Magnesium in PDB 7a2f: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656, PDB code: 7a2f was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.38 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.58, 115, 68.45, 90, 108.36, 90
R / Rfree (%)	18.8 / 22.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 (pdb code 7a2f). 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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656, PDB code: 7a2f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:9.5 occ:1.00 O A:HOH1107 1.9 21.7 1.0 OD1 A:ASP710 2.0 19.7 1.0 O A:HOH1110 2.1 16.7 1.0 O A:HOH1211 2.1 33.8 1.0 O A:HOH1121 2.2 15.6 1.0 O A:HOH1204 2.3 17.8 1.0 CG A:ASP710 3.1 20.4 1.0 O A:HOH1203 3.4 33.5 1.0 OD2 A:ASP710 3.5 21.6 1.0 ZN A:ZN1001 3.8 24.4 1.0 O A:HIS709 4.0 18.4 1.0 NE2 A:HIS745 4.0 20.0 1.0 OG1 A:THR783 4.0 20.6 1.0 CD2 A:HIS709 4.1 16.6 1.0 OD2 A:ASP822 4.2 18.6 1.0 OE2 A:GLU742 4.3 25.4 1.0 CD2 A:HIS745 4.3 20.5 1.0 CB A:ASP710 4.4 20.5 1.0 NE2 A:HIS709 4.5 17.0 1.0 CD2 A:HIS713 4.5 21.4 1.0 CB A:THR783 4.6 19.4 1.0 O A:HOH1209 4.6 26.8 1.0 CA A:ASP710 4.7 20.5 1.0 CD2 A:HIS669 4.8 22.2 1.0 C A:HIS709 4.9 18.4 1.0 NE2 A:HIS669 4.9 20.7 1.0 NE2 A:HIS713 4.9 21.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:7.8 occ:1.00 O B:HOH1118 1.9 21.5 1.0 O B:HOH1152 1.9 19.5 1.0 OD1 B:ASP710 2.0 15.1 1.0 O B:HOH1222 2.1 26.7 1.0 O B:HOH1192 2.2 19.7 1.0 O B:HOH1169 2.3 25.3 1.0 CG B:ASP710 3.1 16.4 1.0 OD2 B:ASP710 3.6 16.8 1.0 O B:HOH1129 3.8 25.4 1.0 ZN B:ZN1002 3.8 24.6 1.0 NE2 B:HIS745 4.0 19.8 1.0 O B:HIS709 4.0 17.9 1.0 OG1 B:THR783 4.1 23.1 1.0 OE2 B:GLU742 4.2 27.4 1.0 CD2 B:HIS709 4.2 16.0 1.0 O B:HOH1227 4.2 39.8 1.0 CD2 B:HIS745 4.4 19.7 1.0 CB B:ASP710 4.4 16.2 1.0 OD2 B:ASP822 4.4 29.3 1.0 CD2 B:HIS713 4.5 20.9 1.0 O B:HOH1197 4.5 23.3 1.0 NE2 B:HIS709 4.6 17.2 1.0 CB B:THR783 4.7 21.9 1.0 CA B:ASP710 4.7 17.4 1.0 NE2 B:HIS713 4.7 21.5 1.0 CD2 B:HIS669 4.8 22.5 1.0 NE2 B:HIS669 4.9 22.0 1.0 C B:HIS709 4.9 18.3 1.0 O B:HOH1233 5.0 38.1 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 To Be Published.