Magnesium in PDB 5im3: Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp

All present enzymatic activity of Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp:
1.17.4.1;

The structure of Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp, PDB code: 5im3 was solved by R.Johansson, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	267.465, 62.577, 173.761, 90.00, 127.81, 90.00
R / Rfree (%)	18.6 / 21.7

The binding sites of Magnesium atom in the Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp (pdb code 5im3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp, PDB code: 5im3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:81.9 occ:0.49 O1G A:DTP1002 1.8 80.8 0.9 O2G A:DTP1001 1.8 86.1 1.0 O2A A:DTP1001 1.8 85.3 1.0 O2A A:DTP1002 2.0 79.8 0.9 O1B A:DTP1002 2.1 79.3 0.9 O1B A:DTP1001 2.2 89.0 1.0 PG A:DTP1002 3.0 79.9 0.9 PB A:DTP1002 3.0 75.5 0.9 PA A:DTP1001 3.1 88.5 1.0 PA A:DTP1002 3.2 76.4 0.9 PG A:DTP1001 3.2 89.8 1.0 PB A:DTP1001 3.2 89.0 1.0 O3B A:DTP1002 3.3 79.9 0.9 O3A A:DTP1002 3.4 76.5 0.9 O3A A:DTP1001 3.5 89.7 1.0 O3B A:DTP1001 3.5 88.0 1.0 O5' A:DTP1001 3.5 88.7 1.0 NH1 A:ARG37 3.7 96.9 1.0 O5' A:DTP1002 3.8 73.2 0.9 O3G A:DTP1001 3.8 92.7 1.0 O3G A:DTP1002 4.0 82.3 0.9 O2G A:DTP1002 4.1 79.1 0.9 O1G A:DTP1001 4.3 88.7 1.0 O1A A:DTP1001 4.3 88.6 1.0 O2B A:DTP1002 4.4 77.2 0.9 O1A A:DTP1002 4.4 75.1 0.9 O2B A:DTP1001 4.5 88.9 1.0 CZ A:ARG37 4.9 95.5 1.0 C5' A:DTP1001 4.9 91.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Class I Ribonucleotide Reductase From Pseudomonas Aeruginosa in Complex with Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:63.8 occ:1.00 O3G B:DTP1002 1.8 65.5 1.0 O1A B:DTP1001 1.8 68.7 1.0 O2G B:DTP1001 1.8 67.8 1.0 O2A B:DTP1002 2.1 64.7 1.0 O1B B:DTP1002 2.1 64.3 1.0 O1B B:DTP1001 2.4 70.7 1.0 PA B:DTP1001 3.1 68.7 1.0 PA B:DTP1002 3.1 60.7 1.0 O5' B:DTP1002 3.1 62.5 1.0 PB B:DTP1002 3.2 61.3 1.0 PG B:DTP1002 3.2 65.8 1.0 PG B:DTP1001 3.3 69.2 1.0 PB B:DTP1001 3.4 68.9 1.0 O3A B:DTP1002 3.4 63.5 1.0 O3B B:DTP1002 3.5 64.7 1.0 O5' B:DTP1001 3.6 66.9 1.0 O3A B:DTP1001 3.7 67.6 1.0 O3B B:DTP1001 3.7 71.9 1.0 O1G B:DTP1002 4.0 66.0 1.0 O3G B:DTP1001 4.1 69.0 1.0 NH1 B:ARG37 4.1 67.6 1.0 O2G B:DTP1002 4.2 64.6 1.0 O1G B:DTP1001 4.2 68.6 1.0 O2A B:DTP1001 4.3 67.0 1.0 O1A B:DTP1002 4.4 66.6 1.0 C5' B:DTP1002 4.5 58.6 1.0 O2B B:DTP1002 4.5 61.8 1.0 NH2 B:ARG37 4.6 65.3 1.0 O2B B:DTP1001 4.7 71.6 1.0 C5' B:DTP1001 4.8 65.6 1.0 CZ B:ARG37 4.9 66.6 1.0

R.Johansson, V.R.Jonna, R.Kumar, N.Nayeri, D.Lundin, B.M.Sjoberg, A.Hofer, D.T.Logan. Structural Mechanism of Allosteric Activity Regulation in A Ribonucleotide Reductase with Double Atp Cones. Structure V. 24 906 2016.
ISSN: ISSN 0969-2126
PubMed: 27133024
DOI: 10.1016/J.STR.2016.03.025