Magnesium in PDB 1nue: X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution

All present enzymatic activity of X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution:
2.7.4.6;

The structure of X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution, PDB code: 1nue was solved by S.Morera, M.-L.Lacombe, X.Yingwu, G.Lebras, J.Janin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.030, 87.370, 162.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / n/a

The binding sites of Magnesium atom in the X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution (pdb code 1nue). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution, PDB code: 1nue:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg161 b:40.9 occ:1.00 O A:HOH218 2.0 48.4 1.0 O A:HOH190 2.0 37.5 1.0 O1A A:GDP160 2.1 25.9 1.0 O A:HOH172 2.1 28.1 1.0 O A:HOH167 2.4 34.5 1.0 O A:HOH210 2.5 33.8 1.0 O1B A:GDP160 3.3 17.2 1.0 PA A:GDP160 3.6 24.1 1.0 OD2 A:ASP121 4.0 32.9 1.0 O A:HOH201 4.3 23.4 1.0 OD2 A:ASP54 4.3 43.1 1.0 O A:HOH163 4.3 10.7 1.0 O3A A:GDP160 4.3 23.7 1.0 PB A:GDP160 4.5 18.1 1.0 O5' A:GDP160 4.5 16.0 1.0 O2A A:GDP160 4.5 27.3 1.0 C5' A:GDP160 4.6 11.5 1.0 CG A:ASP121 4.7 23.4 1.0 CD1 A:LEU55 4.7 15.6 1.0 OD1 A:ASP54 4.9 41.0 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of NM23 Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg161 b:19.1 occ:1.00 O C:HOH199 1.9 15.5 1.0 O C:HOH214 1.9 18.6 1.0 O1A C:GDP160 2.0 13.7 1.0 O C:HOH193 2.0 13.9 1.0 O C:HOH173 2.2 25.9 1.0 O C:HOH195 2.3 15.7 1.0 PA C:GDP160 3.4 12.8 1.0 O1B C:GDP160 3.6 14.5 1.0 OD2 C:ASP54 4.1 26.1 1.0 OD2 C:ASP121 4.1 32.6 1.0 O C:HOH163 4.1 10.5 1.0 O2A C:GDP160 4.1 10.9 1.0 O C:HOH168 4.2 9.7 1.0 O3A C:GDP160 4.2 13.9 1.0 OD1 C:ASP54 4.3 23.7 1.0 O5' C:GDP160 4.5 12.0 1.0 PB C:GDP160 4.5 14.3 1.0 C5' C:GDP160 4.6 8.3 1.0 CD1 C:LEU55 4.7 10.3 1.0 CG C:ASP54 4.7 22.6 1.0 CG C:ASP121 4.8 23.5 1.0

S.Morera, M.L.Lacombe, Y.Xu, G.Lebras, J.Janin. X-Ray Structure of Human Nucleoside Diphosphate Kinase B Complexed with Gdp at 2 A Resolution. Structure V. 3 1307 1995.
ISSN: ISSN 0969-2126
PubMed: 8747457
DOI: 10.1016/S0969-2126(01)00268-4