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Manganese in PDB 1jpr: Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide

Enzymatic activity of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide

All present enzymatic activity of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide:
1.17.4.1;

Protein crystallography data

The structure of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide, PDB code: 1jpr was solved by M.Hogbom, M.E.Andersson, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.826, 84.683, 114.333, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 21.3

Other elements in 1jpr:

The structure of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide also contains other interesting chemical elements:

Mercury (Hg) 14 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide (pdb code 1jpr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide, PDB code: 1jpr:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1jpr

Go back to Manganese Binding Sites List in 1jpr
Manganese binding site 1 out of 4 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:19.8
occ:0.90
 OD1 A:ASP84 2.0 24.2 1.0
OE1 A:GLU115 2.1 21.8 1.0
ND1 A:HIS118 2.2 8.4 1.0
OE2 A:GLU238 2.2 20.3 1.0
O A:HOH1031 2.3 25.5 1.0
CG A:ASP84 2.8 18.4 1.0
CE1 A:HIS118 2.9 7.1 1.0
OD2 A:ASP84 3.0 21.9 1.0
CD A:GLU115 3.1 15.2 1.0
O A:HOH964 3.3 26.1 1.0
CG A:HIS118 3.3 11.5 1.0
CD A:GLU238 3.3 28.3 1.0
MN A:MN404 3.4 17.5 1.0
OE2 A:GLU115 3.5 17.8 1.0
CB A:HIS118 3.8 9.5 1.0
NE2 A:HIS118 4.1 9.8 1.0
CG A:GLU238 4.2 23.1 1.0
OE1 A:GLU238 4.2 20.4 1.0
CZ A:PHE208 4.2 26.2 1.0
CE2 A:PHE208 4.3 27.5 1.0
CB A:ASP84 4.3 12.2 1.0
CD2 A:HIS118 4.3 6.6 1.0
CG A:GLU115 4.4 12.4 1.0
CA A:GLU115 4.4 9.5 1.0
CG2 A:ILE234 4.4 10.7 1.0
CB A:GLU115 4.5 10.4 1.0
CE1 A:HIS241 4.7 8.3 1.0
ND1 A:HIS241 4.7 9.7 1.0
CE1 A:PHE208 4.8 26.9 1.0
OH A:TYR122 4.9 17.9 1.0
CD2 A:PHE208 4.9 27.6 1.0
CA A:ASP84 5.0 12.4 1.0

Manganese binding site 2 out of 4 in 1jpr

Go back to Manganese Binding Sites List in 1jpr
Manganese binding site 2 out of 4 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:17.5
occ:1.00
 OE1 A:GLU238 1.8 20.4 1.0
OE2 A:GLU115 2.0 17.8 1.0
OE2 A:GLU238 2.1 20.3 1.0
OE1 A:GLU204 2.1 25.4 1.0
CD A:GLU238 2.2 28.3 1.0
O A:HOH964 2.3 26.1 1.0
ND1 A:HIS241 2.3 9.7 1.0
CD A:GLU115 2.9 15.2 1.0
CD A:GLU204 3.0 23.4 1.0
OE1 A:GLU115 3.1 21.8 1.0
CE1 A:HIS241 3.3 8.3 1.0
CG A:HIS241 3.4 11.6 1.0
MN A:MN403 3.4 19.8 0.9
CG A:GLU204 3.5 27.4 1.0
CB A:HIS241 3.7 8.6 1.0
CG A:GLU238 3.8 23.1 1.0
NE1 A:TRP111 3.9 9.8 1.0
OE2 A:GLU204 4.0 29.0 1.0
CG A:GLU115 4.3 12.4 1.0
CA A:GLU238 4.4 14.3 1.0
NE2 A:HIS241 4.4 9.6 1.0
O A:HOH1031 4.5 25.5 1.0
CD1 A:TRP111 4.5 8.1 1.0
CD2 A:HIS241 4.5 11.6 1.0
CB A:GLU238 4.6 17.9 1.0
CB A:GLU204 4.6 24.5 1.0
OD1 A:ASP84 4.7 24.2 1.0
CE1 A:HIS118 4.8 7.1 1.0
OE1 A:GLN87 5.0 19.8 1.0
ND1 A:HIS118 5.0 8.4 1.0

