 3 out of 4 in 1pj0

Go back to Iron Binding Sites List in 1pj0
Iron binding site 3 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F 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/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe376

b:20.9
occ:1.00
 ND1 B:HIS118 2.0 13.4 1.0
OE2 B:GLU238 2.0 18.7 1.0
OE2 B:GLU84 2.1 15.2 1.0
OE1 B:GLU115 2.1 15.6 1.0
OE1 B:GLU84 2.3 16.7 1.0
CD B:GLU84 2.5 16.0 1.0
CE1 B:HIS118 2.9 13.8 1.0
CG B:HIS118 3.1 13.0 1.0
CD B:GLU238 3.2 16.8 1.0
CD B:GLU115 3.2 14.9 1.0
CB B:HIS118 3.6 13.2 1.0
OE1 B:GLU238 3.7 17.4 1.0
OE2 B:GLU115 3.7 16.6 1.0
CZ B:PHE208 3.9 23.0 1.0
FE B:FE377 3.9 14.1 1.0
CG B:GLU84 4.0 15.4 1.0
NE2 B:HIS118 4.1 13.4 1.0
CE2 B:PHE208 4.2 23.7 1.0
CD2 B:HIS118 4.2 13.1 1.0
CG2 B:ILE234 4.2 15.7 1.0
CA B:GLU115 4.2 12.7 1.0
CG B:GLU115 4.4 14.2 1.0
CG B:GLU238 4.4 15.7 1.0
CB B:GLU115 4.4 13.0 1.0
CE1 B:PHE208 4.4 22.7 1.0
O B:HOH431 4.7 24.7 1.0
CE1 B:HIS241 4.7 11.6 1.0
ND1 B:HIS241 4.8 11.3 1.0
CB B:GLU84 4.9 14.7 1.0
O B:GLU115 4.9 12.1 1.0
CD2 B:PHE208 5.0 22.6 1.0

Iron binding site 4 out of 4 in 1pj0

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Iron binding site 4 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F 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/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe377

b:14.1
occ:1.00
 OE1 B:GLU238 1.9 17.4 1.0
OE1 B:GLU204 2.0 22.1 1.0
OE2 B:GLU115 2.0 16.6 1.0
ND1 B:HIS241 2.1 11.3 1.0
CD B:GLU204 2.7 20.4 1.0
OE2 B:GLU204 2.8 21.9 1.0
CD B:GLU115 2.8 14.9 1.0
CD B:GLU238 2.9 16.8 1.0
OE1 B:GLU115 3.0 15.6 1.0
CE1 B:HIS241 3.1 11.6 1.0
CG B:HIS241 3.1 12.3 1.0
OE2 B:GLU238 3.3 18.7 1.0
CB B:HIS241 3.4 13.6 1.0
NE1 B:TRP111 3.7 11.7 1.0
CE2 B:PHE208 3.9 23.7 1.0
FE B:FE376 3.9 20.9 1.0
CD1 B:TRP111 4.2 11.4 1.0
CG B:GLU204 4.2 20.3 1.0
CG B:GLU115 4.2 14.2 1.0
NE2 B:HIS241 4.2 10.6 1.0
CD2 B:HIS241 4.2 11.7 1.0
CG B:GLU238 4.2 15.7 1.0
CA B:GLU238 4.3 14.2 1.0
CD2 B:PHE208 4.4 22.6 1.0
CB B:GLU238 4.6 14.9 1.0
CB B:GLU204 4.8 18.6 1.0
CZ B:PHE208 4.8 23.0 1.0
CE2 B:TRP111 4.9 12.2 1.0
CA B:HIS241 5.0 13.8 1.0
N B:GLU238 5.0 14.3 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 13:08:59 2024

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