Magnesium in PDB 3pkp: Q83S Variant of S. Enterica Rmla with Datp

All present enzymatic activity of Q83S Variant of S. Enterica Rmla with Datp:
2.7.7.24;

The structure of Q83S Variant of S. Enterica Rmla with Datp, PDB code: 3pkp 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)	43.39 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.879, 134.313, 175.829, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 26

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Q83S Variant of S. Enterica Rmla with Datp (pdb code 3pkp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Q83S Variant of S. Enterica Rmla with Datp, PDB code: 3pkp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:61.6 occ:1.00 O2A A:DTP500 2.4 59.4 1.0 OD1 A:ASP226 2.4 73.2 1.0 OD2 A:ASP111 2.9 52.0 1.0 OD2 A:ASP226 2.9 77.2 1.0 CG A:ASP226 3.0 77.5 1.0 NH2 A:ARG16 3.5 66.5 1.0 PA A:DTP500 3.7 48.0 1.0 NZ A:LYS26 4.0 57.5 1.0 CG A:ASP111 4.0 57.2 1.0 NH1 A:ARG16 4.1 52.2 1.0 CZ A:ARG16 4.2 71.6 1.0 O1A A:DTP500 4.2 87.0 1.0 CB A:ASP226 4.4 45.8 1.0 OD1 A:ASP111 4.4 38.4 1.0 O3A A:DTP500 4.5 68.7 1.0 CA A:GLY228 4.7 45.8 1.0 C5' A:DTP500 4.8 40.1 1.0 O5' A:DTP500 4.8 97.6 1.0 O A:HOH324 5.0 43.7 1.0

Magnesium binding site 2 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:53.0 occ:1.00 O1A A:DTP500 2.4 87.0 1.0 O2B A:DTP500 2.5 79.7 1.0 O3G A:DTP500 2.8 0.6 1.0 O2G A:DTP500 3.5 0.7 1.0 PG A:DTP500 3.6 51.7 1.0 PB A:DTP500 3.7 69.2 1.0 PA A:DTP500 3.8 48.0 1.0 O3B A:DTP500 3.9 0.3 1.0 NH2 A:ARG16 4.2 66.5 1.0 O3A A:DTP500 4.2 68.7 1.0 O5' A:DTP500 4.4 97.6 1.0 O A:HOH328 4.6 41.2 1.0 O2A A:DTP500 5.0 59.4 1.0

Magnesium binding site 3 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:50.7 occ:1.00 O2A B:DTP500 2.3 55.4 1.0 OD1 B:ASP226 2.4 88.5 1.0 OD2 B:ASP111 2.9 64.0 1.0 OD2 B:ASP226 2.9 0.3 1.0 CG B:ASP226 2.9 0.2 1.0 NH2 B:ARG16 3.5 51.7 1.0 PA B:DTP500 3.6 54.2 1.0 CG B:ASP111 3.8 45.5 1.0 NZ B:LYS26 4.1 68.0 1.0 OD1 B:ASP111 4.2 65.0 1.0 O1A B:DTP500 4.2 68.3 1.0 CZ B:ARG16 4.3 65.9 1.0 NH1 B:ARG16 4.3 54.2 1.0 CB B:ASP226 4.3 39.7 1.0 O3A B:DTP500 4.6 0.8 1.0 C5' B:DTP500 4.6 70.2 1.0 O5' B:DTP500 4.7 57.2 1.0 CA B:GLY228 4.9 37.6 1.0

Magnesium binding site 4 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:50.8 occ:1.00 O1A B:DTP500 2.3 68.3 1.0 O2B B:DTP500 2.5 85.4 1.0 O3G B:DTP500 2.7 0.9 1.0 PG B:DTP500 3.7 56.3 1.0 PB B:DTP500 3.7 64.6 1.0 PA B:DTP500 3.7 54.2 1.0 O2G B:DTP500 3.7 0.1 1.0 O3B B:DTP500 3.8 80.5 1.0 O3A B:DTP500 4.2 0.8 1.0 NH2 B:ARG16 4.2 51.7 1.0 O5' B:DTP500 4.4 57.2 1.0 O A:HOH331 4.8 50.9 1.0 O2A B:DTP500 4.9 55.4 1.0

Magnesium binding site 5 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:61.8 occ:1.00 O2A C:DTP500 2.3 0.3 1.0 OD1 C:ASP226 2.4 83.2 1.0 OD2 C:ASP111 2.9 62.1 1.0 OD2 C:ASP226 2.9 0.1 1.0 CG C:ASP226 3.0 0.8 1.0 NH2 C:ARG16 3.4 43.7 1.0 PA C:DTP500 3.7 65.6 1.0 CG C:ASP111 4.0 80.6 1.0 NZ C:LYS26 4.0 70.3 1.0 CZ C:ARG16 4.1 86.7 1.0 NH1 C:ARG16 4.1 62.3 1.0 O1A C:DTP500 4.2 91.4 1.0 OD1 C:ASP111 4.3 70.9 1.0 CB C:ASP226 4.3 64.8 1.0 O3A C:DTP500 4.5 0.8 1.0 CA C:GLY228 4.7 39.8 1.0 O5' C:DTP500 4.7 70.3 1.0 C5' C:DTP500 4.7 42.2 1.0

