Magnesium in PDB 3em1: Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp

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

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp, PDB code: 3em1 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 / 1.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.343, 70.343, 104.137, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp (pdb code 3em1). 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 Double Mutant Complexed with Dtdp, PDB code: 3em1:
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 Double Mutant Complexed with Dtdp


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 Double Mutant Complexed with Dtdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg142 b:26.3 occ:1.00 O2B A:TYD143 2.3 14.9 1.0 O2A A:TYD143 2.3 15.1 1.0 O A:HOH177 2.4 20.9 1.0 O A:HOH180 2.7 23.7 1.0 PB A:TYD143 3.5 12.2 1.0 PA A:TYD143 3.6 13.9 1.0 O3A A:TYD143 3.8 12.7 1.0 O A:HOH251 3.8 31.7 1.0 O A:HOH154 3.9 12.8 1.0 O1B A:TYD143 4.1 13.3 1.0 O A:HOH169 4.1 18.6 1.0 NH1 A:ARG86 4.2 14.4 1.0 CE1 A:HIS116 4.3 14.7 1.0 OD2 A:ASP119 4.5 33.8 1.0 C5' A:TYD143 4.5 14.1 1.0 O5' A:TYD143 4.5 13.3 1.0 NE2 A:HIS53 4.7 21.0 1.0 ND1 A:HIS116 4.7 12.6 1.0 O1A A:TYD143 4.7 17.4 1.0 O A:HOH191 4.7 17.4 1.0 O A:HOH173 4.8 14.3 1.0 O3B A:TYD143 4.8 14.2 1.0 NH2 A:ARG86 4.8 16.9 1.0 CZ A:ARG86 4.8 14.2 1.0 CG A:ASP119 4.9 26.2 1.0 CB A:ASP119 4.9 20.5 1.0 O A:ALA117 5.0 14.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mimivirus Ndk +Kpn-N62L Double Mutant Complexed with Dtdp


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 Double Mutant Complexed with Dtdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg142 b:25.7 occ:1.00 O2A B:TYD143 2.3 15.2 1.0 O2B B:TYD143 2.3 17.1 1.0 O B:HOH353 2.4 32.2 1.0 O B:HOH258 2.4 18.7 1.0 O B:HOH343 2.6 24.1 1.0 PA B:TYD143 3.5 15.0 1.0 O B:HOH304 3.5 28.2 1.0 PB B:TYD143 3.5 14.0 1.0 O3A B:TYD143 3.8 14.0 1.0 O B:HOH240 3.9 14.7 1.0 O1B B:TYD143 4.1 14.1 1.0 NH1 B:ARG86 4.2 15.6 1.0 O B:HOH284 4.3 17.7 1.0 CE1 B:HIS116 4.4 12.5 1.0 C5' B:TYD143 4.4 14.1 1.0 OD2 B:ASP119 4.5 29.8 1.0 O5' B:TYD143 4.5 13.7 1.0 NE2 B:HIS53 4.6 18.3 1.0 O1A B:TYD143 4.6 18.1 1.0 O B:HOH351 4.6 31.9 1.0 ND1 B:HIS116 4.7 12.8 1.0 NH2 B:ARG86 4.8 20.6 1.0 O B:HOH350 4.8 27.5 1.0 O3B B:TYD143 4.8 14.9 1.0 O B:HOH235 4.8 13.3 1.0 O B:HOH253 4.8 15.4 1.0 CZ B:ARG86 4.8 15.5 1.0 CG B:ASP119 4.9 24.4 1.0 CB B:ASP119 4.9 20.8 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