Atomistry » Magnesium » PDB 1lnz-1mez » 1lwx
Atomistry »
  Magnesium »
    PDB 1lnz-1mez »
      1lwx »

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

Enzymatic activity of Azt Diphosphate Binding to Nucleoside Diphosphate Kinase

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

Protein crystallography data

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

Magnesium Binding Sites:

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 1lwx

Go back to Magnesium Binding Sites List in 1lwx
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 1lwx

Go back to Magnesium Binding Sites List in 1lwx
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

Reference:

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
Page generated: Tue Aug 13 08:35:39 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy