Magnesium in PDB 4ix5: Crystal Structure of A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp

The structure of Crystal Structure of A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp, PDB code: 4ix5 was solved by J.Guo, X.Wei, M.Li, X.Pan, W.Chang, Z.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.63 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.860, 132.610, 55.180, 90.00, 116.64, 90.00
R / Rfree (%)	17.2 / 20.1

The binding sites of Magnesium atom in the Crystal Structure of A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp (pdb code 4ix5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp, PDB code: 4ix5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A STT7 Homolog From Micromonas Algae 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 A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:15.0 occ:1.00 O B:HOH832 2.1 13.1 1.0 O A:HOH874 2.1 11.9 1.0 O A:HOH873 2.1 13.4 1.0 O B:HOH726 2.2 14.3 1.0 O B:HOH833 2.2 11.7 1.0 O B:HOH831 2.3 16.5 1.0 OE1 B:GLU255 3.8 19.7 1.0 O B:HOH751 4.0 19.2 1.0 O B:HOH723 4.0 17.0 1.0 OE2 A:GLU422 4.1 18.3 1.0 O B:HOH707 4.2 17.4 1.0 O B:HOH716 4.2 16.3 1.0 OD2 A:ASP418 4.2 13.1 1.0 O B:HOH703 4.3 14.6 1.0 CB A:ASP418 4.3 12.0 1.0 O B:HOH704 4.3 16.6 1.0 O A:HOH875 4.3 20.5 1.0 OE1 A:GLU422 4.3 19.4 1.0 CB B:ALA204 4.6 12.9 1.0 CD A:GLU422 4.7 19.2 1.0 CD B:GLU255 4.7 22.7 1.0 CG A:ASP418 4.7 12.9 1.0 OE2 B:GLU255 4.8 20.6 1.0 CA B:ALA204 5.0 15.7 1.0 O B:GLU255 5.0 16.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A STT7 Homolog From Micromonas Algae 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 A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:50.2 occ:1.00 O2A A:ANP603 2.2 47.1 1.0 O A:HOH1037 2.4 49.9 1.0 O2B A:ANP603 2.5 65.5 1.0 OD1 A:ASN323 2.5 10.6 1.0 OD2 A:ASP338 2.8 34.8 1.0 O A:HOH1036 3.1 51.8 1.0 O1G A:ANP603 3.4 60.3 1.0 CG A:ASN323 3.4 12.8 1.0 O B:HOH972 3.5 38.6 1.0 PA A:ANP603 3.5 40.0 1.0 ND2 A:ASN323 3.6 11.3 1.0 CG A:ASP338 3.6 28.2 1.0 PB A:ANP603 3.7 64.9 1.0 CB A:ASP338 3.8 12.7 1.0 O3A A:ANP603 4.0 59.9 1.0 PG A:ANP603 4.2 57.3 1.0 O3G A:ANP603 4.2 55.2 1.0 N3B A:ANP603 4.4 43.8 1.0 O5' A:ANP603 4.5 41.9 1.0 O B:HOH970 4.5 35.1 1.0 OD1 A:ASP318 4.5 12.3 1.0 O1A A:ANP603 4.6 45.1 1.0 CE A:LYS320 4.7 17.3 1.0 C5' A:ANP603 4.7 32.8 1.0 OD1 A:ASP338 4.7 17.9 1.0 CB A:ASN323 4.8 8.4 1.0 O1B A:ANP603 4.9 66.2 1.0 O A:HOH1026 5.0 49.1 1.0 CD1 A:ILE337 5.0 12.5 1.0 NZ A:LYS320 5.0 12.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A STT7 Homolog From Micromonas Algae 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 A STT7 Homolog From Micromonas Algae in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:45.2 occ:1.00 O2A B:ANP602 2.0 60.5 1.0 O2G B:ANP602 2.4 58.0 1.0 O B:HOH978 2.5 54.4 1.0 OD1 B:ASN323 2.5 14.1 1.0 OD2 B:ASP338 2.6 38.8 1.0 O B:HOH974 2.6 40.8 1.0 O2B B:ANP602 2.9 64.7 1.0 O B:HOH975 3.1 42.8 1.0 CG B:ASN323 3.4 15.6 1.0 CG B:ASP338 3.4 27.3 1.0 PA B:ANP602 3.5 48.6 1.0 ND2 B:ASN323 3.5 17.1 1.0 CB B:ASP338 3.6 15.5 1.0 PG B:ANP602 3.9 60.4 1.0 PB B:ANP602 4.0 66.5 1.0 O3A B:ANP602 4.1 63.0 1.0 O A:HOH1042 4.1 43.1 1.0 O5' B:ANP602 4.3 39.0 1.0 N3B B:ANP602 4.4 50.8 1.0 O1A B:ANP602 4.5 50.4 1.0 OD2 B:ASP318 4.5 18.5 1.0 OD1 B:ASP338 4.5 20.9 1.0 O1G B:ANP602 4.5 61.9 1.0 C5' B:ANP602 4.6 33.6 1.0 CB B:ASN323 4.8 12.1 1.0 CE B:LYS320 4.9 19.5 1.0 CD1 B:ILE337 4.9 19.4 1.0 O B:HOH969 4.9 42.8 1.0

J.Guo, X.Wei, M.Li, X.Pan, W.Chang, Z.Liu. Structure of the Catalytic Domain of A State Transition Kinase Homolog From Micromonas Algae Protein Cell V. 4 607 2013.
ISSN: ISSN 1674-800X
PubMed: 23794031
DOI: 10.1007/S13238-013-3034-9