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Iron in PDB 1r65: Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli

Enzymatic activity of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli

All present enzymatic activity of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli, PDB code: 1r65 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) 25.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.170, 84.220, 114.220, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.6

Other elements in 1r65:

The structure of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli also contains other interesting chemical elements:

Mercury (Hg) 13 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli (pdb code 1r65). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli, PDB code: 1r65:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1r65

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Iron binding site 1 out of 4 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


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 Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:39.7
occ:1.00
 OD1 A:ASP84 2.0 32.6 1.0
ND1 A:HIS118 2.1 19.7 1.0
OE1 A:GLU115 2.1 34.3 1.0
OE2 A:GLU238 2.2 35.1 1.0
CG A:ASP84 2.8 29.9 1.0
OD2 A:ASP84 2.9 29.7 1.0
CE1 A:HIS118 2.9 17.6 1.0
CD A:GLU115 3.0 27.5 1.0
CG A:HIS118 3.2 18.5 1.0
CD A:GLU238 3.3 31.5 1.0
OE2 A:GLU115 3.4 33.0 1.0
CZ A:PHE208 3.7 35.7 1.0
CB A:HIS118 3.7 19.7 1.0
FE A:FE2802 3.8 43.0 1.0
OE1 A:GLU238 3.9 34.4 1.0
NE2 A:HIS118 4.1 16.8 1.0
CE1 A:PHE208 4.2 33.6 1.0
CB A:ASP84 4.2 27.7 1.0
CE2 A:PHE208 4.3 35.3 1.0
CD2 A:HIS118 4.3 17.6 1.0
CG A:GLU115 4.3 27.5 1.0
CG2 A:ILE234 4.3 19.6 1.0
CG A:GLU238 4.3 28.4 1.0
CA A:GLU115 4.4 22.8 1.0
CB A:GLU115 4.5 22.5 1.0
CE1 A:HIS241 4.8 21.6 1.0
CA A:ASP84 4.9 25.6 1.0
OH A:TYR122 4.9 31.6 1.0
ND1 A:HIS241 4.9 20.2 1.0

Iron binding site 2 out of 4 in 1r65

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Iron binding site 2 out of 4 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


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 Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:43.0
occ:1.00
 OE1 A:GLU238 1.8 34.4 1.0
OE2 A:GLU115 2.1 33.0 1.0
ND1 A:HIS241 2.2 20.2 1.0
OE1 A:GLU204 2.6 38.3 1.0
OE2 A:GLU204 2.7 37.8 1.0
CD A:GLU238 2.7 31.5 1.0
OE2 A:GLU238 2.8 35.1 1.0
CD A:GLU115 3.0 27.5 1.0
CD A:GLU204 3.0 37.3 1.0
CE1 A:HIS241 3.1 21.6 1.0
OE1 A:GLU115 3.2 34.3 1.0
CG A:HIS241 3.2 24.2 1.0
CB A:HIS241 3.6 21.3 1.0
NE1 A:TRP111 3.6 25.6 1.0
FE A:FE2801 3.8 39.7 1.0
CG A:GLU238 4.1 28.4 1.0
CE2 A:PHE208 4.1 35.3 1.0
CD1 A:TRP111 4.2 24.1 1.0
NE2 A:HIS241 4.2 22.2 1.0
CG A:GLU115 4.3 27.5 1.0
CD2 A:HIS241 4.3 21.9 1.0
CA A:GLU238 4.4 25.9 1.0
CG A:GLU204 4.5 36.9 1.0
CB A:GLU238 4.6 26.6 1.0
CD2 A:PHE208 4.7 33.9 1.0
CZ A:PHE208 4.8 35.7 1.0
CE2 A:TRP111 4.8 25.9 1.0
OD1 A:ASP84 4.9 32.6 1.0

Iron binding site 3 out of 4 in 1r65

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Iron binding site 3 out of 4 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


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 Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:52.1
occ:1.00
 OD1 B:ASP84 2.1 34.3 1.0
ND1 B:HIS118 2.1 24.6 1.0
OE2 B:GLU115 2.3 34.6 1.0
OE2 B:GLU238 2.4 35.9 1.0
OD2 B:ASP84 2.5 34.2 1.0
CG B:ASP84 2.6 32.2 1.0
CE1 B:HIS118 2.8 24.6 1.0
CG B:HIS118 3.3 22.6 1.0
CD B:GLU115 3.3 30.1 1.0
CD B:GLU238 3.4 33.0 1.0
CZ B:PHE208 3.5 42.8 1.0
OE1 B:GLU115 3.7 37.6 1.0
FE B:FE2804 3.7 49.2 1.0
CB B:HIS118 3.8 22.2 1.0
CG2 B:ILE234 4.0 23.0 1.0
NE2 B:HIS118 4.1 23.1 1.0
OE1 B:GLU238 4.1 36.0 1.0
CB B:ASP84 4.1 28.4 1.0
CE1 B:PHE208 4.1 41.5 1.0
CE2 B:PHE208 4.1 41.3 1.0
CG B:GLU238 4.3 31.2 1.0
CD2 B:HIS118 4.3 24.7 1.0
CG B:GLU115 4.5 27.2 1.0
CA B:GLU115 4.6 24.1 1.0
CB B:GLU115 4.7 25.1 1.0
CA B:ASP84 4.8 26.5 1.0
OH B:TYR122 4.9 31.1 1.0
CE1 B:HIS241 5.0 21.6 1.0

Iron binding site 4 out of 4 in 1r65

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Iron binding site 4 out of 4 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


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 Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe804

b:49.2
occ:1.00
 OE1 B:GLU238 1.9 36.0 1.0
OE1 B:GLU115 2.0 37.6 1.0
ND1 B:HIS241 2.2 18.7 1.0
OE2 B:GLU238 2.4 35.9 1.0
CD B:GLU238 2.4 33.0 1.0
OE2 B:GLU204 2.8 40.4 1.0
CD B:GLU115 3.0 30.1 1.0
CE1 B:HIS241 3.1 21.6 1.0
OE1 B:GLU204 3.2 43.5 1.0
OE2 B:GLU115 3.2 34.6 1.0
CG B:HIS241 3.3 20.9 1.0
CD B:GLU204 3.4 43.1 1.0
CB B:HIS241 3.6 22.1 1.0
FE B:FE2803 3.7 52.1 1.0
NE1 B:TRP111 3.7 24.5 1.0
CG B:GLU238 3.9 31.2 1.0
CE2 B:PHE208 4.1 41.3 1.0
NE2 B:HIS241 4.3 21.2 1.0
CD1 B:TRP111 4.3 22.4 1.0
CA B:GLU238 4.3 24.5 1.0
CG B:GLU115 4.4 27.2 1.0
CD2 B:HIS241 4.4 20.8 1.0
CB B:GLU238 4.5 27.7 1.0
OD1 B:ASP84 4.6 34.3 1.0
CD2 B:PHE208 4.6 38.8 1.0
CZ B:PHE208 4.8 42.8 1.0
CE1 B:HIS118 4.8 24.6 1.0
CE2 B:TRP111 4.9 25.2 1.0
CG B:GLU204 4.9 40.0 1.0
N B:GLU238 4.9 23.5 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 13:59:58 2024

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