Magnesium in PDB 3ejm: Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp:
2.7.4.6;

The structure of Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp, PDB code: 3ejm was solved by S.Jeudy, A.Lartigue, J.M.Claverie, C.Abergel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.96 / 1.95
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.153, 70.153, 104.937, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp (pdb code 3ejm). 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 Mimivirus Ndk +Kpn Mutant Complexed with Gdp, PDB code: 3ejm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp


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 Mimivirus Ndk +Kpn Mutant Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:37.5 occ:1.00 O1A A:GDP201 2.3 32.5 1.0 O A:HOH308 2.4 27.7 1.0 O1B A:GDP201 2.4 28.4 1.0 O A:HOH240 2.6 31.1 1.0 PA A:GDP201 3.6 31.5 1.0 PB A:GDP201 3.6 30.1 1.0 O3A A:GDP201 3.9 30.9 1.0 O A:HOH214 4.0 21.1 1.0 OD2 A:ASP119 4.0 36.2 1.0 O A:HOH230 4.0 25.3 1.0 NH1 A:ARG86 4.2 24.2 1.0 O3B A:GDP201 4.2 29.1 1.0 CE1 A:HIS116 4.3 23.4 1.0 C5' A:GDP201 4.5 30.0 1.0 O5' A:GDP201 4.6 30.7 1.0 CG A:ASP119 4.6 33.3 1.0 O2A A:GDP201 4.6 33.6 1.0 NE2 A:HIS53 4.6 30.4 1.0 ND1 A:HIS116 4.7 20.7 1.0 NH2 A:ARG86 4.7 24.9 1.0 CB A:ASP119 4.7 29.7 1.0 O A:HOH251 4.7 25.8 1.0 CZ A:ARG86 4.8 23.7 1.0 O2B A:GDP201 4.8 29.4 1.0 O A:HOH234 4.9 20.7 1.0 O A:ALA117 5.0 21.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn Mutant Complexed with Gdp


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 Mimivirus Ndk +Kpn Mutant Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:37.3 occ:1.00 O B:HOH322 2.4 23.4 1.0 O1A B:GDP202 2.4 23.3 1.0 O1B B:GDP202 2.5 24.6 1.0 O B:HOH306 2.7 34.5 1.0 O B:HOH279 3.5 38.1 1.0 PA B:GDP202 3.6 28.6 1.0 PB B:GDP202 3.7 23.9 1.0 O B:HOH213 3.9 21.3 1.0 O3A B:GDP202 4.0 29.2 1.0 OD2 B:ASP119 4.0 32.2 1.0 NH1 B:ARG86 4.1 22.5 1.0 O B:HOH256 4.2 24.2 1.0 CE1 B:HIS116 4.3 20.2 1.0 O3B B:GDP202 4.3 22.9 1.0 CG B:ASP119 4.5 29.0 1.0 NH2 B:ARG86 4.6 25.5 1.0 O2A B:GDP202 4.6 31.7 1.0 CZ B:ARG86 4.7 26.5 1.0 CB B:ASP119 4.7 27.4 1.0 C5' B:GDP202 4.7 29.9 1.0 ND1 B:HIS116 4.7 18.4 1.0 O5' B:GDP202 4.7 28.5 1.0 NE2 B:HIS53 4.8 28.1 1.0 O B:HOH224 4.8 24.7 1.0 O2B B:GDP202 4.9 22.3 1.0 O B:ALA117 4.9 18.5 1.0

S.Jeudy, A.Lartigue, J.M.Claverie, C.Abergel. Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase. J.Virol. V. 83 7142 2009.
ISSN: ISSN 0022-538X
PubMed: 19439473
DOI: 10.1128/JVI.00511-09