Magnesium in PDB 3emt: Crystal Structure of the Mimivirus Ndk +Kpn-R107G Double Mutant Complexed with Dgdp

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

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-R107G Double Mutant Complexed with Dgdp, PDB code: 3emt 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)	60.81 / 1.60
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.212, 70.212, 104.668, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 19.7

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

Magnesium binding site 1 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn-R107G Double Mutant Complexed with Dgdp


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-R107G Double Mutant Complexed with Dgdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:20.7 occ:1.00 O2A A:DGI201 2.2 20.3 1.0 O2B A:DGI201 2.2 16.5 1.0 O A:HOH233 2.4 21.1 1.0 O A:HOH236 2.7 27.0 1.0 PB A:DGI201 3.6 13.9 1.0 PA A:DGI201 3.6 15.4 1.0 O3A A:DGI201 3.9 11.8 1.0 O A:HOH213 3.9 12.4 1.0 O A:HOH226 4.0 16.9 1.0 NH1 A:ARG86 4.1 12.7 1.0 OD2 A:ASP119 4.1 28.9 1.0 O3B A:DGI201 4.3 14.9 1.0 CE1 A:HIS116 4.4 13.4 1.0 NH2 A:ARG86 4.6 13.8 1.0 CG A:ASP119 4.6 21.3 1.0 CB A:ASP119 4.6 16.2 1.0 C5' A:DGI201 4.6 15.2 1.0 O1A A:DGI201 4.6 17.1 1.0 CZ A:ARG86 4.7 10.8 1.0 O5' A:DGI201 4.7 12.8 1.0 ND1 A:HIS116 4.8 12.3 1.0 O A:HOH245 4.8 19.1 1.0 O1B A:DGI201 4.8 12.8 1.0 O A:ALA117 4.9 12.3 1.0 O A:HOH229 4.9 12.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn-R107G Double Mutant Complexed with Dgdp


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-R107G Double Mutant Complexed with Dgdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:21.0 occ:1.00 O1A B:DGI201 2.2 18.7 1.0 O2B B:DGI201 2.3 15.9 1.0 O B:HOH224 2.4 17.3 1.0 O B:HOH269 2.7 29.4 1.0 PA B:DGI201 3.5 14.9 1.0 PB B:DGI201 3.5 14.3 1.0 O B:HOH256 3.5 27.6 1.0 O3A B:DGI201 3.8 12.6 1.0 O B:HOH211 3.9 13.7 1.0 NH1 B:ARG86 4.1 14.9 1.0 O B:HOH244 4.2 15.6 1.0 O1B B:DGI201 4.2 11.6 1.0 OD2 B:ASP119 4.3 27.2 1.0 CE1 B:HIS116 4.4 10.7 1.0 O B:HOH289 4.5 28.5 1.0 C5' B:DGI201 4.6 13.6 1.0 O5' B:DGI201 4.6 13.6 1.0 NH2 B:ARG86 4.6 18.1 1.0 CZ B:ARG86 4.7 13.4 1.0 O2A B:DGI201 4.7 21.3 1.0 CB B:ASP119 4.7 15.8 1.0 ND1 B:HIS116 4.7 11.2 1.0 CG B:ASP119 4.7 21.8 1.0 O B:HOH221 4.8 18.5 1.0 O B:HOH205 4.8 12.4 1.0 NE2 B:HIS53 4.9 17.5 1.0 O3B B:DGI201 4.9 13.6 1.0 O B:ALA117 4.9 11.5 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