Cobalt in PDB 3o0o: Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin

All present enzymatic activity of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin:
1.17.4.1;

The structure of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin, PDB code: 3o0o was solved by K.-M.Larsson, D.T.Logan, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.94 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.020, 124.230, 107.170, 90.00, 102.57, 90.00
R / Rfree (%)	20.2 / 23.8

The structure of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Cobalt atom in the Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin (pdb code 3o0o). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin, PDB code: 3o0o:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1004 b:80.5 occ:0.81 CO A:B121004 0.0 80.5 0.8 N24 A:B121004 1.9 71.8 0.5 N21 A:B121004 1.9 69.8 0.3 N22 A:B121004 1.9 76.3 0.7 N23 A:B121004 1.9 76.9 0.5 N3B A:B121004 2.1 59.3 1.0 C19 A:B121004 2.8 71.3 0.5 C9 A:B121004 2.9 77.5 0.6 C5' A:5AD1005 2.9 68.4 0.8 C11 A:B121004 2.9 77.4 0.6 C4 A:B121004 2.9 70.7 0.7 C16 A:B121004 2.9 73.6 0.5 C1 A:B121004 2.9 66.2 1.0 C14 A:B121004 3.0 76.5 0.7 C6 A:B121004 3.0 74.5 0.7 C2B A:B121004 3.0 64.2 0.7 C9B A:B121004 3.2 63.9 0.8 C10 A:B121004 3.2 77.2 0.6 C5 A:B121004 3.4 72.1 0.7 C15 A:B121004 3.4 76.1 0.6 C20 A:B121004 3.7 50.9 1.0 C4B A:B121004 3.7 66.7 0.5 C2 A:B121004 4.1 52.5 0.4 C4' A:5AD1005 4.1 68.2 0.7 C18 A:B121004 4.2 73.2 0.7 C8 A:B121004 4.2 79.6 0.5 C3 A:B121004 4.2 71.9 0.7 C17 A:B121004 4.2 75.2 0.6 C12 A:B121004 4.2 78.2 0.4 N1B A:B121004 4.2 68.6 0.7 C13 A:B121004 4.2 77.2 0.6 C7 A:B121004 4.3 41.8 0.5 C8B A:B121004 4.3 67.8 0.5 C26 A:B121004 4.4 66.2 0.7 O4' A:5AD1005 4.4 68.5 0.7 C35 A:B121004 4.9 71.2 0.7 C37 A:B121004 4.9 66.4 0.8 C41 A:B121004 4.9 79.9 0.9 C53 A:B121004 4.9 43.6 0.6 C54 A:B121004 5.0 76.2 0.8

Cobalt binding site 2 out of 2 in the Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosylcobalamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1004 b:49.8 occ:0.86 CO B:B121004 0.0 49.8 0.9 N24 B:B121004 1.9 39.3 0.3 N21 B:B121004 1.9 44.4 0.6 N23 B:B121004 1.9 46.9 0.5 N22 B:B121004 1.9 52.0 0.8 N3B B:B121004 2.2 57.1 1.0 C5' B:5AD1005 2.6 59.0 0.9 C19 B:B121004 2.8 40.0 0.6 C11 B:B121004 2.9 50.9 0.8 C9 B:B121004 2.9 58.1 0.6 C4 B:B121004 2.9 46.1 1.0 C16 B:B121004 2.9 38.4 1.0 C1 B:B121004 2.9 41.5 0.7 C14 B:B121004 3.0 44.7 0.8 C6 B:B121004 3.0 52.3 0.7 C2B B:B121004 3.1 59.0 0.8 C10 B:B121004 3.2 55.2 0.8 C9B B:B121004 3.3 63.6 0.8 C5 B:B121004 3.4 51.4 0.8 C15 B:B121004 3.4 40.4 0.6 C4' B:5AD1005 3.6 62.6 1.0 C20 B:B121004 3.7 51.1 1.0 C4B B:B121004 3.8 66.2 1.0 O4' B:5AD1005 3.9 67.5 0.8 C2 B:B121004 4.1 35.9 0.7 C18 B:B121004 4.2 36.8 0.9 C8 B:B121004 4.2 62.0 0.8 C3 B:B121004 4.2 38.3 1.0 C12 B:B121004 4.2 48.3 0.8 C17 B:B121004 4.2 47.5 0.7 C13 B:B121004 4.2 47.1 0.8 C7 B:B121004 4.3 54.7 0.8 N1B B:B121004 4.4 57.7 0.8 C8B B:B121004 4.4 61.5 0.7 C26 B:B121004 4.5 35.1 0.8 C35 B:B121004 4.9 54.9 0.8 C37 B:B121004 4.9 70.2 1.0 C3' B:5AD1005 4.9 62.2 1.0 C53 B:B121004 4.9 27.4 0.7 C41 B:B121004 5.0 65.2 1.0 C54 B:B121004 5.0 52.8 1.0

K.M.Larsson, D.T.Logan, P.Nordlund. Structural Basis For Adenosylcobalamin Activation in Adocbl-Dependent Ribonucleotide Reductases. Acs Chem.Biol. V. 5 933 2010.
ISSN: ISSN 1554-8929
PubMed: 20672854
DOI: 10.1021/CB1000845