Magnesium in PDB 3w6o: Crystal Structure of Human DLP1 in Complex with Gmp-Pcp

All present enzymatic activity of Crystal Structure of Human DLP1 in Complex with Gmp-Pcp:
3.6.5.5;

The structure of Crystal Structure of Human DLP1 in Complex with Gmp-Pcp, PDB code: 3w6o was solved by H.Kishida, S.Sugio, 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 (°)	51.240, 109.070, 128.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.5

The structure of Crystal Structure of Human DLP1 in Complex with Gmp-Pcp also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Human DLP1 in Complex with Gmp-Pcp (pdb code 3w6o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human DLP1 in Complex with Gmp-Pcp, PDB code: 3w6o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human DLP1 in Complex with Gmp-Pcp


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 Human DLP1 in Complex with Gmp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:8.9 occ:1.00 O3G A:GCP801 1.9 10.1 1.0 O1B A:GCP801 1.9 8.8 1.0 O A:HOH913 2.0 7.5 1.0 OG A:SER39 2.1 9.5 1.0 OG1 A:THR59 2.1 8.7 1.0 O A:HOH902 2.2 9.2 1.0 CB A:THR59 3.1 9.3 1.0 PB A:GCP801 3.2 7.8 1.0 CB A:SER39 3.2 8.7 1.0 PG A:GCP801 3.2 9.7 1.0 C3B A:GCP801 3.5 7.7 1.0 N A:SER39 3.9 8.1 1.0 N A:THR59 4.0 9.2 1.0 OD2 A:ASP146 4.1 11.0 1.0 CA A:SER39 4.1 8.9 1.0 OD1 A:ASP146 4.1 10.6 1.0 CG2 A:THR59 4.1 9.0 1.0 O A:HOH918 4.2 9.0 1.0 CA A:THR59 4.2 9.3 1.0 O2B A:GCP801 4.2 8.4 1.0 O1G A:GCP801 4.2 9.5 1.0 O2G A:GCP801 4.2 8.9 1.0 O2A A:GCP801 4.3 9.5 1.0 O3A A:GCP801 4.4 9.3 1.0 O A:LEU147 4.4 9.3 1.0 CG A:ASP146 4.5 10.9 1.0 O A:PRO52 4.6 11.6 1.0 CB A:LYS38 4.7 8.9 1.0 PA A:GCP801 4.7 9.4 1.0 CE A:LYS38 4.8 9.4 1.0 NZ A:LYS38 4.9 9.2 1.0 CB A:VAL58 4.9 9.4 1.0 C A:LYS38 4.9 8.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human DLP1 in Complex with Gmp-Pcp


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 Human DLP1 in Complex with Gmp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:8.4 occ:1.00 O1B B:GCP801 1.9 8.1 1.0 O3G B:GCP801 1.9 8.7 1.0 O B:HOH934 2.0 7.2 1.0 OG1 B:THR59 2.1 7.3 1.0 OG B:SER39 2.1 8.9 1.0 O B:HOH936 2.2 6.5 1.0 CB B:THR59 3.1 9.0 1.0 PB B:GCP801 3.2 8.9 1.0 CB B:SER39 3.2 8.6 1.0 PG B:GCP801 3.2 9.3 1.0 C3B B:GCP801 3.4 8.2 1.0 N B:SER39 3.8 7.5 1.0 N B:THR59 3.9 9.5 1.0 OD2 B:ASP146 4.0 11.9 1.0 CA B:SER39 4.0 8.7 1.0 OD1 B:ASP146 4.1 12.4 1.0 O B:HOH1007 4.1 11.4 1.0 CA B:THR59 4.1 9.0 1.0 CG2 B:THR59 4.1 8.1 1.0 O2B B:GCP801 4.2 7.4 1.0 O2G B:GCP801 4.2 8.8 1.0 O1G B:GCP801 4.3 10.8 1.0 O2A B:GCP801 4.3 9.2 1.0 O3A B:GCP801 4.4 8.3 1.0 CG B:ASP146 4.4 10.4 1.0 O B:LEU147 4.4 8.8 1.0 O B:PRO52 4.5 11.6 1.0 CB B:LYS38 4.7 9.2 1.0 CE B:LYS38 4.7 9.1 1.0 PA B:GCP801 4.7 9.0 1.0 C B:LYS38 4.9 8.0 1.0 CB B:VAL58 4.9 8.9 1.0 NZ B:LYS38 5.0 10.1 1.0

H.Kishida, S.Sugio. Crystal Structure of Gtpase Domain Fused with Minimal Stalks From Human Dynamin-1-Like Protein (DLP1) in Complex with Several Nucleotide Analogues Curr Top Pept Protein Res. V. 14 67 2013.
ISSN: ISSN 0972-4524