Magnesium in PDB 6lj3: Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion

The structure of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion, PDB code: 6lj3 was solved by R.Liang, G.Q.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.24 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.040, 68.427, 117.969, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 23.5

The binding sites of Magnesium atom in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion (pdb code 6lj3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion, PDB code: 6lj3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:30.6 occ:1.00 O A:HOH307 2.0 17.6 1.0 O2A A:DUP202 2.1 37.5 1.0 O B:HOH400 2.2 33.6 1.0 O1B A:DUP202 2.2 40.0 1.0 O2G A:DUP202 2.3 37.6 1.0 O A:HOH327 2.4 25.4 1.0 PA A:DUP202 3.4 34.2 1.0 PB A:DUP202 3.4 35.6 1.0 PG A:DUP202 3.5 39.2 1.0 O A:HOH344 3.8 24.0 1.0 N3A A:DUP202 3.8 33.8 1.0 O1G A:DUP202 3.9 45.6 1.0 O3B A:DUP202 4.0 41.1 1.0 NE A:ARG71 4.0 21.0 1.0 OD1 A:ASP33 4.1 25.1 1.0 OE1 A:GLN120 4.1 15.3 1.0 O B:HOH355 4.2 23.4 1.0 O B:HOH327 4.2 16.4 1.0 OD2 A:ASP33 4.2 24.9 1.0 NH2 A:ARG71 4.3 23.9 1.0 O5' A:DUP202 4.3 31.6 1.0 C5' A:DUP202 4.3 26.6 1.0 O1A A:DUP202 4.5 31.6 1.0 CG A:ASP33 4.6 20.4 1.0 CZ A:ARG71 4.7 22.7 1.0 O2B A:DUP202 4.7 32.4 1.0 OD2 B:ASP91 4.7 23.9 1.0 O3G A:DUP202 4.8 40.1 1.0 CD A:GLN120 4.8 15.3 1.0 CG A:ARG71 4.9 19.3 1.0 NE2 A:GLN120 5.0 15.5 1.0 CD A:ARG71 5.0 20.7 1.0

Magnesium binding site 2 out of 3 in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:31.8 occ:1.00 O B:HOH333 2.1 28.4 1.0 O1A B:DUP202 2.1 30.0 1.0 O B:HOH318 2.1 17.5 1.0 O B:HOH394 2.1 30.1 1.0 O1B B:DUP202 2.2 32.4 1.0 O3G B:DUP202 2.3 37.0 1.0 PG B:DUP202 3.4 39.8 1.0 PB B:DUP202 3.4 34.0 1.0 O B:HOH362 3.4 44.3 1.0 PA B:DUP202 3.4 31.3 1.0 O1G B:DUP202 3.7 43.1 1.0 O B:HOH393 3.8 36.4 1.0 O3B B:DUP202 3.8 36.6 1.0 N3A B:DUP202 3.9 32.7 1.0 O B:HOH310 4.0 36.7 1.0 NE B:ARG71 4.1 18.3 1.0 C5' B:DUP202 4.2 26.4 1.0 OD1 B:ASP33 4.2 17.9 1.0 NH2 B:ARG71 4.2 21.7 1.0 OD2 B:ASP33 4.3 21.9 1.0 OE1 B:GLN120 4.3 14.3 1.0 O C:HOH319 4.4 22.2 1.0 O5' B:DUP202 4.4 29.5 1.0 O2A B:DUP202 4.5 29.7 1.0 CZ B:ARG71 4.6 19.1 1.0 O2G B:DUP202 4.7 42.1 1.0 O2B B:DUP202 4.7 36.5 1.0 CG B:ASP33 4.7 18.0 1.0 OD2 C:ASP91 4.9 29.4 1.0

Magnesium binding site 3 out of 3 in the Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Full Length Asfv Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:30.4 occ:1.00 O A:HOH347 1.8 35.2 1.0 O1A A:DUP201 1.9 28.2 1.0 O2G A:DUP201 2.0 25.9 1.0 O1B A:DUP201 2.0 22.6 1.0 O A:HOH377 2.3 20.6 1.0 O C:HOH309 2.4 17.2 1.0 PA A:DUP201 3.1 23.3 1.0 PG A:DUP201 3.1 29.5 1.0 PB A:DUP201 3.1 24.4 1.0 O3B A:DUP201 3.4 28.4 1.0 N3A A:DUP201 3.7 23.1 1.0 O1G A:DUP201 3.7 32.6 1.0 NH1 A:ARG149 3.8 34.6 1.0 O C:HOH316 4.0 22.5 1.0 O A:HOH336 4.0 27.3 1.0 C5' A:DUP201 4.1 24.3 1.0 O2A A:DUP201 4.1 28.4 1.0 O5' A:DUP201 4.2 25.5 1.0 OD1 C:ASP33 4.2 23.4 1.0 O A:HOH314 4.3 24.0 1.0 NE C:ARG71 4.3 25.9 1.0 CG2 A:THR157 4.3 44.6 1.0 NH2 C:ARG71 4.4 27.6 1.0 OE1 C:GLN120 4.4 13.4 1.0 O3G A:DUP201 4.4 31.2 1.0 OD2 C:ASP33 4.5 26.1 1.0 O2B A:DUP201 4.5 24.1 1.0 OD2 A:ASP91 4.6 27.2 1.0 CZ A:ARG149 4.8 33.0 1.0 CG C:ASP33 4.8 21.8 1.0 CZ C:ARG71 4.9 27.8 1.0 CB A:THR157 4.9 47.7 1.0

R.Liang, G.Wang, D.Zhang, G.Ye, M.Li, Y.Shi, J.Shi, H.Chen, G.Peng. Structural Comparisons of Host and African Swine Fever Virus Dutpases Reveal New Clues For Inhibitor Development. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33139328
DOI: 10.1074/JBC.RA120.014005