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Iron in PDB 1mxr: High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form

Enzymatic activity of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form

All present enzymatic activity of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form:
1.17.4.1;

Protein crystallography data

The structure of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form, PDB code: 1mxr was solved by M.A.Andersson, M.Hogbom, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.83 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.844, 84.975, 114.318, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.5

Other elements in 1mxr:

The structure of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form also contains other interesting chemical elements:

Mercury (Hg) 11 atoms

Iron Binding Sites:

The binding sites of Iron atom in the High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form (pdb code 1mxr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form, PDB code: 1mxr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1mxr

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Iron binding site 1 out of 4 in the High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:12.6
occ:1.00
 O A:HOH3440 1.9 14.3 1.0
OD2 A:ASP84 2.0 19.0 1.0
OE1 A:GLU115 2.0 14.6 1.0
ND1 A:HIS118 2.1 11.2 1.0
O A:HOH3051 2.3 15.8 1.0
CG A:ASP84 2.7 17.1 1.0
OD1 A:ASP84 2.9 16.5 1.0
CE1 A:HIS118 3.0 11.8 1.0
CD A:GLU115 3.1 12.4 1.0
O A:HOH3041 3.2 15.3 1.0
CG A:HIS118 3.2 10.4 1.0
FE A:FE1004 3.4 11.5 1.0
OE2 A:GLU115 3.5 10.5 1.0
CB A:HIS118 3.7 10.4 1.0
OE1 A:GLU238 4.1 16.4 1.0
CB A:ASP84 4.1 13.6 1.0
NE2 A:HIS118 4.1 11.6 1.0
CD2 A:HIS118 4.3 10.5 1.0
CG2 A:ILE234 4.3 13.2 1.0
CG A:GLU115 4.4 10.6 1.0
OE2 A:GLU238 4.5 12.9 1.0
CA A:GLU115 4.5 10.3 1.0
CE1 A:HIS241 4.5 11.1 1.0
CZ A:PHE208 4.5 15.5 1.0
CD A:GLU238 4.5 14.9 1.0
CE2 A:PHE208 4.6 16.6 1.0
ND1 A:HIS241 4.6 11.3 1.0
CB A:GLU115 4.6 10.6 1.0
OH A:TYR122 4.7 21.0 1.0

Iron binding site 2 out of 4 in 1mxr

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Iron binding site 2 out of 4 in the High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1004

b:11.5
occ:1.00
 O A:HOH3440 1.9 14.3 1.0
OE2 A:GLU204 2.0 13.3 1.0
OE2 A:GLU115 2.0 10.5 1.0
OE2 A:GLU238 2.1 12.9 1.0
ND1 A:HIS241 2.2 11.3 1.0
O A:HOH3041 2.3 15.3 1.0
CD A:GLU115 3.0 12.4 1.0
CD A:GLU204 3.0 12.3 1.0
CD A:GLU238 3.0 14.9 1.0
CE1 A:HIS241 3.1 11.1 1.0
CG A:HIS241 3.3 10.8 1.0
OE1 A:GLU115 3.3 14.6 1.0
OE1 A:GLU238 3.3 16.4 1.0
FE A:FE1003 3.4 12.6 1.0
CG A:GLU204 3.6 12.3 1.0
CB A:HIS241 3.7 11.1 1.0
NE1 A:TRP111 4.0 11.0 1.0
OE1 A:GLU204 4.0 14.5 1.0
O A:HOH3051 4.3 15.8 1.0
NE2 A:HIS241 4.3 11.2 1.0
CG A:GLU115 4.3 10.6 1.0
CG A:GLU238 4.3 14.4 1.0
CD2 A:HIS241 4.4 10.8 1.0
OD1 A:ASP84 4.4 16.5 1.0
CB A:GLU204 4.4 13.5 1.0
CA A:GLU238 4.5 11.1 1.0
CD1 A:TRP111 4.5 10.3 1.0
OE1 A:GLN87 4.7 17.5 1.0
CB A:GLU238 4.7 11.0 1.0
CE1 A:HIS118 4.8 11.8 1.0
ND1 A:HIS118 4.8 11.2 1.0

