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Manganese in PDB 6sf5: Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis

Enzymatic activity of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis

All present enzymatic activity of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis:
1.17.4.1;

Protein crystallography data

The structure of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis, PDB code: 6sf5 was solved by M.Hasan, I.Rozman Grinberg, B.M.Sjoberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.82 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.060, 80.602, 158.228, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis (pdb code 6sf5). 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-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis, PDB code: 6sf5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6sf5

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Manganese binding site 1 out of 4 in the Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:32.0
occ:1.00
 OE2 A:GLU298 2.1 36.2 1.0
OE1 A:GLU200 2.2 35.4 1.0
ND1 A:HIS203 2.2 31.4 1.0
OE2 A:GLU170 2.2 33.4 1.0
OE1 A:GLU170 2.3 34.8 1.0
O A:HOH768 2.3 36.8 1.0
CD A:GLU170 2.6 36.6 1.0
OE2 A:GLU200 2.8 46.3 1.0
CD A:GLU200 2.8 33.8 1.0
CD A:GLU298 3.2 40.1 1.0
CE1 A:HIS203 3.2 30.6 1.0
CG A:HIS203 3.3 30.8 1.0
CB A:HIS203 3.5 28.1 1.0
OE1 A:GLU298 3.7 35.8 1.0
MN A:MN502 3.9 31.7 1.0
CG A:GLU170 4.1 31.5 1.0
NZ A:LYS174 4.2 35.8 1.0
CG A:GLU298 4.3 34.3 1.0
CG A:GLU200 4.3 28.2 1.0
NE2 A:HIS203 4.4 31.3 1.0
CD2 A:HIS203 4.4 32.3 1.0
CG2 A:THR294 4.4 30.2 1.0
O A:HOH761 4.5 53.4 1.0
O A:HOH740 4.7 41.1 1.0
CD1 A:LEU267 4.8 34.9 1.0
CA A:GLU200 4.9 29.7 1.0
CD A:LYS174 4.9 40.8 1.0
O A:HOH601 4.9 56.6 1.0

Manganese binding site 2 out of 4 in 6sf5

Go back to Manganese Binding Sites List in 6sf5
Manganese binding site 2 out of 4 in the Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:31.7
occ:1.00
 OE1 A:GLU298 2.0 35.8 1.0
OE2 A:GLU200 2.1 46.3 1.0
ND1 A:HIS301 2.1 31.1 1.0
OE2 A:GLU263 2.2 35.2 1.0
O A:HOH601 2.2 56.6 1.0
CD A:GLU263 2.9 42.1 1.0
CD A:GLU298 3.0 40.1 1.0
CE1 A:HIS301 3.0 30.7 1.0
OE1 A:GLU263 3.1 36.0 1.0
OE2 A:GLU298 3.2 36.2 1.0
CD A:GLU200 3.2 33.8 1.0
CG A:HIS301 3.3 31.0 1.0
O A:HOH761 3.6 53.4 1.0
CB A:HIS301 3.7 28.7 1.0
O A:HOH768 3.8 36.8 1.0
MN A:MN501 3.9 32.0 1.0
NE1 A:TRP177 4.0 31.5 1.0
OE1 A:GLU200 4.0 35.4 1.0
CG A:GLU200 4.1 28.2 1.0
O A:HOH740 4.2 41.1 1.0
NE2 A:HIS301 4.2 31.3 1.0
CG A:GLU263 4.3 29.0 1.0
CD2 A:HIS301 4.3 31.6 1.0
CG A:GLU298 4.4 34.3 1.0
CD1 A:TRP177 4.5 33.5 1.0
O A:HOH844 4.5 56.4 1.0
CA A:GLU298 4.6 28.2 1.0
CB A:GLU298 4.9 29.6 1.0
CB A:GLU263 4.9 29.5 1.0

