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

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

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Cdp, PDB code: 3etm 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 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.325, 70.325, 104.279, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.8

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


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 Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.5 occ:1.00 O2A A:CDP201 2.4 12.9 1.0 O A:HOH200 2.4 16.5 1.0 O1B A:CDP201 2.5 10.4 1.0 O A:HOH205 2.7 24.4 1.0 PA A:CDP201 3.6 12.8 1.0 PB A:CDP201 3.7 11.2 1.0 O A:HOH187 3.9 16.9 1.0 O A:HOH161 3.9 12.2 1.0 O3A A:CDP201 4.0 12.1 1.0 OD2 A:ASP119 4.1 23.4 1.0 O A:HOH217 4.2 35.8 1.0 O3B A:CDP201 4.3 14.0 1.0 CE1 A:HIS116 4.3 13.1 1.0 NH1 A:ARG86 4.3 12.1 1.0 CG A:ASP119 4.5 19.5 1.0 CB A:ASP119 4.6 13.3 1.0 O A:HOH229 4.6 12.8 1.0 O1A A:CDP201 4.6 14.9 1.0 NH2 A:ARG86 4.7 9.3 1.0 ND1 A:HIS116 4.7 8.2 1.0 O5' A:CDP201 4.7 14.2 1.0 CZ A:ARG86 4.8 13.6 1.0 NE2 A:HIS53 4.8 15.2 1.0 O A:ALA117 4.9 11.4 1.0 O A:HOH192 4.9 9.0 1.0 O2B A:CDP201 4.9 12.8 1.0

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


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 Cdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:24.2 occ:1.00 O2A B:CDP201 2.3 13.6 1.0 O B:HOH203 2.4 13.5 1.0 O B:HOH221 2.6 15.7 1.0 O1B B:CDP201 2.6 14.4 1.0 PA B:CDP201 3.6 15.3 1.0 PB B:CDP201 3.7 12.8 1.0 O B:HOH155 3.8 27.0 1.0 O B:HOH160 3.9 10.8 1.0 O3A B:CDP201 4.0 15.2 1.0 O5' B:CDP201 4.0 15.2 1.0 CE1 B:HIS116 4.1 8.4 1.0 O3B B:CDP201 4.1 12.8 1.0 O B:HOH253 4.2 13.2 1.0 OD2 B:ASP119 4.2 22.8 1.0 ND1 B:HIS116 4.4 7.7 1.0 NH1 B:ARG86 4.5 13.4 1.0 NE2 B:HIS53 4.6 13.7 1.0 O B:HOH177 4.6 12.2 1.0 CG B:ASP119 4.7 18.7 1.0 O B:HOH145 4.7 9.0 1.0 O B:HOH156 4.8 25.2 1.0 O1A B:CDP201 4.8 17.9 1.0 CB B:ASP119 4.9 15.7 1.0 O B:ALA117 4.9 11.1 1.0 NH2 B:ARG86 5.0 12.8 1.0 O2B B:CDP201 5.0 12.0 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