Magnesium in PDB 7mxb: Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp

The structure of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp, PDB code: 7mxb was solved by M.N.Lisa, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.02 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.663, 42.741, 175.327, 90, 95.31, 90
R / Rfree (%)	20.9 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp (pdb code 7mxb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp, PDB code: 7mxb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp


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 S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:31.3 occ:1.00 MG A:MAP901 0.0 31.3 1.0 O1B A:MAP901 2.0 23.1 1.0 O2A A:MAP901 2.0 25.2 1.0 O A:HOH1164 2.0 21.3 1.0 O A:HOH1060 2.2 28.2 1.0 OE2 A:GLU305 2.2 24.2 1.0 O1G A:MAP901 2.3 23.3 1.0 PB A:MAP901 2.8 29.3 1.0 PA A:MAP901 3.1 26.3 1.0 O3A A:MAP901 3.1 27.4 1.0 PG A:MAP901 3.2 28.8 1.0 N3B A:MAP901 3.3 30.6 1.0 CD A:GLU305 3.4 29.0 1.0 O2G A:MAP901 3.8 28.2 1.0 C5' A:MAP901 3.8 21.8 1.0 O5' A:MAP901 3.9 26.8 1.0 O A:HOH1093 4.1 19.9 1.0 OE1 A:GLU305 4.2 38.0 1.0 O1A A:MAP901 4.2 23.8 1.0 CG A:GLU305 4.3 22.8 1.0 O A:HOH1224 4.3 27.6 1.0 O2B A:MAP901 4.3 31.3 1.0 NZ A:LYS303 4.3 20.1 1.0 N A:GLY185 4.4 29.7 1.0 O A:HOH1009 4.5 37.3 1.0 CA A:GLY184 4.6 29.9 1.0 O3G A:MAP901 4.6 26.8 1.0 CE A:LYS303 4.8 18.4 1.0 O A:HOH1233 4.8 44.7 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp


