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

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

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Dudp, PDB code: 3fcv 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)	29.23 / 2.40
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.407, 70.407, 104.846, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Dudp (pdb code 3fcv). 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 Dudp, PDB code: 3fcv:
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 Dudp


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 Dudp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:25.7 occ:1.00 O1A A:DUD201 2.8 18.2 1.0 O A:HOH193 2.8 18.1 1.0 O A:HOH198 2.8 24.6 1.0 O1B A:DUD201 3.0 17.1 1.0 OD2 A:ASP119 3.0 27.2 1.0 O A:HOH197 3.5 20.8 1.0 CG A:ASP119 3.9 22.9 1.0 PA A:DUD201 4.1 18.1 1.0 CB A:ASP119 4.3 18.9 1.0 PB A:DUD201 4.4 15.7 1.0 NH1 A:ARG86 4.5 16.1 1.0 O A:HOH151 4.7 13.6 1.0 O2A A:DUD201 4.7 16.3 1.0 NE2 A:HIS53 4.8 19.4 1.0 NH2 A:ARG86 4.8 17.0 1.0 O A:HOH175 4.8 17.6 1.0 O3A A:DUD201 4.8 17.5 1.0 OD1 A:ASP119 4.9 21.4 1.0 CZ A:ARG86 4.9 16.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Dudp


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 Dudp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:23.6 occ:1.00 O B:HOH188 2.9 19.3 1.0 O B:HOH156 2.9 16.9 1.0 O1A B:DUD201 3.1 17.9 1.0 NE2 B:HIS53 3.2 18.1 1.0 CD2 B:TYR50 3.9 18.9 1.0 CE2 B:TYR50 3.9 18.7 1.0 O B:HOH172 4.0 18.3 1.0 CD2 B:HIS53 4.0 20.2 1.0 O B:HOH160 4.0 17.4 1.0 CE1 B:HIS116 4.2 16.6 1.0 CE1 B:HIS53 4.3 18.9 1.0 C5' B:DUD201 4.3 17.5 1.0 PA B:DUD201 4.5 16.8 1.0 O1B B:DUD201 4.6 18.2 1.0 ND1 B:HIS116 4.7 16.9 1.0 OE2 B:GLU127 4.8 17.5 1.0 O5' B:DUD201 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