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Manganese in PDB 3n3b: Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide

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

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

Protein crystallography data

The structure of Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide, PDB code: 3n3b 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) 40.56 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.723, 91.348, 144.114, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 27.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide (pdb code 3n3b). 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 with A Trapped Peroxide, PDB code: 3n3b:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3n3b

Go back to Manganese Binding Sites List in 3n3b
Manganese binding site 1 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide


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 with A Trapped Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn320

b:22.9
occ:1.00
 OE1 B:GLU98 2.1 17.1 1.0
O B:HOH375 2.1 60.1 1.0
OE2 B:GLU192 2.1 18.0 1.0
OD1 B:ASP67 2.2 21.5 1.0
OE1 B:GLU158 2.3 24.2 1.0
ND1 B:HIS101 2.5 16.1 1.0
CD B:GLU192 3.2 18.0 1.0
CD B:GLU98 3.2 16.8 1.0
CG B:ASP67 3.3 21.8 1.0
CE1 B:HIS101 3.3 16.3 1.0
CD B:GLU158 3.3 24.2 1.0
CG B:HIS101 3.6 16.2 1.0
OE2 B:GLU158 3.6 24.4 1.0
OD2 B:ASP67 3.6 22.0 1.0
MN B:MN321 3.6 23.0 1.0
OE2 B:GLU98 3.8 17.2 1.0
CB B:HIS101 3.9 16.1 1.0
CG B:GLU192 4.0 17.8 1.0
OE1 B:GLU192 4.1 17.9 1.0
CA B:GLU98 4.4 15.8 1.0
NE2 B:HIS101 4.5 16.2 1.0
CG B:GLU98 4.5 16.2 1.0
CB B:ASP67 4.6 21.8 1.0
CB B:GLU98 4.6 15.8 1.0
CG B:GLU158 4.6 23.7 1.0
CD2 B:HIS101 4.6 16.2 1.0
CE1 B:PHE162 4.8 23.3 1.0
CG2 B:ILE188 4.8 18.8 1.0
CZ B:PHE162 4.9 23.3 1.0

Manganese binding site 2 out of 4 in 3n3b

Go back to Manganese Binding Sites List in 3n3b
Manganese binding site 2 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide


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 with A Trapped Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn321

b:23.0
occ:1.00
 OE2 B:GLU98 2.0 17.2 1.0
O B:HOH381 2.1 48.5 1.0
OE2 B:GLU158 2.1 24.4 1.0
OE1 B:GLU192 2.2 17.9 1.0
ND1 B:HIS195 2.3 16.3 1.0
OE2 B:GLU192 2.5 18.0 1.0
CD B:GLU192 2.7 18.0 1.0
CD B:GLU98 2.9 16.8 1.0
CD B:GLU158 3.0 24.2 1.0
OE1 B:GLU98 3.2 17.1 1.0
CE1 B:HIS195 3.2 16.1 1.0
CG B:HIS195 3.3 16.6 1.0
OE1 B:GLU158 3.5 24.2 1.0
CB B:HIS195 3.6 17.1 1.0
MN B:MN320 3.6 22.9 1.0
O B:HOH389 3.8 18.7 1.0
O B:HOH374 4.1 38.2 1.0
CG B:GLU158 4.2 23.7 1.0
CG B:GLU192 4.2 17.8 1.0
CB B:GLU158 4.3 23.5 1.0
CG B:GLU98 4.3 16.2 1.0
NE2 B:HIS195 4.4 16.0 1.0
OE1 B:GLN70 4.4 23.4 1.0
CD2 B:HIS195 4.4 16.4 1.0
CG2 B:ILE94 4.6 16.0 1.0
CA B:GLU192 4.8 17.9 1.0
CB B:GLU192 4.9 17.9 1.0
O B:HOH347 5.0 24.5 1.0

Manganese binding site 3 out of 4 in 3n3b

Go back to Manganese Binding Sites List in 3n3b
Manganese binding site 3 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide


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 with A Trapped Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn320

b:21.5
occ:1.00
 OE1 A:GLU98 2.1 17.1 1.0
OD1 A:ASP67 2.2 23.9 1.0
OE2 A:GLU192 2.2 20.0 1.0
OE1 A:GLU158 2.2 22.5 1.0
O A:HOH361 2.2 10.1 1.0
ND1 A:HIS101 2.5 18.4 1.0
CD A:GLU98 3.2 17.3 1.0
CD A:GLU192 3.2 19.9 1.0
CE1 A:HIS101 3.2 18.1 1.0
CG A:ASP67 3.2 24.1 1.0
CD A:GLU158 3.3 22.8 1.0
CG A:HIS101 3.6 18.5 1.0
OD2 A:ASP67 3.6 24.3 1.0
OE2 A:GLU98 3.7 17.4 1.0
OE2 A:GLU158 3.8 22.8 1.0
MN A:MN321 3.8 19.0 1.0
CB A:HIS101 3.9 18.5 1.0
CG A:GLU192 4.0 19.8 1.0
OE1 A:GLU192 4.1 19.9 1.0
CA A:GLU98 4.4 16.7 1.0
NE2 A:HIS101 4.4 18.4 1.0
CG A:GLU98 4.5 16.9 1.0
CG A:GLU158 4.5 23.0 1.0
CB A:ASP67 4.5 24.1 1.0
CD2 A:HIS101 4.6 18.4 1.0
CB A:GLU98 4.6 16.9 1.0
CG2 A:ILE188 4.7 21.7 1.0
CE1 A:PHE162 4.9 24.2 1.0
CZ A:PHE162 5.0 24.2 1.0
CA A:ASP67 5.0 24.1 1.0

Manganese binding site 4 out of 4 in 3n3b

Go back to Manganese Binding Sites List in 3n3b
Manganese binding site 4 out of 4 in the Ribonucleotide Reductase Dimanganese(II)-Nrdf From Escherichia Coli in Complex with Reduced Nrdi with A Trapped Peroxide


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 with A Trapped Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn321

b:19.0
occ:1.00
 OE2 A:GLU98 2.0 17.4 1.0
O A:HOH334 2.1 32.2 1.0
OE1 A:GLU192 2.2 19.9 1.0
OE2 A:GLU158 2.2 22.8 1.0
ND1 A:HIS195 2.4 17.5 1.0
OE2 A:GLU192 2.6 20.0 1.0
CD A:GLU192 2.7 19.9 1.0
CD A:GLU98 3.0 17.3 1.0
CD A:GLU158 3.0 22.8 1.0
CE1 A:HIS195 3.3 17.3 1.0
OE1 A:GLU98 3.3 17.1 1.0
CG A:HIS195 3.4 17.9 1.0
OE1 A:GLU158 3.4 22.5 1.0
CB A:HIS195 3.7 18.1 1.0
MN A:MN320 3.8 21.5 1.0
O A:HOH335 3.9 46.1 1.0
O A:HOH343 4.2 15.2 1.0
CG A:GLU158 4.2 23.0 1.0
CG A:GLU192 4.2 19.8 1.0
CB A:GLU158 4.3 23.0 1.0
CG A:GLU98 4.4 16.9 1.0
NE2 A:HIS195 4.5 17.2 1.0
OE1 A:GLN70 4.5 24.0 1.0
CD2 A:HIS195 4.5 17.5 1.0
CG2 A:ILE94 4.6 16.2 1.0
CA A:GLU192 4.9 19.7 1.0
CB A:GLU192 4.9 19.8 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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