Magnesium in PDB 1mn9: Ndp Kinase Mutant (H122G) Complex with Rtp

All present enzymatic activity of Ndp Kinase Mutant (H122G) Complex with Rtp:
2.7.4.6;

The structure of Ndp Kinase Mutant (H122G) Complex with Rtp, PDB code: 1mn9 was solved by S.Gallois-Montbrun, Y.Chen, H.Dutartre, S.Morera, C.Guerreiro, L.Mulard, B.Schneider, J.Janin, B.Canard, M.Veron, D.Deville-Bonne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.20 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.731, 71.731, 153.818, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.9

The binding sites of Magnesium atom in the Ndp Kinase Mutant (H122G) Complex with Rtp (pdb code 1mn9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ndp Kinase Mutant (H122G) Complex with Rtp, PDB code: 1mn9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ndp Kinase Mutant (H122G) Complex with Rtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ndp Kinase Mutant (H122G) Complex with Rtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg164 b:27.7 occ:1.00 O A:HOH1001 1.9 26.0 1.0 O A:HOH1003 1.9 43.5 1.0 O A:HOH1002 2.0 14.6 1.0 O2A A:RTP160 2.2 48.7 1.0 O1B A:RTP160 2.4 49.5 1.0 O3G A:RTP160 2.8 56.9 1.0 PA A:RTP160 3.4 48.5 1.0 PB A:RTP160 3.4 50.5 1.0 O3A A:RTP160 3.7 50.3 1.0 PG A:RTP160 3.7 58.0 1.0 O3B A:RTP160 3.7 54.9 1.0 OD2 A:ASP125 3.7 44.8 1.0 OE2 A:GLU58 4.0 69.4 1.0 O2G A:RTP160 4.1 57.1 1.0 O1A A:RTP160 4.3 48.2 1.0 NH2 A:ARG92 4.3 35.6 1.0 NE2 A:HIS59 4.4 61.9 1.0 O5' A:RTP160 4.6 46.3 1.0 NH1 A:ARG92 4.6 36.3 1.0 CG A:ASP125 4.7 44.5 1.0 C5' A:RTP160 4.7 44.4 1.0 CD A:GLU58 4.8 69.0 1.0 O2B A:RTP160 4.8 49.6 1.0 CZ A:ARG92 4.8 35.6 1.0 CB A:ASP125 4.9 42.3 1.0 O1G A:RTP160 5.0 55.3 1.0

Magnesium binding site 2 out of 3 in the Ndp Kinase Mutant (H122G) Complex with Rtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ndp Kinase Mutant (H122G) Complex with Rtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg163 b:41.8 occ:1.00 O2A A:RTP161 1.9 59.7 1.0 O A:HOH1016 1.9 31.8 1.0 O3G A:RTP161 2.0 66.5 1.0 O1B A:RTP161 2.8 63.8 1.0 PG A:RTP161 3.3 66.3 1.0 PA A:RTP161 3.3 59.8 1.0 O3B A:RTP161 3.4 65.3 1.0 PB A:RTP161 3.6 64.0 1.0 O3A A:RTP161 3.8 62.1 1.0 OE2 B:GLU58 3.9 70.6 1.0 C5' A:RTP161 3.9 58.1 1.0 NE2 B:HIS59 4.0 65.5 1.0 O2G A:RTP161 4.1 67.0 1.0 O5' A:RTP161 4.1 59.3 1.0 O1G A:RTP161 4.3 65.0 1.0 O1A A:RTP161 4.4 58.9 1.0 OD2 B:ASP125 4.4 47.9 1.0 CE1 B:TYR56 4.6 57.1 1.0 CD B:GLU58 4.7 70.0 1.0 CD2 B:HIS59 4.8 65.6 1.0 CD1 B:TYR56 4.8 56.9 1.0 CE1 B:HIS59 5.0 65.4 1.0

Magnesium binding site 3 out of 3 in the Ndp Kinase Mutant (H122G) Complex with Rtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ndp Kinase Mutant (H122G) Complex with Rtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg165 b:41.3 occ:1.00 O2A A:RTP162 2.3 58.9 1.0 O1B A:RTP162 2.5 65.9 1.0 O3G A:RTP162 2.7 74.8 1.0 PB A:RTP162 3.5 66.1 1.0 PA A:RTP162 3.5 61.5 1.0 PG A:RTP162 3.5 74.1 1.0 OD2 C:ASP125 3.6 43.6 1.0 O2G A:RTP162 3.7 73.5 1.0 O3B A:RTP162 3.7 69.9 1.0 O3A A:RTP162 3.8 64.9 1.0 OE2 C:GLU58 3.9 71.2 1.0 O1A A:RTP162 4.4 62.4 1.0 NH2 C:ARG92 4.5 44.0 1.0 NH1 C:ARG92 4.5 44.4 1.0 CG C:ASP125 4.5 43.6 1.0 NE2 C:HIS59 4.6 65.0 1.0 O5' A:RTP162 4.7 58.9 1.0 CB C:ASP125 4.8 42.7 1.0 O C:GLY123 4.8 31.2 1.0 CD C:GLU58 4.8 71.6 1.0 CZ C:ARG92 4.8 43.3 1.0 C5' A:RTP162 4.9 56.5 1.0 O1G A:RTP162 4.9 71.2 1.0 O2B A:RTP162 4.9 65.9 1.0

S.Gallois-Montbrun, Y.Chen, H.Dutartre, M.Sophys, S.Morera, C.Guerreiro, B.Schneider, L.Mulard, J.Janin, M.Veron, D.Deville-Bonne, B.Canard. Structural Analysis of the Activation of Ribavirin Analogs By Ndp Kinase: Comparison with Other Ribavirin Targets Mol.Pharmacol. V. 63 538 2003.
ISSN: ISSN 0026-895X
PubMed: 12606760
DOI: 10.1124/MOL.63.3.538