Manganese binding site 3 out of 4 in 6sf5

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Manganese binding site 3 out of 4 in the Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:39.2
occ:1.00
 OE2 B:GLU298 2.0 46.3 1.0
OE1 B:GLU200 2.2 50.1 1.0
O B:HOH682 2.2 45.9 1.0
ND1 B:HIS203 2.3 38.8 1.0
OE2 B:GLU170 2.3 46.8 1.0
OE1 B:GLU170 2.3 41.3 1.0
CD B:GLU170 2.6 45.7 1.0
OE2 B:GLU200 2.8 54.7 1.0
CD B:GLU200 2.9 48.2 1.0
CD B:GLU298 3.1 52.0 1.0
CE1 B:HIS203 3.2 38.3 1.0
CG B:HIS203 3.3 36.1 1.0
CB B:HIS203 3.6 33.1 1.0
OE1 B:GLU298 3.7 45.7 1.0
MN B:MN502 3.9 39.0 1.0
CG B:GLU170 4.1 39.2 1.0
NZ B:LYS174 4.2 41.0 1.0
CG B:GLU298 4.2 39.5 1.0
CG B:GLU200 4.4 42.9 1.0
NE2 B:HIS203 4.4 38.7 1.0
CG2 B:THR294 4.4 35.0 1.0
CD2 B:HIS203 4.4 37.7 1.0
O B:HOH673 4.6 63.1 1.0
O B:HOH681 4.6 53.4 1.0
CD1 B:LEU267 4.8 40.4 1.0
CD B:LYS174 4.9 47.5 1.0
CA B:GLU200 4.9 32.3 1.0
CE1 B:HIS301 5.0 37.1 1.0

Manganese binding site 4 out of 4 in 6sf5

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Manganese binding site 4 out of 4 in the Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mn-Containing Form of the Ribonucleotide Reductase Nrdb Protein From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:39.0
occ:1.00
 OE1 B:GLU298 2.0 45.7 1.0
OE1 B:GLU263 2.1 45.2 1.0
ND1 B:HIS301 2.1 38.1 1.0
OE2 B:GLU200 2.1 54.7 1.0
CD B:GLU263 2.9 53.4 1.0
CD B:GLU298 3.0 52.0 1.0
CE1 B:HIS301 3.0 37.1 1.0
OE2 B:GLU263 3.0 48.5 1.0
CG B:HIS301 3.2 38.1 1.0
OE2 B:GLU298 3.3 46.3 1.0
CD B:GLU200 3.3 48.2 1.0
CB B:HIS301 3.6 36.6 1.0
O B:HOH682 3.7 45.9 1.0
O B:HOH673 3.9 63.1 1.0
MN B:MN501 3.9 39.2 1.0
NE1 B:TRP177 4.0 40.3 1.0
O B:HOH707 4.0 68.6 1.0
OE1 B:GLU200 4.1 50.1 1.0
CG B:GLU200 4.2 42.9 1.0
NE2 B:HIS301 4.2 37.2 1.0
O B:HOH681 4.2 53.4 1.0
CG B:GLU263 4.2 47.9 1.0
CD2 B:HIS301 4.3 38.2 1.0
CG B:GLU298 4.4 39.5 1.0
CD1 B:TRP177 4.5 41.0 1.0
CA B:GLU298 4.5 37.3 1.0
CB B:GLU263 4.8 42.4 1.0
CB B:GLU298 4.8 38.2 1.0

Reference:

I.Rozman Grinberg, S.Berglund, M.Hasan, D.Lundin, F.M.Ho, A.Magnuson, D.T.Logan, B.M.Sjoberg, G.Berggren. Class Id Ribonucleotide Reductase Utilizes A MN2(IV,III) Cofactor and Undergoes Large Conformational Changes on Metal Loading. J.Biol.Inorg.Chem. V. 24 863 2019.
ISSN: ESSN 1432-1327
PubMed: 31414238
DOI: 10.1007/S00775-019-01697-8
Page generated: Sun Oct 6 07:06:54 2024

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