Magnesium in PDB 3o0q: Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosine

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

The structure of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosine, PDB code: 3o0q 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)	23.12 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.120, 124.380, 106.820, 90.00, 103.43, 90.00
R / Rfree (%)	17.6 / 21

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

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosine (pdb code 3o0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosine, PDB code: 3o0q:
Jump to Magnesium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:27.8 occ:1.00 O1A A:TTP1001 2.1 22.3 1.0 O2B A:TTP1001 2.2 25.4 1.0 O2G A:TTP1001 2.3 27.3 1.0 O A:HOH705 2.3 24.1 1.0 O A:HOH706 2.4 29.4 1.0 O A:HOH707 2.4 22.2 1.0 PB A:TTP1001 3.2 24.9 1.0 PG A:TTP1001 3.3 27.1 1.0 PA A:TTP1001 3.3 21.2 1.0 O3G A:TTP1001 3.6 27.4 1.0 O3A A:TTP1001 3.6 22.0 1.0 O3B A:TTP1001 3.7 27.1 1.0 O A:HOH830 4.1 48.1 1.0 O A:HOH680 4.2 36.7 1.0 NH2 A:ARG171 4.3 22.4 1.0 O A:ASP141 4.3 21.6 1.0 CB A:SER142 4.3 21.1 1.0 O2A A:TTP1001 4.3 19.8 1.0 C5' A:TTP1001 4.4 20.7 1.0 O5' A:TTP1001 4.4 21.0 1.0 O A:HOH708 4.5 36.2 1.0 O1B A:TTP1001 4.5 24.8 1.0 O1G A:TTP1001 4.7 21.9 1.0 CA A:SER142 4.9 17.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermotoga Maritima Ribonucleotide Reductase, Nrdj, in Complex with Dttp, Gdp and Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:46.3 occ:1.00 O1A B:TTP1001 2.4 25.5 1.0 O2B B:TTP1001 2.4 44.6 1.0 O B:HOH703 2.9 37.5 1.0 O B:HOH704 2.9 59.2 1.0 O2G B:TTP1001 3.5 46.4 1.0 PA B:TTP1001 3.7 25.2 1.0 CB B:SER142 3.8 21.2 1.0 PB B:TTP1001 3.8 45.1 1.0 O2A B:TTP1001 4.2 22.2 1.0 O3A B:TTP1001 4.3 24.0 1.0 PG B:TTP1001 4.4 40.4 1.0 O3G B:TTP1001 4.5 39.1 1.0 O B:ASP141 4.6 20.1 1.0 O3B B:TTP1001 4.6 36.3 1.0 CA B:SER142 4.7 20.1 1.0 O B:HOH931 4.8 41.6 1.0 O1B B:TTP1001 4.8 42.0 1.0 OG B:SER142 4.8 25.6 1.0 O B:HOH837 4.9 25.8 1.0 NZ A:LYS158 5.0 33.2 1.0 O5' B:TTP1001 5.0 22.7 1.0 O B:HOH952 5.0 32.1 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