Manganese binding site 3 out of 4 in 1jpr

Go back to Manganese Binding Sites List in 1jpr
Manganese binding site 3 out of 4 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:19.8
occ:0.80
 OE1 B:GLU115 2.1 17.6 1.0
ND1 B:HIS118 2.1 11.1 1.0
OD2 B:ASP84 2.2 18.5 1.0
O B:HOH1077 2.3 31.4 1.0
OE2 B:GLU238 2.4 21.2 1.0
OD1 B:ASP84 2.5 23.1 1.0
CG B:ASP84 2.6 17.9 1.0
CE1 B:HIS118 2.9 11.9 1.0
O B:HOH984 3.1 24.8 1.0
CD B:GLU115 3.1 14.8 1.0
CG B:HIS118 3.3 11.5 1.0
MN B:MN402 3.4 16.8 1.0
CD B:GLU238 3.5 25.8 1.0
OE2 B:GLU115 3.6 19.5 1.0
CB B:HIS118 3.8 9.4 1.0
CB B:ASP84 4.1 14.6 1.0
NE2 B:HIS118 4.1 13.2 1.0
CG B:GLU238 4.2 23.2 1.0
CD2 B:HIS118 4.3 11.1 1.0
CZ B:PHE208 4.3 23.4 1.0
CG B:GLU115 4.4 9.7 1.0
CA B:GLU115 4.4 10.5 1.0
OE1 B:GLU238 4.4 18.7 1.0
CE2 B:PHE208 4.4 25.1 1.0
CG2 B:ILE234 4.5 13.2 1.0
CB B:GLU115 4.5 10.7 1.0
CE1 B:HIS241 4.6 12.2 1.0
ND1 B:HIS241 4.7 8.8 1.0
OH B:TYR122 4.8 16.4 1.0
CE1 B:PHE208 4.9 26.2 1.0
CA B:ASP84 4.9 11.0 1.0

Manganese binding site 4 out of 4 in 1jpr

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Manganese binding site 4 out of 4 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:16.8
occ:1.00
 OE2 B:GLU238 1.8 21.2 1.0
OE2 B:GLU204 2.1 20.9 1.0
OE2 B:GLU115 2.1 19.5 1.0
OE1 B:GLU238 2.1 18.7 1.0
CD B:GLU238 2.2 25.8 1.0
O B:HOH984 2.2 24.8 1.0
ND1 B:HIS241 2.2 8.8 1.0
CD B:GLU115 2.9 14.8 1.0
OE1 B:GLU115 3.1 17.6 1.0
CD B:GLU204 3.1 18.6 1.0
CE1 B:HIS241 3.1 12.2 1.0
CG B:HIS241 3.3 10.9 1.0
MN B:MN401 3.4 19.8 0.8
CB B:HIS241 3.7 12.3 1.0
CG B:GLU204 3.7 22.8 1.0
CG B:GLU238 3.7 23.2 1.0
NE1 B:TRP111 3.9 9.4 1.0
OE1 B:GLU204 4.1 23.1 1.0
O B:HOH1077 4.2 31.4 1.0
NE2 B:HIS241 4.3 8.5 1.0
CG B:GLU115 4.3 9.7 1.0
CD2 B:HIS241 4.4 10.6 1.0
OD1 B:ASP84 4.4 23.1 1.0
CA B:GLU238 4.4 12.6 1.0
CD1 B:TRP111 4.4 8.9 1.0
CB B:GLU204 4.5 22.6 1.0
CB B:GLU238 4.5 14.6 1.0
CE1 B:HIS118 4.8 11.9 1.0
OE1 B:GLN87 4.9 20.0 1.0
ND1 B:HIS118 4.9 11.1 1.0

Reference:

M.Hogbom, M.E.Andersson, P.Nordlund. Crystal Structures of Oxidized Dinuclear Manganese Centres in Mn-Substituted Class I Ribonucleotide Reductase From Escherichia Coli: Carboxylate Shifts with Implications For O2 Activation and Radical Generation. J.Biol.Inorg.Chem. V. 6 315 2001.
ISSN: ISSN 0949-8257
PubMed: 11315567
DOI: 10.1007/S007750000205
Page generated: Sat Oct 5 11:12:56 2024

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