Magnesium in PDB 3w6n: Crystal Structure of Human DLP1 in Complex with Gmp-Pn.Pi

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

The structure of Crystal Structure of Human DLP1 in Complex with Gmp-Pn.Pi, PDB code: 3w6n 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 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.340, 109.020, 128.820, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The structure of Crystal Structure of Human DLP1 in Complex with Gmp-Pn.Pi 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-Pn.Pi (pdb code 3w6n). 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-Pn.Pi, PDB code: 3w6n:
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-Pn.Pi


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-Pn.Pi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:6.0 occ:1.00 O3 A:PO4802 2.0 18.6 1.0 O1B A:GNH801 2.0 11.7 1.0 OG1 A:THR59 2.1 11.8 1.0 OG A:SER39 2.1 10.4 1.0 O A:HOH904 2.1 14.7 1.0 O A:HOH905 2.3 13.6 1.0 CB A:THR59 3.2 13.1 1.0 CB A:SER39 3.3 10.4 1.0 PB A:GNH801 3.3 12.2 1.0 P A:PO4802 3.5 19.3 1.0 N3B A:GNH801 3.7 12.4 1.0 O2 A:PO4802 4.0 21.5 1.0 N A:THR59 4.0 13.9 1.0 N A:SER39 4.1 10.2 1.0 OD2 A:ASP146 4.1 16.0 1.0 OD1 A:ASP146 4.2 14.2 1.0 CA A:THR59 4.2 13.3 1.0 CA A:SER39 4.2 10.4 1.0 O A:HOH999 4.2 14.7 1.0 CG2 A:THR59 4.3 12.6 1.0 O2A A:GNH801 4.3 12.1 1.0 O1 A:PO4802 4.3 24.3 1.0 O2B A:GNH801 4.3 11.6 1.0 O4 A:PO4802 4.5 23.7 1.0 O3A A:GNH801 4.5 11.1 1.0 CG A:ASP146 4.6 14.9 1.0 O A:PRO52 4.6 19.3 1.0 O A:LEU147 4.8 11.9 1.0 CB A:VAL58 4.8 14.8 1.0 CE A:LYS38 4.8 15.1 1.0 PA A:GNH801 4.9 13.0 1.0 NZ A:LYS38 4.9 13.8 1.0 CB A:LYS38 4.9 11.4 1.0

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


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-Pn.Pi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:5.0 occ:1.00 O3 B:PO4802 2.0 16.7 1.0 O1B B:GNH801 2.0 12.3 1.0 OG1 B:THR59 2.1 12.2 1.0 OG B:SER39 2.1 9.7 1.0 O B:HOH934 2.2 11.2 1.0 O B:HOH951 2.3 12.1 1.0 CB B:THR59 3.2 13.5 1.0 CB B:SER39 3.3 9.6 1.0 PB B:GNH801 3.4 11.3 1.0 P B:PO4802 3.4 19.6 1.0 N3B B:GNH801 3.7 10.3 1.0 N B:THR59 3.9 15.3 1.0 O2 B:PO4802 4.0 19.1 1.0 N B:SER39 4.0 9.7 1.0 OD2 B:ASP146 4.1 15.7 1.0 OD1 B:ASP146 4.1 16.5 1.0 O1 B:PO4802 4.1 21.0 1.0 CA B:THR59 4.2 13.8 1.0 CA B:SER39 4.2 9.6 1.0 O2A B:GNH801 4.3 12.5 1.0 CG2 B:THR59 4.3 12.8 1.0 O2B B:GNH801 4.4 10.2 1.0 O B:HOH978 4.5 18.3 1.0 CG B:ASP146 4.5 14.4 1.0 O3A B:GNH801 4.5 12.1 1.0 O4 B:PO4802 4.5 24.0 1.0 O B:PRO52 4.7 28.6 1.0 NZ B:LYS38 4.7 10.6 1.0 O B:LEU147 4.7 12.0 1.0 CB B:VAL58 4.8 18.4 1.0 CE B:LYS38 4.8 10.9 1.0 CB B:LYS38 4.8 10.1 1.0 PA B:GNH801 4.9 13.1 1.0 CG1 B:VAL58 4.9 17.1 1.0 C B:VAL58 5.0 17.1 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