Magnesium in PDB 3pkq: Q83D Variant of S. Enterica Rmla with Dgtp

All present enzymatic activity of Q83D Variant of S. Enterica Rmla with Dgtp:
2.7.7.24;

The structure of Q83D Variant of S. Enterica Rmla with Dgtp, PDB code: 3pkq was solved by A.Chang, R.Moretti, C.A.Bingman, J.S.Thorson, G.N.Phillips Jr., Center Foreukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.71 / 2.40
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	109.400, 109.400, 110.075, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27.1

The binding sites of Magnesium atom in the Q83D Variant of S. Enterica Rmla with Dgtp (pdb code 3pkq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Q83D Variant of S. Enterica Rmla with Dgtp, PDB code: 3pkq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Q83D Variant of S. Enterica Rmla with Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Q83D Variant of S. Enterica Rmla with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:77.8 occ:1.00 O2A A:DGT500 2.7 85.8 0.8 OD2 A:ASP111 2.7 38.3 1.0 OD1 A:ASP226 2.8 68.0 1.0 O5' A:DGT500 3.1 84.9 0.8 CG A:ASP111 3.5 29.3 1.0 CG A:ASP226 3.5 71.9 1.0 PA A:DGT500 3.5 51.4 0.8 OD2 A:ASP226 3.5 63.7 1.0 OD1 A:ASP111 3.7 31.1 1.0 NZ A:LYS26 3.7 42.9 1.0 C5' A:DGT500 4.1 63.7 0.8 NH2 A:ARG16 4.1 51.5 1.0 O3A A:DGT500 4.4 75.8 0.8 O A:HOH354 4.5 39.2 1.0 O1A A:DGT500 4.8 0.9 0.8 CB A:ASP111 4.8 30.7 1.0 CB A:ASP226 4.9 79.1 1.0 C3' A:DGT500 4.9 34.8 0.8 CE A:LYS26 4.9 32.6 1.0

Magnesium binding site 2 out of 5 in the Q83D Variant of S. Enterica Rmla with Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Q83D Variant of S. Enterica Rmla with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:75.9 occ:1.00 OD2 B:ASP111 2.6 46.8 1.0 O2A B:DGT500 2.7 72.4 0.9 OD1 B:ASP226 2.8 75.3 1.0 O5' B:DGT500 3.2 78.8 0.9 CG B:ASP226 3.4 65.6 1.0 CG B:ASP111 3.5 27.5 1.0 OD2 B:ASP226 3.5 73.1 1.0 PA B:DGT500 3.6 57.1 0.9 OD1 B:ASP111 3.6 28.6 1.0 NZ B:LYS26 3.7 39.5 1.0 C5' B:DGT500 4.2 45.5 0.9 NH2 B:ARG16 4.2 35.0 1.0 O3A B:DGT500 4.4 71.5 0.9 O B:HOH326 4.5 45.0 1.0 CB B:ASP111 4.8 23.2 1.0 CB B:ASP226 4.8 76.7 1.0 O1A B:DGT500 4.8 97.2 0.9 CE B:LYS26 4.9 34.6 1.0 C3' B:DGT500 5.0 36.8 0.9 CA B:GLY228 5.0 60.0 1.0

Magnesium binding site 3 out of 5 in the Q83D Variant of S. Enterica Rmla with Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Q83D Variant of S. Enterica Rmla with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:64.7 occ:1.00 O2B B:DGT500 2.3 79.4 0.9 O1A B:DGT500 2.6 97.2 0.9 O3G B:DGT500 2.8 71.0 0.9 PB B:DGT500 3.6 50.7 0.9 PA B:DGT500 3.6 57.1 0.9 PG B:DGT500 4.0 59.0 0.9 O2A B:DGT500 4.0 72.4 0.9 O3A B:DGT500 4.1 71.5 0.9 O3B B:DGT500 4.2 0.5 0.9 O2G B:DGT500 4.5 50.1 0.9 O1B B:DGT500 4.8 61.0 0.9 C8 B:DGT500 4.9 73.6 0.9 N7 B:DGT500 5.0 50.4 0.9

Magnesium binding site 4 out of 5 in the Q83D Variant of S. Enterica Rmla with Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Q83D Variant of S. Enterica Rmla with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:64.8 occ:1.00 O2A C:DGT500 2.6 89.6 0.9 OD2 C:ASP111 2.7 50.2 1.0 OD1 C:ASP226 2.8 65.2 1.0 O5' C:DGT500 3.2 89.0 0.9 PA C:DGT500 3.5 67.5 0.9 CG C:ASP111 3.5 49.4 1.0 CG C:ASP226 3.5 80.4 1.0 OD2 C:ASP226 3.6 60.5 1.0 NZ C:LYS26 3.6 50.5 1.0 OD1 C:ASP111 3.7 35.2 1.0 NH2 C:ARG16 4.1 63.1 1.0 C5' C:DGT500 4.2 47.8 0.9 O3A C:DGT500 4.3 73.6 0.9 O1A C:DGT500 4.7 0.3 0.9 CB C:ASP111 4.8 33.6 1.0 CB C:ASP226 4.9 0.7 1.0 CE C:LYS26 4.9 43.8 1.0 C3' C:DGT500 4.9 48.6 0.9 CA C:GLY228 5.0 80.7 1.0

Magnesium binding site 5 out of 5 in the Q83D Variant of S. Enterica Rmla with Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Q83D Variant of S. Enterica Rmla with Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:73.4 occ:1.00 O2B D:DGT500 2.6 75.8 0.8 O1A D:DGT500 2.7 0.2 0.8 O3G D:DGT500 2.8 68.7 0.8 PA D:DGT500 3.7 74.2 0.8 PB D:DGT500 3.9 67.7 0.8 O2A D:DGT500 3.9 90.9 0.8 PG D:DGT500 4.1 67.0 0.8 O3A D:DGT500 4.2 53.2 0.8 O3B D:DGT500 4.4 92.7 0.8 O2G D:DGT500 4.7 69.5 0.8 NH2 D:ARG16 4.8 42.5 1.0

R.Moretti, A.Chang, P.Peltier-Pain, C.A.Bingman, G.N.Phillips, J.S.Thorson. Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase Rmla Via Directed Evolution. J.Biol.Chem. V. 286 13235 2011.
ISSN: ISSN 0021-9258
PubMed: 21317292
DOI: 10.1074/JBC.M110.206433