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Manganese in PDB 3n3a: Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi

Enzymatic activity of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi

All present enzymatic activity of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi, PDB code: 3n3a was solved by A.K.Boal, J.A.Cotruvo Jr., J.Stubbe, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.58 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.863, 90.678, 143.837, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi (pdb code 3n3a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi, PDB code: 3n3a:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3n3a

Go back to Manganese Binding Sites List in 3n3a
Manganese binding site 1 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn320

b:20.8
occ:1.00
 OE2 B:GLU98 2.1 18.9 1.0
OE2 B:GLU158 2.2 26.0 1.0
O B:HOH429 2.2 15.1 1.0
OE1 B:GLU192 2.2 20.9 1.0
ND1 B:HIS195 2.3 18.3 1.0
OE2 B:GLU192 2.3 19.2 1.0
CD B:GLU192 2.6 19.6 1.0
CD B:GLU98 3.0 18.3 1.0
CD B:GLU158 3.1 24.3 1.0
OE1 B:GLU98 3.2 18.3 1.0
CE1 B:HIS195 3.3 19.1 1.0
CG B:HIS195 3.3 19.9 1.0
CB B:HIS195 3.5 19.9 1.0
OE1 B:GLU158 3.6 22.5 1.0
MN B:MN321 3.7 20.5 1.0
O B:HOH348 3.9 24.8 1.0
CG B:GLU192 4.1 20.2 1.0
O B:HOH440 4.2 17.0 1.0
CG B:GLU158 4.3 23.1 1.0
CB B:GLU158 4.4 23.3 1.0
OE1 B:GLN70 4.4 23.9 1.0
NE2 B:HIS195 4.4 18.7 1.0
CG B:GLU98 4.4 17.0 1.0
CD2 B:HIS195 4.4 18.9 1.0
CG2 B:ILE94 4.6 19.3 1.0
O B:HOH338 4.7 17.0 1.0
CE1 B:HIS101 4.8 18.2 1.0
CA B:GLU192 4.9 20.1 1.0
CB B:GLU192 4.9 20.4 1.0

Manganese binding site 2 out of 4 in 3n3a

Go back to Manganese Binding Sites List in 3n3a
Manganese binding site 2 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn321

b:20.5
occ:1.00
 OE1 B:GLU98 2.1 18.3 1.0
OD1 B:ASP67 2.1 23.3 1.0
OE2 B:GLU192 2.2 19.2 1.0
OE1 B:GLU158 2.2 22.5 1.0
ND1 B:HIS101 2.2 18.4 1.0
O B:HOH430 2.3 15.0 1.0
CE1 B:HIS101 3.0 18.2 1.0
CG B:ASP67 3.2 22.4 1.0
CD B:GLU158 3.2 24.3 1.0
CD B:GLU192 3.2 19.6 1.0
CD B:GLU98 3.3 18.3 1.0
CG B:HIS101 3.4 18.9 1.0
OE2 B:GLU158 3.5 26.0 1.0
OD2 B:ASP67 3.5 23.1 1.0
MN B:MN320 3.7 20.8 1.0
CB B:HIS101 3.8 19.4 1.0
OE2 B:GLU98 3.8 18.9 1.0
CG B:GLU192 3.9 20.2 1.0
OE1 B:GLU192 4.1 20.9 1.0
NE2 B:HIS101 4.2 19.4 1.0
CD2 B:HIS101 4.4 17.4 1.0
CA B:GLU98 4.4 18.0 1.0
CB B:ASP67 4.5 21.6 1.0
CG B:GLU158 4.5 23.1 1.0
CG B:GLU98 4.5 17.0 1.0
CB B:GLU98 4.7 17.4 1.0
CG2 B:ILE188 4.7 21.0 1.0
CE1 B:PHE162 4.9 27.0 1.0
ND1 B:HIS195 4.9 18.3 1.0
CZ B:PHE162 5.0 26.4 1.0

