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

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

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Dcdp, PDB code: 3evm 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 / 1.80
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.323, 70.323, 104.207, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.8

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


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 Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.5 occ:1.00 O2A A:YYY201 2.3 9.5 1.0 O3B A:YYY201 2.4 8.1 1.0 O A:HOH204 2.4 13.7 1.0 O A:HOH210 2.7 19.5 1.0 PA A:YYY201 3.6 10.8 1.0 PB A:YYY201 3.6 9.0 1.0 O A:HOH209 3.9 25.3 1.0 O3A A:YYY201 3.9 11.2 1.0 O A:HOH158 3.9 8.8 1.0 O A:HOH189 4.0 14.4 1.0 O2B A:YYY201 4.2 10.0 1.0 NH1 A:ARG86 4.2 7.3 1.0 OD2 A:ASP119 4.3 24.9 1.0 CE1 A:HIS116 4.3 10.3 1.0 O5' A:YYY201 4.7 12.8 1.0 C5' A:YYY201 4.7 10.6 1.0 ND1 A:HIS116 4.7 9.2 1.0 CG A:ASP119 4.7 18.6 1.0 O1A A:YYY201 4.7 12.3 1.0 NE2 A:HIS53 4.7 15.0 1.0 O A:HOH196 4.7 6.8 1.0 CB A:ASP119 4.8 14.8 1.0 NH2 A:ARG86 4.8 10.1 1.0 O A:HOH227 4.8 12.7 1.0 CZ A:ARG86 4.8 12.4 1.0 O A:ALA117 4.8 8.5 1.0 O1B A:YYY201 4.8 7.7 1.0

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


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 Dcdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:24.4 occ:1.00 O2A B:YYY201 2.3 10.1 1.0 O B:HOH197 2.4 10.6 1.0 O3B B:YYY201 2.5 12.9 1.0 O B:HOH213 2.6 19.2 1.0 PA B:YYY201 3.6 13.2 1.0 O B:HOH155 3.6 24.2 1.0 PB B:YYY201 3.7 11.0 1.0 O B:HOH163 3.8 9.5 1.0 O3A B:YYY201 3.9 14.5 1.0 O2B B:YYY201 4.1 14.3 1.0 O B:HOH236 4.2 17.2 1.0 CE1 B:HIS116 4.2 9.5 1.0 OD2 B:ASP119 4.2 28.2 1.0 NH1 B:ARG86 4.4 12.6 1.0 C5' B:YYY201 4.5 11.4 1.0 NE2 B:HIS53 4.5 13.7 1.0 O5' B:YYY201 4.6 12.5 1.0 ND1 B:HIS116 4.6 8.4 1.0 O B:HOH186 4.6 14.0 1.0 O1A B:YYY201 4.7 12.3 1.0 CG B:ASP119 4.8 17.4 1.0 O B:HOH148 4.8 7.4 1.0 NH2 B:ARG86 4.9 12.7 1.0 CB B:ASP119 4.9 14.7 1.0 O1B B:YYY201 4.9 8.4 1.0 CE1 B:HIS53 4.9 11.5 1.0 O B:ALA117 4.9 10.4 1.0 CZ B:ARG86 5.0 14.1 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