Magnesium in PDB 3dkd: Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Gdp

All present enzymatic activity of Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Gdp:
2.7.4.6;

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Gdp, PDB code: 3dkd 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)	30.00 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.070, 70.070, 103.221, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.6

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Gdp (pdb code 3dkd). 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-N62L-R107G Triple Mutant Complexed with Gdp, PDB code: 3dkd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple 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-N62L-R107G Triple Mutant Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg142 b:25.5 occ:1.00 O A:HOH174 2.2 20.6 1.0 O1B A:GDP143 2.3 12.0 1.0 O1A A:GDP143 2.6 13.2 1.0 O A:HOH150 2.6 21.0 1.0 PB A:GDP143 3.6 10.8 1.0 O A:HOH149 3.7 15.8 1.0 PA A:GDP143 3.8 12.3 1.0 NH1 A:ARG86 3.9 15.2 1.0 O A:HOH172 4.0 17.6 1.0 O3A A:GDP143 4.0 11.1 1.0 CE1 A:HIS116 4.2 13.2 1.0 O3B A:GDP143 4.3 12.1 1.0 OD2 A:ASP119 4.4 24.1 1.0 NH2 A:ARG86 4.5 15.7 1.0 CZ A:ARG86 4.5 14.7 1.0 ND1 A:HIS116 4.5 12.5 1.0 O A:HOH224 4.5 35.7 1.0 CB A:ASP119 4.6 19.6 1.0 O A:ALA117 4.6 14.3 1.0 CG A:ASP119 4.6 20.8 1.0 O A:HOH176 4.7 12.7 1.0 O2B A:GDP143 4.7 11.9 1.0 O2A A:GDP143 4.8 13.8 1.0 O A:HOH182 4.8 20.8 1.0 C5' A:GDP143 4.9 12.7 1.0 O5' A:GDP143 4.9 11.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple 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-N62L-R107G Triple Mutant Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg142 b:29.1 occ:1.00 O B:HOH202 2.0 17.2 1.0 O1B B:GDP143 2.2 12.0 1.0 O1A B:GDP143 2.4 13.2 1.0 PB B:GDP143 3.5 10.8 1.0 PA B:GDP143 3.6 12.3 1.0 O B:HOH206 3.7 20.0 1.0 O3A B:GDP143 3.8 11.1 1.0 NH1 B:ARG86 3.9 17.7 1.0 O B:HOH229 4.1 21.8 1.0 CE1 B:HIS116 4.2 12.7 1.0 O3B B:GDP143 4.2 12.1 1.0 OD2 B:ASP119 4.2 23.2 1.0 ND1 B:HIS116 4.5 12.2 1.0 CZ B:ARG86 4.5 16.8 1.0 NH2 B:ARG86 4.6 17.6 1.0 O2A B:GDP143 4.6 13.8 1.0 O2B B:GDP143 4.6 11.9 1.0 O B:ALA117 4.7 14.1 1.0 CB B:ASP119 4.7 19.8 1.0 O B:HOH201 4.7 12.8 1.0 O5' B:GDP143 4.7 11.7 1.0 C5' B:GDP143 4.7 12.7 1.0 CG B:ASP119 4.7 20.4 1.0 O B:HOH208 4.9 18.6 1.0 OE2 B:GLU52 5.0 26.8 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