Magnesium in PDB 5ckw: Crystal Structure of LEGK4_AMPPNP Kinase

The structure of Crystal Structure of LEGK4_AMPPNP Kinase, PDB code: 5ckw was solved by A.Flayhan, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.35 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.684, 76.871, 86.441, 90.00, 98.19, 90.00
R / Rfree (%)	20.4 / 25.8

The structure of Crystal Structure of LEGK4_AMPPNP Kinase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of LEGK4_AMPPNP Kinase (pdb code 5ckw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of LEGK4_AMPPNP Kinase, PDB code: 5ckw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.5 occ:1.00 OD1 B:ASN200 2.2 46.2 1.0 O B:HOH675 2.2 48.0 1.0 O2A B:ANP501 2.2 38.1 1.0 N3B B:ANP501 2.4 72.1 1.0 OD2 B:ASP213 2.6 49.2 1.0 CG B:ASN200 3.2 40.9 1.0 CG B:ASP213 3.4 49.1 1.0 PB B:ANP501 3.5 65.5 1.0 PA B:ANP501 3.5 42.8 1.0 O3G B:ANP501 3.6 0.9 1.0 PG B:ANP501 3.6 0.7 1.0 ND2 B:ASN200 3.6 33.5 1.0 O2B B:ANP501 3.7 67.8 1.0 O3A B:ANP501 3.8 46.7 1.0 CB B:ASP213 3.8 52.1 1.0 O B:HOH642 4.1 19.4 0.7 MG B:MG503 4.2 33.5 1.0 OD1 B:ASP213 4.3 42.9 1.0 O2G B:ANP501 4.4 1.0 1.0 O B:GLY199 4.4 49.4 1.0 O1A B:ANP501 4.5 29.9 1.0 CB B:ASN200 4.6 37.7 1.0 O5' B:ANP501 4.6 57.9 1.0 C5' B:ANP501 4.7 50.2 1.0 O3' B:ANP501 4.7 46.8 1.0 O1G B:ANP501 4.8 0.1 1.0 O1B B:ANP501 4.8 57.7 1.0 CA B:ASN200 4.8 41.5 1.0 C3' B:ANP501 4.9 42.8 1.0 OD2 B:ASP195 5.0 39.5 1.0 C B:GLY199 5.0 44.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:33.5 occ:1.00 O B:HOH642 1.9 19.4 0.7 O B:HOH649 2.0 72.9 1.0 O2B B:ANP501 2.4 67.8 1.0 OD2 B:ASP213 2.5 49.2 1.0 OD1 B:ASP213 2.6 42.9 1.0 CG B:ASP213 2.9 49.1 1.0 PB B:ANP501 3.7 65.5 1.0 O B:HOH675 3.9 48.0 1.0 N3B B:ANP501 4.0 72.1 1.0 MG B:MG502 4.2 40.5 1.0 OD2 B:ASP195 4.4 39.5 1.0 CB B:ASP213 4.4 52.1 1.0 NZ B:LYS104 4.4 40.1 1.0 O2G B:ANP501 4.5 1.0 1.0 O1B B:ANP501 4.6 57.7 1.0 O3A B:ANP501 4.8 46.7 1.0 O2A B:ANP501 4.9 38.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:79.8 occ:1.00 O2B A:ANP501 2.0 0.1 1.0 OD1 A:ASN200 2.3 83.6 1.0 O A:HOH648 2.6 60.0 1.0 O3A A:ANP501 2.8 0.9 1.0 PB A:ANP501 2.9 0.5 1.0 CG A:ASN200 3.2 71.9 1.0 OD2 A:ASP213 3.4 87.9 1.0 ND2 A:ASN200 3.5 66.5 1.0 O A:GLY199 3.7 67.8 1.0 N3B A:ANP501 3.8 0.2 1.0 PA A:ANP501 3.9 91.8 1.0 O5' A:ANP501 4.0 97.6 1.0 CG A:ASP213 4.1 78.2 1.0 O1B A:ANP501 4.1 0.5 1.0 O2G A:ANP501 4.4 0.6 1.0 O1A A:ANP501 4.5 90.9 1.0 C A:GLY199 4.5 69.8 1.0 CB A:ASP213 4.5 77.0 1.0 C5' A:ANP501 4.6 94.3 1.0 CB A:ASN200 4.6 65.6 1.0 PG A:ANP501 4.8 0.5 1.0 OD1 A:ASP213 4.9 74.7 1.0 NZ A:LYS197 4.9 62.0 1.0 CA A:ASN200 4.9 69.0 1.0 O A:HOH618 5.0 69.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:77.5 occ:1.00 OD2 A:ASP213 2.8 87.9 1.0 OD1 A:ASP213 2.8 74.7 1.0 O1B A:ANP501 3.0 0.5 1.0 O A:HOH603 3.0 65.3 1.0 CG A:ASP213 3.2 78.2 1.0 OD2 A:ASP195 3.4 89.5 1.0 OG A:SER216 3.7 83.5 1.0 PB A:ANP501 4.1 0.5 1.0 O2B A:ANP501 4.1 0.1 1.0 CG A:ASP195 4.2 77.8 1.0 CB A:ASP195 4.5 69.6 1.0 N A:GLY215 4.6 81.2 1.0 CB A:ASP213 4.6 77.0 1.0 CA A:GLY215 4.7 82.6 1.0 ND2 A:ASN200 4.8 66.5 1.0 O3A A:ANP501 4.8 0.9 1.0 CB A:SER216 4.8 87.7 1.0 O A:TRP228 4.8 80.1 1.0 N A:SER216 4.9 81.4 1.0 O A:ASP213 4.9 82.4 1.0 C A:GLY215 5.0 86.6 1.0

A.Flayhan, C.Berge, N.Bailo, P.Doublet, R.Bayliss, L.Terradot. The Structure of Legionella Pneumophila LEGK4 Type Four Secretion System (T4SS) Effector Reveals A Novel Dimeric Eukaryotic-Like Kinase. Sci Rep V. 5 14602 2015.
ISSN: ESSN 2045-2322
PubMed: 26419332
DOI: 10.1038/SREP14602