Magnesium in PDB 5idm: Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+

The structure of Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+, PDB code: 5idm was solved by B.N.Dubey, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.280, 62.110, 103.890, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.9

The binding sites of Magnesium atom in the Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+ (pdb code 5idm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+, PDB code: 5idm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:8.0 occ:1.00 O1G A:ANP601 2.0 10.6 1.0 O1B A:ANP601 2.1 7.9 1.0 O2A A:ANP601 2.1 6.8 1.0 OD1 A:ASN434 2.1 6.1 1.0 O A:HOH802 2.1 6.4 1.0 O A:HOH818 2.1 5.2 1.0 PB A:ANP601 3.1 8.2 1.0 CG A:ASN434 3.1 6.2 1.0 PG A:ANP601 3.2 11.2 1.0 PA A:ANP601 3.2 7.0 1.0 O3A A:ANP601 3.4 7.6 1.0 ND2 A:ASN434 3.5 6.0 1.0 N3B A:ANP601 3.6 9.2 1.0 O A:HOH741 4.0 7.2 1.0 O5' A:ANP601 4.0 7.0 1.0 O A:HOH860 4.0 10.4 1.0 O3G A:ANP601 4.0 11.8 1.0 O A:HOH829 4.2 26.1 1.0 O2G A:ANP601 4.3 11.5 1.0 CA A:GLY509 4.4 6.7 1.0 CB A:ASN434 4.5 6.3 1.0 O1A A:ANP601 4.5 7.1 1.0 O2B A:ANP601 4.5 8.1 1.0 O A:ASN430 4.5 6.8 1.0 OD2 A:ASP437 4.6 10.3 1.0 CG2 A:VAL433 4.6 7.6 1.0 CA A:ASN434 4.7 6.5 1.0 N A:ASN434 4.8 6.6 1.0 N A:GLY509 4.9 6.9 1.0 NZ A:LYS500 5.0 15.2 1.0

Magnesium binding site 2 out of 2 in the Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bifunctional Histidine Kinase Ccka (Domain, Ca) in Complex with C-Di- Gmp and Amppnp/MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:12.0 occ:1.00 O2G B:ANP600 2.0 12.0 1.0 O2A B:ANP600 2.0 8.9 1.0 O2B B:ANP600 2.1 10.1 1.0 OD1 B:ASN434 2.1 9.2 1.0 O B:HOH783 2.1 9.5 1.0 O B:HOH789 2.2 5.7 1.0 CG B:ASN434 3.1 9.3 1.0 PB B:ANP600 3.1 10.2 1.0 PG B:ANP600 3.1 12.0 1.0 PA B:ANP600 3.2 9.1 1.0 O3A B:ANP600 3.3 9.7 1.0 ND2 B:ASN434 3.4 9.2 1.0 N3B B:ANP600 3.6 10.8 1.0 O1G B:ANP600 3.7 12.2 1.0 NZ B:LYS500 3.9 13.0 1.0 O B:HOH847 4.0 14.2 1.0 O5' B:ANP600 4.0 8.8 1.0 CA B:GLY509 4.3 9.2 1.0 O B:HOH761 4.3 33.1 1.0 O3G B:ANP600 4.4 11.7 1.0 CB B:ASN434 4.4 9.6 1.0 O1A B:ANP600 4.4 9.1 1.0 O1B B:ANP600 4.5 10.2 1.0 O B:ASN430 4.5 9.5 1.0 N B:GLY509 4.7 9.4 1.0 CA B:ASN434 4.7 10.0 1.0 OD2 B:ASP437 4.8 16.9 1.0 N B:ASN434 4.9 10.1 1.0

B.N.Dubey, C.Lori, S.Ozaki, G.Fucile, I.Plaza-Menacho, U.Jenal, T.Schirmer. Cyclic Di-Gmp Mediates A Histidine Kinase/Phosphatase Switch By Noncovalent Domain Cross-Linking. Sci Adv V. 2 00823 2016.
ISSN: ESSN 2375-2548
PubMed: 27652341
DOI: 10.1126/SCIADV.1600823