Magnesium in PDB 5jd9: Bacillus Cereus Coth Kinase

The structure of Bacillus Cereus Coth Kinase, PDB code: 5jd9 was solved by D.R.Tomchick, V.S.Tagliabracci, A.Sreelatha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.81 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.757, 63.516, 118.284, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.1

The binding sites of Magnesium atom in the Bacillus Cereus Coth Kinase (pdb code 5jd9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Bacillus Cereus Coth Kinase, PDB code: 5jd9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Bacillus Cereus Coth Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacillus Cereus Coth Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:25.4 occ:1.00 O A:HOH526 1.9 21.6 1.0 OD1 A:ASN238 2.0 31.5 1.0 O A:ASN238 2.1 18.8 1.0 O A:HOH680 2.2 23.3 1.0 O A:HOH652 2.3 15.4 1.0 NE2 A:HIS233 2.4 16.9 1.0 CG A:ASN238 2.9 36.4 1.0 C A:ASN238 3.0 18.6 1.0 CD2 A:HIS233 3.2 17.5 1.0 HD2 A:HIS233 3.3 21.0 1.0 HA A:ASN238 3.3 20.2 1.0 CE1 A:HIS233 3.4 19.4 1.0 CA A:ASN238 3.5 16.9 1.0 CB A:ASN238 3.5 22.9 1.0 HB3 A:ASN238 3.5 27.4 1.0 O A:HOH517 3.5 21.4 1.0 HE1 A:HIS233 3.6 23.2 1.0 HA A:PHE203 3.9 18.5 1.0 ND2 A:ASN238 4.0 53.2 1.0 HD21 A:ASN238 4.1 63.9 1.0 N A:LEU239 4.1 16.0 1.0 O A:HOH705 4.2 28.5 1.0 HG2 A:GLN180 4.2 24.3 1.0 HA A:LEU239 4.2 18.5 1.0 O A:HOH779 4.3 38.0 1.0 OE2 A:GLU183 4.3 54.0 1.0 HD1 A:PHE203 4.4 24.4 1.0 HB2 A:ASN238 4.4 27.4 1.0 CG A:HIS233 4.4 13.9 1.0 O A:LYS202 4.5 19.8 1.0 ND1 A:HIS233 4.5 19.3 1.0 HB3 A:GLN180 4.5 20.2 1.0 HD22 A:ASN238 4.6 63.9 1.0 CA A:LEU239 4.7 15.4 1.0 HD2 A:PHE240 4.7 14.1 1.0 HD23 A:LEU239 4.8 21.9 1.0 HE2 A:PHE240 4.8 15.0 1.0 H A:LEU239 4.8 19.1 1.0 O A:PHE203 4.8 15.2 1.0 CA A:PHE203 4.9 15.4 1.0 N A:ASN238 4.9 17.5 1.0

Magnesium binding site 2 out of 4 in the Bacillus Cereus Coth Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacillus Cereus Coth Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.9 occ:1.00 OD1 A:ASP279 2.0 21.8 1.0 O A:HOH589 2.1 19.9 1.0 O A:HOH576 2.1 16.2 1.0 O A:HOH668 2.1 20.4 1.0 O A:HOH822 2.1 21.9 1.0 CG A:ASP279 3.1 25.1 1.0 OD2 A:ASP279 3.5 21.2 1.0 O A:HOH802 3.8 37.7 1.0 HA A:ASP279 4.0 18.4 1.0 O A:HOH834 4.1 18.1 1.0 O A:ALA275 4.2 14.0 1.0 O A:LEU278 4.3 21.4 1.0 CB A:ASP279 4.3 17.5 1.0 CA A:ASP279 4.5 15.3 1.0 N A:ASP279 4.6 14.7 1.0 C A:LEU278 4.7 14.9 1.0 HB1 A:ALA275 4.7 16.2 1.0 HA A:ALA275 4.8 14.4 1.0 HB2 A:ASP279 4.9 21.1 1.0 HB3 A:ASP279 4.9 21.1 1.0 H A:ASP279 5.0 17.6 1.0

