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Manganese in PDB 3n39: Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Nrdi

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

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

Protein crystallography data

The structure of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Nrdi, PDB code: 3n39 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) 33.84 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.403, 90.721, 143.787, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 27.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Nrdi (pdb code 3n39). 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 Nrdi, PDB code: 3n39:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3n39

Go back to Manganese Binding Sites List in 3n39
Manganese binding site 1 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with 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 Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn320

b:36.1
occ:1.00
 OE1 B:GLU98 1.9 36.0 1.0
O B:HOH323 2.2 12.7 1.0
OD1 B:ASP67 2.2 43.4 1.0
OE2 B:GLU192 2.2 35.5 1.0
OE1 B:GLU158 2.2 44.0 1.0
ND1 B:HIS101 2.3 32.1 1.0
CD B:GLU98 3.0 35.8 1.0
CE1 B:HIS101 3.1 32.5 1.0
CG B:ASP67 3.2 43.7 1.0
CD B:GLU158 3.3 43.8 1.0
CD B:GLU192 3.3 35.4 1.0
CG B:HIS101 3.4 33.2 1.0
OE2 B:GLU98 3.5 36.1 1.0
OD2 B:ASP67 3.6 43.9 1.0
OE2 B:GLU158 3.7 43.5 1.0
MN B:MN321 3.7 39.4 1.0
CB B:HIS101 3.8 34.3 1.0
OE1 B:GLU192 4.1 35.9 1.0
CG B:GLU192 4.2 35.0 1.0
NE2 B:HIS101 4.3 32.6 1.0
CA B:GLU98 4.3 34.6 1.0
CG B:GLU98 4.3 35.1 1.0
CD2 B:HIS101 4.5 32.6 1.0
CB B:GLU98 4.5 34.7 1.0
CB B:ASP67 4.5 43.7 1.0
CG B:GLU158 4.6 43.5 1.0
CG2 B:ILE188 4.8 37.4 1.0
CE1 B:PHE162 4.8 43.5 1.0
CZ B:PHE162 4.9 43.5 1.0
CA B:ASP67 5.0 43.8 1.0

Manganese binding site 2 out of 4 in 3n39

Go back to Manganese Binding Sites List in 3n39
Manganese binding site 2 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with 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 Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn321

b:39.4
occ:1.00
 OE2 B:GLU98 2.0 36.1 1.0
OE2 B:GLU158 2.0 43.5 1.0
OE1 B:GLU192 2.3 35.9 1.0
ND1 B:HIS195 2.3 33.1 1.0
O B:HOH322 2.3 20.0 1.0
OE2 B:GLU192 2.6 35.5 1.0
CD B:GLU192 2.8 35.4 1.0
CD B:GLU158 2.9 43.8 1.0
CD B:GLU98 3.0 35.8 1.0
CE1 B:HIS195 3.3 33.4 1.0
CG B:HIS195 3.3 33.5 1.0
OE1 B:GLU158 3.4 44.0 1.0
OE1 B:GLU98 3.4 36.0 1.0
CB B:HIS195 3.5 33.9 1.0
MN B:MN320 3.7 36.1 1.0
CG B:GLU158 4.2 43.5 1.0
CG B:GLU192 4.3 35.0 1.0
CB B:GLU158 4.3 43.3 1.0
CG B:GLU98 4.4 35.1 1.0
NE2 B:HIS195 4.4 33.2 1.0
OE1 B:GLN70 4.4 43.7 1.0
CD2 B:HIS195 4.4 33.2 1.0
CG2 B:ILE94 4.5 33.7 1.0
CA B:GLU192 4.8 35.0 1.0
CB B:GLU192 4.9 35.0 1.0

Manganese binding site 3 out of 4 in 3n39

Go back to Manganese Binding Sites List in 3n39
Manganese binding site 3 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with 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 Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn320

b:36.7
occ:1.00
 OE2 A:GLU98 2.0 34.8 1.0
O A:HOH323 2.0 30.3 1.0
OE2 A:GLU158 2.1 43.1 1.0
OE1 A:GLU192 2.1 36.1 1.0
ND1 A:HIS195 2.2 37.1 1.0
OE2 A:GLU192 2.6 35.9 1.0
CD A:GLU192 2.7 36.3 1.0
CD A:GLU158 2.9 43.6 1.0
CD A:GLU98 3.0 35.0 1.0
CE1 A:HIS195 3.2 37.4 1.0
CG A:HIS195 3.2 37.5 1.0
OE1 A:GLU158 3.2 43.5 1.0
OE1 A:GLU98 3.3 35.7 1.0
CB A:HIS195 3.6 37.9 1.0
MN A:MN321 3.7 38.1 1.0
CG A:GLU158 4.1 43.2 1.0
CG A:GLU192 4.2 36.5 1.0
NE2 A:HIS195 4.3 38.0 1.0
CG2 A:ILE94 4.3 37.2 1.0
CB A:GLU158 4.3 43.0 1.0
CG A:GLU98 4.4 34.7 1.0
CD2 A:HIS195 4.4 37.7 1.0
OE1 A:GLN70 4.5 45.3 1.0
CA A:GLU192 4.8 37.2 1.0
CB A:GLU192 4.9 37.0 1.0
CE1 A:HIS101 5.0 33.1 1.0

Manganese binding site 4 out of 4 in 3n39

Go back to Manganese Binding Sites List in 3n39
Manganese binding site 4 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with 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 Nrdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn321

b:38.1
occ:1.00
 OE1 A:GLU98 1.9 35.7 1.0
O A:HOH322 2.1 26.9 1.0
OE2 A:GLU192 2.2 35.9 1.0
OD1 A:ASP67 2.2 41.0 1.0
OE1 A:GLU158 2.3 43.5 1.0
ND1 A:HIS101 2.4 33.4 1.0
CD A:GLU98 3.1 35.0 1.0
CE1 A:HIS101 3.2 33.1 1.0
CD A:GLU192 3.3 36.3 1.0
CG A:ASP67 3.3 40.6 1.0
CD A:GLU158 3.4 43.6 1.0
CG A:HIS101 3.4 33.6 1.0
OE2 A:GLU98 3.6 34.8 1.0
MN A:MN320 3.7 36.7 1.0
OD2 A:ASP67 3.7 40.5 1.0
CB A:HIS101 3.8 33.7 1.0
OE2 A:GLU158 3.9 43.1 1.0
OE1 A:GLU192 4.1 36.1 1.0
CG A:GLU192 4.1 36.5 1.0
CA A:GLU98 4.3 34.2 1.0
CG A:GLU98 4.3 34.7 1.0
NE2 A:HIS101 4.4 33.0 1.0
CB A:GLU98 4.5 34.4 1.0
CD2 A:HIS101 4.5 33.0 1.0
CB A:ASP67 4.6 40.5 1.0
CG A:GLU158 4.7 43.2 1.0
CG2 A:ILE188 4.7 37.5 1.0
CE1 A:PHE162 4.8 42.0 1.0
ND1 A:HIS195 4.9 37.1 1.0
CE1 A:HIS195 5.0 37.4 1.0
CA A:ASP67 5.0 40.8 1.0
O A:MET97 5.0 34.1 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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