Iron binding site 3 out of 4 in 1mxr

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Iron binding site 3 out of 4 in the High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:13.2
occ:1.00
 O B:HOH2388 2.0 15.0 1.0
OE1 B:GLU115 2.0 14.5 1.0
OD2 B:ASP84 2.1 17.9 1.0
ND1 B:HIS118 2.1 11.6 1.0
O B:HOH2055 2.3 17.0 1.0
CG B:ASP84 2.7 17.5 1.0
OD1 B:ASP84 2.9 17.6 1.0
CE1 B:HIS118 2.9 13.3 1.0
CD B:GLU115 3.0 11.1 1.0
O B:HOH2031 3.2 14.8 1.0
CG B:HIS118 3.2 11.0 1.0
FE B:FE1002 3.4 11.3 1.0
OE2 B:GLU115 3.4 11.4 1.0
CB B:HIS118 3.7 11.1 1.0
OE2 B:GLU238 4.0 16.1 1.0
CB B:ASP84 4.1 14.8 1.0
NE2 B:HIS118 4.1 10.9 1.0
CD2 B:HIS118 4.3 11.5 1.0
CG2 B:ILE234 4.3 14.6 1.0
CG B:GLU115 4.4 9.9 1.0
OE1 B:GLU238 4.5 12.5 1.0
CE1 B:HIS241 4.5 11.2 1.0
CD B:GLU238 4.5 12.7 1.0
CA B:GLU115 4.5 11.3 1.0
CZ B:PHE208 4.5 16.0 1.0
ND1 B:HIS241 4.6 10.3 1.0
CE2 B:PHE208 4.6 14.6 1.0
OH B:TYR122 4.6 21.0 1.0
CB B:GLU115 4.7 12.2 1.0

Iron binding site 4 out of 4 in 1mxr

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Iron binding site 4 out of 4 in the High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High Resolution Structure of Ribonucleotide Reductase R2 From E. Coli in Its Oxidised (Met) Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:11.3
occ:1.00
 O B:HOH2388 1.9 15.0 1.0
OE2 B:GLU115 2.0 11.4 1.0
OE1 B:GLU238 2.0 12.5 1.0
OE1 B:GLU204 2.1 13.5 1.0
ND1 B:HIS241 2.2 10.3 1.0
O B:HOH2031 2.2 14.8 1.0
CD B:GLU238 3.0 12.7 1.0
CD B:GLU115 3.0 11.1 1.0
CD B:GLU204 3.1 11.9 1.0
CE1 B:HIS241 3.1 11.2 1.0
CG B:HIS241 3.3 9.8 1.0
OE2 B:GLU238 3.3 16.1 1.0
FE B:FE1001 3.4 13.2 1.0
OE1 B:GLU115 3.4 14.5 1.0
CG B:GLU204 3.6 13.8 1.0
CB B:HIS241 3.7 11.9 1.0
NE1 B:TRP111 4.0 11.0 1.0
OE2 B:GLU204 4.1 13.3 1.0
O B:HOH2055 4.2 17.0 1.0
NE2 B:HIS241 4.2 11.4 1.0
CG B:GLU115 4.3 9.9 1.0
CG B:GLU238 4.3 14.7 1.0
CD2 B:HIS241 4.4 10.5 1.0
OD1 B:ASP84 4.4 17.6 1.0
CB B:GLU204 4.5 13.7 1.0
CD1 B:TRP111 4.5 10.9 1.0
CA B:GLU238 4.5 13.1 1.0
OE1 B:GLN87 4.6 17.4 1.0
CB B:GLU238 4.7 11.5 1.0
CE1 B:HIS118 4.8 13.3 1.0
ND1 B:HIS118 4.8 11.6 1.0
CG B:GLN87 5.0 11.7 1.0

Reference:

M.Hogbom, M.Galander, M.Andersson, M.Kolberg, W.Hofbauer, G.Lassmann, P.Nordlund, F.Lendzian. Displacement of the Tyrosyl Radical Cofactor in Ribonucleotide Reductase Obtained By Single-Crystal High-Field Epr and 1.4-A X-Ray Data. Proc.Natl.Acad.Sci.Usa V. 100 3209 2003.
ISSN: ISSN 0027-8424
PubMed: 12624184
DOI: 10.1073/PNAS.0536684100
Page generated: Sun Dec 13 14:24:34 2020

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