Manganese binding site 3 out of 4 in 3n3a

Go back to Manganese Binding Sites List in 3n3a
Manganese binding site 3 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn320

b:21.7
occ:1.00
 OE2 A:GLU98 2.1 22.1 1.0
OE1 A:GLU192 2.2 27.1 1.0
OE2 A:GLU158 2.2 23.9 1.0
O A:HOH388 2.3 16.9 1.0
ND1 A:HIS195 2.3 18.2 1.0
OE2 A:GLU192 2.4 24.8 1.0
CD A:GLU192 2.6 24.3 1.0
CD A:GLU98 3.0 22.3 1.0
CD A:GLU158 3.1 26.2 1.0
CE1 A:HIS195 3.2 18.5 1.0
OE1 A:GLU98 3.2 21.9 1.0
CG A:HIS195 3.3 18.4 1.0
OE1 A:GLU158 3.5 26.5 1.0
CB A:HIS195 3.6 18.8 1.0
MN A:MN321 3.7 23.4 1.0
O A:HOH347 4.0 21.2 1.0
CG A:GLU192 4.2 24.1 1.0
O A:HOH391 4.2 20.8 1.0
CG A:GLU158 4.3 25.6 1.0
NE2 A:HIS195 4.3 19.1 1.0
OE1 A:GLN70 4.4 27.1 1.0
CB A:GLU158 4.4 26.2 1.0
CG A:GLU98 4.4 19.5 1.0
CD2 A:HIS195 4.4 18.1 1.0
CG2 A:ILE94 4.6 19.9 1.0
O A:HOH412 4.8 28.9 1.0
CA A:GLU192 4.8 22.6 1.0
CE1 A:HIS101 4.9 21.4 1.0
CB A:GLU192 4.9 22.9 1.0

Manganese binding site 4 out of 4 in 3n3a

Go back to Manganese Binding Sites List in 3n3a
Manganese binding site 4 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn321

b:23.4
occ:1.00
 OD1 A:ASP67 2.1 26.7 1.0
OE2 A:GLU192 2.2 24.8 1.0
OE1 A:GLU98 2.2 21.9 1.0
OE1 A:GLU158 2.2 26.5 1.0
O A:HOH401 2.3 16.9 1.0
ND1 A:HIS101 2.3 20.9 1.0
CE1 A:HIS101 3.1 21.4 1.0
CD A:GLU192 3.2 24.3 1.0
CG A:ASP67 3.2 28.1 1.0
CD A:GLU158 3.2 26.2 1.0
CD A:GLU98 3.4 22.3 1.0
CG A:HIS101 3.4 21.2 1.0
OD2 A:ASP67 3.6 26.8 1.0
OE2 A:GLU158 3.6 23.9 1.0
MN A:MN320 3.7 21.7 1.0
CB A:HIS101 3.8 21.9 1.0
CG A:GLU192 3.8 24.1 1.0
OE2 A:GLU98 3.9 22.1 1.0
OE1 A:GLU192 4.0 27.1 1.0
NE2 A:HIS101 4.3 20.7 1.0
CA A:GLU98 4.4 20.1 1.0
CD2 A:HIS101 4.5 21.7 1.0
CB A:ASP67 4.5 27.8 1.0
CG A:GLU158 4.6 25.6 1.0
CG A:GLU98 4.6 19.5 1.0
CB A:GLU98 4.7 20.1 1.0
CG2 A:ILE188 4.7 24.3 1.0
CE1 A:PHE162 4.9 27.7 1.0
CA A:ASP67 4.9 27.6 1.0
CZ A:PHE162 5.0 28.7 1.0
ND1 A:HIS195 5.0 18.2 1.0

Reference:

A.K.Boal, J.A.Cotruvo, J.Stubbe, A.C.Rosenzweig. Structural Basis For Activation of Class Ib Ribonucleotide Reductase. Science V. 329 1526 2010.
ISSN: ISSN 0036-8075
PubMed: 20688982
DOI: 10.1126/SCIENCE.1190187
Page generated: Sat Oct 5 17:17:04 2024

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