Magnesium in PDB 1lwx: Azt Diphosphate Binding to Nucleoside Diphosphate Kinase

All present enzymatic activity of Azt Diphosphate Binding to Nucleoside Diphosphate Kinase:
2.7.4.6;

The structure of Azt Diphosphate Binding to Nucleoside Diphosphate Kinase, PDB code: 1lwx was solved by J.Janin, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.590, 71.590, 152.700, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 28

The binding sites of Magnesium atom in the Azt Diphosphate Binding to Nucleoside Diphosphate Kinase (pdb code 1lwx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Azt Diphosphate Binding to Nucleoside Diphosphate Kinase, PDB code: 1lwx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Azt Diphosphate Binding to Nucleoside Diphosphate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Azt Diphosphate Binding to Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg157 b:26.8 occ:1.00 O A:HOH283 1.9 21.9 1.0 O A:HOH282 2.0 28.2 1.0 O1A A:AZD156 2.5 25.5 1.0 O1B A:AZD156 2.5 32.2 1.0 PB A:AZD156 3.6 26.6 1.0 NH2 A:ARG92 3.7 24.5 1.0 PA A:AZD156 3.7 23.2 1.0 O3B A:AZD156 3.8 30.6 1.0 OE2 A:GLU58 4.0 37.0 1.0 O3A A:AZD156 4.0 31.6 1.0 C5' A:AZD156 4.2 21.1 1.0 ND1 A:HIS122 4.3 11.8 1.0 OD2 A:ASP125 4.3 29.7 1.0 O5' A:AZD156 4.4 23.9 1.0 CE1 A:HIS122 4.4 11.8 1.0 NE2 A:HIS59 4.4 26.2 1.0 CE1 A:TYR56 4.8 25.9 1.0 CZ A:ARG92 4.8 23.2 1.0 O2B A:AZD156 4.9 25.4 1.0 CD A:GLU58 4.9 39.1 1.0 O A:GLY123 4.9 11.3 1.0 O2A A:AZD156 5.0 30.4 1.0

Magnesium binding site 2 out of 2 in the Azt Diphosphate Binding to Nucleoside Diphosphate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Azt Diphosphate Binding to Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg157 b:33.3 occ:1.00 O C:HOH231 2.2 21.9 1.0 O C:HOH281 2.3 41.7 1.0 O1B C:AZD156 2.6 24.9 1.0 O1A C:AZD156 2.8 28.5 1.0 PB C:AZD156 3.6 21.5 1.0 O3B C:AZD156 3.6 23.6 1.0 CE1 C:HIS122 3.7 2.0 1.0 ND1 C:HIS122 3.8 9.9 1.0 PA C:AZD156 4.0 25.1 1.0 O3A C:AZD156 4.1 24.9 1.0 O C:GLY123 4.1 16.4 1.0 C5' C:AZD156 4.2 30.5 1.0 NH1 C:ARG92 4.3 21.4 1.0 OE2 C:GLU58 4.4 68.5 1.0 OD2 C:ASP125 4.5 23.7 1.0 CE1 C:TYR56 4.6 35.9 1.0 O C:HOH201 4.6 12.2 1.0 O5' C:AZD156 4.7 28.8 1.0 O2B C:AZD156 4.9 19.5 1.0 NE2 C:HIS122 4.9 10.2 1.0 NE2 C:HIS59 4.9 59.3 1.0

Y.Xu, O.Sellam, S.Morera, S.Sarfati, R.Biondi, M.Veron, J.Janin. X-Ray Analysis of Azido-Thymidine Diphosphate Binding to Nucleoside Diphosphate Kinase. Proc.Natl.Acad.Sci.Usa V. 94 7162 1997.
ISSN: ISSN 0027-8424
PubMed: 9207061
DOI: 10.1073/PNAS.94.14.7162