Magnesium binding site 3 out of 4 in the Bacillus Cereus Coth Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacillus Cereus Coth Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:28.9 occ:1.00 O A:HOH674 2.1 40.1 1.0 O A:HOH506 2.1 31.3 1.0 OD2 A:ASP246 2.2 32.9 1.0 O A:HOH555 2.2 26.9 1.0 O A:HOH825 2.2 28.2 1.0 O A:HOH717 2.3 30.2 1.0 CG A:ASP246 3.0 26.3 1.0 OD1 A:ASP246 3.2 40.0 1.0 O A:HOH827 3.8 41.2 1.0 HD21 A:ASN228 3.9 29.8 1.0 HE1 A:HIS48 3.9 25.5 1.0 O A:HOH586 4.1 15.4 1.0 OD1 A:ASP248 4.2 21.1 1.0 HG12 A:VAL255 4.3 22.5 1.0 OD1 A:ASN228 4.4 17.3 1.0 CB A:ASP246 4.4 8.9 1.0 O A:HOH819 4.5 28.8 1.0 HB3 A:ASP246 4.5 10.7 1.0 O A:ASP246 4.5 11.0 1.0 O A:HOH691 4.6 36.7 1.0 ND2 A:ASN228 4.6 24.8 1.0 CE1 A:HIS48 4.8 21.2 1.0 HG11 A:VAL255 4.9 22.5 1.0 HB2 A:ASP246 4.9 10.7 1.0 CG A:ASN228 4.9 16.8 1.0

Magnesium binding site 4 out of 4 in the Bacillus Cereus Coth Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacillus Cereus Coth Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:45.0 occ:1.00 O A:PHE61 2.0 14.4 1.0 O A:HOH547 2.0 21.6 1.0 O A:HOH650 2.3 25.2 1.0 O A:HOH760 2.3 32.8 1.0 O A:HOH629 2.4 31.4 1.0 HA A:TYR62 3.1 16.0 1.0 C A:PHE61 3.2 11.8 1.0 HB2 A:LYS71 3.8 20.4 1.0 CA A:TYR62 3.9 13.4 1.0 N A:TYR62 4.0 12.1 1.0 HA A:LYS65 4.1 19.1 1.0 O A:HOH538 4.2 24.2 1.0 O A:LYS65 4.3 16.9 1.0 CA A:PHE61 4.3 10.9 1.0 HD1 A:TYR62 4.4 20.7 1.0 H A:PHE61 4.4 12.5 1.0 N A:PHE61 4.4 10.4 1.0 O A:LYS71 4.4 11.8 1.0 O A:HOH832 4.4 44.5 1.0 HB2 A:PHE61 4.5 13.2 1.0 O A:TYR62 4.5 16.3 1.0 HB3 A:MET60 4.5 17.1 1.0 HB3 A:LYS65 4.7 26.2 1.0 C A:TYR62 4.7 14.3 1.0 CB A:LYS71 4.7 17.0 1.0 HG2 A:LYS65 4.7 33.2 1.0 HD2 A:LYS71 4.7 36.9 1.0 H A:TYR62 4.8 14.6 1.0 CA A:LYS65 4.9 15.9 1.0 HB2 A:TYR62 4.9 16.0 1.0 CB A:PHE61 4.9 11.0 1.0 C A:MET60 4.9 12.1 1.0 CB A:TYR62 5.0 13.3 1.0

K.B.Nguyen, A.Sreelatha, E.S.Durrant, J.Lopez-Garrido, A.Muszewska, M.Dudkiewicz, M.Grynberg, S.Yee, K.Pogliano, D.R.Tomchick, K.Pawowski, J.E.Dixon, V.S.Tagliabracci. Phosphorylation of Spore Coat Proteins By A Family of Atypical Protein Kinases. Proc.Natl.Acad.Sci.Usa V. 113 E3482 2016.
ISSN: ESSN 1091-6490
PubMed: 27185916
DOI: 10.1073/PNAS.1605917113