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 S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:29.3 occ:1.00 OD2 A:ASP301 2.0 13.9 1.0 OD2 A:ASP318 2.0 19.6 1.0 O A:HOH1141 2.0 19.3 1.0 O A:HOH1093 2.1 19.9 1.0 O3G A:MAP901 2.1 26.8 1.0 O A:HOH1066 2.2 26.6 1.0 CG A:ASP318 3.0 22.9 1.0 CG A:ASP301 3.2 18.5 1.0 PG A:MAP901 3.2 28.8 1.0 N3B A:MAP901 3.4 30.6 1.0 OD1 A:ASP318 3.5 24.9 1.0 O1G A:MAP901 3.6 23.3 1.0 CB A:ASP301 3.9 16.9 1.0 OD1 A:ASP301 4.1 23.2 1.0 CB A:ASP318 4.3 21.6 1.0 O1A A:MAP901 4.4 23.8 1.0 CE A:LYS303 4.4 18.4 1.0 ND2 A:ASN306 4.4 17.6 1.0 O2G A:MAP901 4.6 28.2 1.0 NZ A:LYS303 4.6 20.1 1.0 O A:TYR332 4.7 29.0 1.0 O2A A:MAP901 4.9 25.2 1.0 NZ A:LYS205 4.9 34.8 1.0 CB A:ALA321 4.9 19.9 1.0 CE A:MET208 5.0 55.5 1.0 PB A:MAP901 5.0 29.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:27.4 occ:1.00 O A:HOH1058 2.0 15.9 1.0 O A:HOH1088 2.0 22.0 1.0 O A:HOH1126 2.1 18.8 1.0 O A:GLY199 2.2 21.3 1.0 O A:HOH1333 2.2 23.4 1.0 O A:HOH1192 2.3 20.5 1.0 C A:GLY199 3.3 24.0 1.0 CA A:GLY199 3.8 20.8 1.0 OE1 A:GLU145 3.8 36.9 1.0 OE2 A:GLU145 4.0 39.6 1.0 CD A:GLU145 4.3 39.4 1.0 O A:HOH1272 4.4 26.7 1.0 O A:HOH1150 4.4 23.7 1.0 N A:ARG200 4.4 20.0 1.0 O A:HOH1219 4.5 23.8 1.0 CA A:ARG200 4.8 24.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:27.4 occ:1.00 MG B:MAP901 0.0 27.4 1.0 O1B B:MAP901 1.9 21.4 1.0 O2A B:MAP901 2.0 24.2 1.0 O B:HOH1056 2.1 27.5 1.0 OE2 B:GLU305 2.2 27.3 1.0 O B:HOH1171 2.2 23.7 1.0 O1G B:MAP901 2.4 22.2 1.0 PB B:MAP901 2.8 28.0 1.0 PA B:MAP901 3.1 32.8 1.0 O3A B:MAP901 3.1 21.8 1.0 CD B:GLU305 3.3 33.7 1.0 PG B:MAP901 3.4 23.4 1.0 N3B B:MAP901 3.5 32.3 1.0 C5' B:MAP901 3.8 26.7 1.0 O5' B:MAP901 3.9 27.0 1.0 O3G B:MAP901 4.0 28.8 1.0 O B:HOH1198 4.0 27.6 1.0 O B:HOH1015 4.1 32.4 1.0 OE1 B:GLU305 4.1 42.4 1.0 O B:HOH1066 4.2 17.6 1.0 O1A B:MAP901 4.2 29.3 1.0 CG B:GLU305 4.2 30.6 1.0 O2B B:MAP901 4.3 29.3 1.0 O B:HOH1284 4.4 44.7 1.0 NZ B:LYS303 4.4 26.0 1.0 N B:GLY185 4.7 40.5 1.0 CA B:GLY184 4.8 34.0 1.0 O2G B:MAP901 4.8 26.5 1.0 CE B:LYS303 4.9 24.2 1.0 O B:HOH1170 5.0 32.3 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:27.4 occ:1.00 OD2 B:ASP301 2.0 19.2 1.0 OD2 B:ASP318 2.1 22.2 1.0 O2G B:MAP901 2.1 26.5 1.0 O B:HOH1066 2.1 17.6 1.0 O B:HOH1095 2.1 22.7 1.0 O B:HOH1120 2.3 20.9 1.0 CG B:ASP318 3.1 22.2 1.0 CG B:ASP301 3.1 25.1 1.0 PG B:MAP901 3.3 23.4 1.0 OD1 B:ASP318 3.5 27.1 1.0 N3B B:MAP901 3.6 32.3 1.0 O1G B:MAP901 3.7 22.2 1.0 CB B:ASP301 3.8 22.1 1.0 O B:HOH1366 3.9 31.2 1.0 O B:TYR332 4.1 34.4 1.0 OD1 B:ASP301 4.1 24.6 1.0 O B:HOH1165 4.2 30.0 1.0 CB B:ASP318 4.4 21.7 1.0 O1A B:MAP901 4.4 29.3 1.0 CE B:LYS303 4.5 24.2 1.0 ND2 B:ASN306 4.6 19.7 1.0 O3G B:MAP901 4.6 28.8 1.0 NZ B:LYS303 4.7 26.0 1.0 CB B:ALA321 4.8 24.3 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the S/T Protein Kinase Pkng From Corynebacterium Glutamicum in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:29.2 occ:1.00 O B:HOH1214 2.0 19.5 1.0 O B:HOH1126 2.0 21.2 1.0 O B:GLY199 2.1 12.8 1.0 O B:HOH1106 2.1 16.5 1.0 O B:HOH1274 2.2 14.8 1.0 O B:HOH1136 2.2 19.6 1.0 C B:GLY199 3.1 16.2 1.0 CA B:GLY199 3.6 17.6 1.0 OE1 B:GLU145 3.7 33.8 1.0 OE2 B:GLU145 3.8 33.6 1.0 CD B:GLU145 4.2 31.4 1.0 N B:ARG200 4.3 14.9 1.0 O B:HOH1205 4.3 21.3 1.0 O B:HOH1381 4.4 34.2 1.0 O B:HOH1153 4.5 21.0 1.0 CA B:ARG200 4.7 20.6 1.0 O B:HOH1351 4.9 23.9 1.0 N B:ILE201 4.9 12.7 1.0

M.N.Lisa, A.Sogues, N.Barilone, M.Baumgart, M.Gil, M.Grana, R.Duran, R.M.Biondi, M.Bellinzoni, M.Bott, P.M.Alzari. A Tetratricopeptide Repeat Scaffold Couples Signal Detection to Odhi Phosphorylation in Metabolic Control By the Protein Kinase Pkng Mbio 2021.
ISSN: ESSN 2150-7511
PubMed: 34607462
DOI: 10.1128/MBIO.01717-21