Magnesium in PDB 1ndp: Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase

All present enzymatic activity of Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase:
2.7.4.6;

The structure of Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase, PDB code: 1ndp was solved by J.Janin, S.Morera, C.Dumas, I.Lascu, G.Lebras, M.Veron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	73.180, 73.180, 158.450, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase (pdb code 1ndp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase, PDB code: 1ndp:

Magnesium binding site 1 out of 1 in the Adenosine 5'-Diphosphate Binding and the Active Site of 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 Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg161 b:16.2 occ:1.00 O B:HOH218 2.0 18.9 1.0 O B:HOH204 2.0 10.1 1.0 O1A B:ADP160 2.0 14.2 1.0 O B:HOH244 2.1 27.9 1.0 O B:HOH220 2.1 20.3 1.0 O1B B:ADP160 2.3 11.0 1.0 PA B:ADP160 3.3 11.5 1.0 PB B:ADP160 3.4 14.2 1.0 O B:HOH187 3.5 11.4 1.0 O3A B:ADP160 3.5 15.8 1.0 O2A B:ADP160 4.0 14.1 1.0 OE2 B:GLU58 4.0 27.4 1.0 NE2 B:HIS59 4.1 5.6 1.0 NH1 B:ARG92 4.1 11.6 1.0 O B:HOH198 4.2 17.4 1.0 NH2 B:ARG92 4.2 15.7 1.0 O3B B:ADP160 4.3 13.1 1.0 OD2 B:ASP125 4.3 24.9 1.0 O5' B:ADP160 4.4 9.0 1.0 O2B B:ADP160 4.6 17.4 1.0 CZ B:ARG92 4.6 25.8 1.0 CE1 B:HIS59 4.6 5.0 1.0 C5' B:ADP160 4.6 6.3 1.0 O B:HOH210 4.7 10.2 1.0 CD B:GLU58 4.9 29.1 1.0 O B:HOH206 5.0 16.6 1.0

S.Morera, I.Lascu, C.Dumas, G.Lebras, P.Briozzo, M.Veron, J.Janin. Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase. Biochemistry V. 33 459 1994.
ISSN: ISSN 0006-2960
PubMed: 8286376
DOI: 10.1021/BI00168A010