Magnesium binding site 6 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.0 occ:1.00 O1A C:DTP500 2.4 91.4 1.0 O2B C:DTP500 2.5 69.0 1.0 O2G C:DTP500 2.6 0.4 1.0 O3G C:DTP500 3.1 0.9 1.0 PB C:DTP500 3.7 74.1 1.0 PG C:DTP500 3.7 73.5 1.0 PA C:DTP500 3.8 65.6 1.0 O3B C:DTP500 3.9 0.9 1.0 O3A C:DTP500 4.2 0.8 1.0 NH2 C:ARG16 4.3 43.7 1.0 O5' C:DTP500 4.4 70.3 1.0 O1G C:DTP500 5.0 83.1 1.0

Magnesium binding site 7 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:67.6 occ:1.00 OD1 D:ASP226 2.2 82.0 1.0 O2A D:DTP500 2.4 78.0 1.0 OD2 D:ASP226 2.5 78.2 1.0 CG D:ASP226 2.6 87.1 1.0 OD2 D:ASP111 2.8 66.1 1.0 CG D:ASP111 3.7 75.2 1.0 PA D:DTP500 3.7 56.6 1.0 NH2 D:ARG16 3.9 71.7 1.0 OD1 D:ASP111 3.9 64.3 1.0 CB D:ASP226 4.1 62.8 1.0 NZ D:LYS26 4.2 75.5 1.0 O1A D:DTP500 4.3 65.6 1.0 C5' D:DTP500 4.5 60.4 1.0 NH1 D:ARG16 4.6 61.2 1.0 O5' D:DTP500 4.6 68.2 1.0 CZ D:ARG16 4.6 78.9 1.0 O3A D:DTP500 4.7 0.0 1.0 CA D:ASP226 5.0 74.5 1.0

Magnesium binding site 8 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:66.6 occ:1.00 O1A D:DTP500 2.3 65.6 1.0 O2B D:DTP500 2.5 95.0 1.0 O3G D:DTP500 2.6 64.7 1.0 O2G D:DTP500 3.5 0.1 1.0 PG D:DTP500 3.5 66.0 1.0 PB D:DTP500 3.7 74.1 1.0 PA D:DTP500 3.7 56.6 1.0 O3B D:DTP500 3.8 87.9 1.0 NH2 D:ARG16 4.1 71.7 1.0 O3A D:DTP500 4.2 0.0 1.0 O5' D:DTP500 4.4 68.2 1.0 O1G D:DTP500 4.9 76.8 1.0 O2A D:DTP500 4.9 78.0 1.0

Magnesium binding site 9 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg501 b:64.6 occ:1.00 OD1 I:ASP226 2.2 56.2 1.0 O I:HOH313 2.2 41.8 1.0 O2A I:DTP500 2.3 82.5 1.0 OD2 I:ASP226 2.4 82.6 1.0 OD2 I:ASP111 2.6 50.0 1.0 CG I:ASP226 2.6 69.2 1.0 CG I:ASP111 3.4 68.3 1.0 OD1 I:ASP111 3.6 42.0 1.0 PA I:DTP500 3.7 51.8 1.0 CB I:ASP226 4.1 49.1 1.0 C5' I:DTP500 4.2 74.1 1.0 O I:HOH301 4.2 48.9 1.0 NH2 I:ARG16 4.3 73.7 1.0 NZ I:LYS26 4.3 56.8 1.0 O1A I:DTP500 4.4 73.8 1.0 O5' I:DTP500 4.5 65.9 1.0 O3A I:DTP500 4.7 0.1 1.0 CB I:ASP111 4.8 37.8 1.0 CA I:ASP226 4.9 97.2 1.0

Magnesium binding site 10 out of 16 in the Q83S Variant of S. Enterica Rmla with Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Q83S Variant of S. Enterica Rmla with Datp within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg502 b:55.1 occ:1.00 O1A I:DTP500 2.3 73.8 1.0 O2B I:DTP500 2.5 1.0 1.0 O3G I:DTP500 2.8 0.3 1.0 O2G I:DTP500 3.6 0.8 1.0 PA I:DTP500 3.6 51.8 1.0 PG I:DTP500 3.6 59.7 1.0 O3B I:DTP500 3.7 81.0 1.0 PB I:DTP500 3.8 48.0 1.0 O I:HOH308 4.1 42.7 1.0 NH2 I:ARG16 4.2 73.7 1.0 O3A I:DTP500 4.2 0.1 1.0 O5' I:DTP500 4.3 65.9 1.0 O J:HOH313 4.5 51.6 1.0 O2A I:DTP500 4.8 82.5 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