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

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

The structure of Crystal Structure of the Mimivirus Ndk +Kpn-N62L-R107G Triple Mutant Complexed with Tdp, PDB code: 3ddi was solved by S.Jeudy, A.Lartigue, J.M.Claverie, A.Abergel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	70.084, 70.084, 103.313, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.8

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


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 Tdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg142 b:47.0 occ:1.00 O A:HOH236 2.6 25.6 1.0 O2B A:TYD201 2.6 26.3 1.0 O1A A:TYD201 2.7 28.2 1.0 O A:HOH206 3.6 20.4 1.0 OD2 A:ASP119 3.6 38.6 1.0 PB A:TYD201 4.0 24.2 1.0 O A:HOH213 4.0 18.1 1.0 CG A:ASP119 4.0 30.9 1.0 PA A:TYD201 4.1 28.0 1.0 NH1 A:ARG86 4.2 21.5 1.0 CB A:ASP119 4.2 25.0 1.0 CE1 A:HIS116 4.3 18.6 1.0 O3A A:TYD201 4.5 22.4 1.0 O1B A:TYD201 4.5 24.4 1.0 NH2 A:ARG86 4.6 21.9 1.0 CZ A:ARG86 4.6 26.0 1.0 O A:HOH229 4.6 20.0 1.0 ND1 A:HIS116 4.7 19.3 1.0 O A:ALA117 4.7 17.1 1.0 OD1 A:ASP119 4.8 27.5 1.0 NE2 A:HIS53 4.9 25.4 1.0 N A:ASP119 5.0 21.6 1.0

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


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 Tdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg142 b:33.6 occ:1.00 O1A B:TYD201 2.3 25.1 1.0 O B:HOH240 2.4 25.2 1.0 O B:HOH226 2.5 26.4 1.0 O2B B:TYD201 2.5 22.6 1.0 PA B:TYD201 3.7 26.4 1.0 PB B:TYD201 3.7 24.4 1.0 O B:HOH214 4.1 20.5 1.0 O3A B:TYD201 4.1 28.1 1.0 O B:HOH223 4.1 23.1 1.0 OD2 B:ASP119 4.1 32.6 1.0 CE1 B:HIS116 4.2 20.0 1.0 O1B B:TYD201 4.3 20.4 1.0 NH1 B:ARG86 4.4 24.1 1.0 OE2 B:GLU52 4.4 37.7 1.0 NE2 B:HIS53 4.5 25.6 1.0 O B:HOH225 4.5 18.6 1.0 ND1 B:HIS116 4.6 16.1 1.0 CG B:ASP119 4.6 25.9 1.0 C5' B:TYD201 4.7 24.7 1.0 O5' B:TYD201 4.7 27.0 1.0 O2A B:TYD201 4.7 28.3 1.0 CB B:ASP119 4.8 26.5 1.0 NH2 B:ARG86 4.8 23.8 1.0 O B:HOH208 4.9 19.1 1.0 CZ B:ARG86 4.9 24.0 1.0 O B:ALA117 4.9 18.8 1.0 O3B B:TYD201 5.0 18.8 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