Magnesium in PDB 8vn6: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S, PDB code: 8vn6 was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.99 / 1.54
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.65, 113.65, 88.31, 90, 90, 120
R / Rfree (%)	18 / 19.7

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Magnesium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S (pdb code 8vn6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S, PDB code: 8vn6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:16.6 occ:0.15 NA C:NA502 0.0 16.6 0.8 OD1 B:ASN319 2.2 18.3 1.0 O B:HOH541 2.3 16.2 1.0 O B:HOH591 2.3 21.7 1.0 O B:HOH531 2.4 21.3 1.0 O3' C:DA413 2.4 16.3 0.8 O3' C:DA413 2.4 16.6 0.1 OP3 C:DG414 2.4 17.4 0.1 OP1 C:DG414 2.5 17.5 0.8 P C:DG414 3.0 18.4 0.8 CG B:ASN319 3.4 16.2 1.0 C3' C:DA413 3.6 17.0 0.8 P C:DG414 3.7 17.3 0.1 C3' C:DA413 3.7 17.0 0.1 O B:ASN319 3.7 16.5 1.0 O5' C:DG414 3.9 18.2 0.8 N B:HIS298 3.9 15.0 1.0 C4' C:DA413 4.0 16.2 0.8 ND2 B:ASN319 4.0 16.8 1.0 C4' C:DA413 4.0 16.4 0.1 OP1 C:DG414 4.1 19.7 0.1 O5' C:DG414 4.1 18.0 0.1 OG B:SER297 4.2 19.3 1.0 O C:HOH644 4.2 28.7 1.0 C B:ASN319 4.2 18.1 1.0 OP2 C:DG414 4.2 19.5 0.8 O B:HIS298 4.2 17.4 1.0 C2' C:DA413 4.3 16.7 0.8 C2' C:DA413 4.4 16.8 0.1 OD1 B:ASN323 4.5 16.9 1.0 CA B:SER297 4.5 18.3 1.0 CB B:ASN319 4.5 15.0 1.0 CA B:ASN319 4.6 15.7 1.0 C5' C:DA413 4.7 16.3 0.8 C B:SER297 4.7 16.9 1.0 CB B:HIS298 4.7 16.4 1.0 C5' C:DA413 4.7 16.4 0.1 CA B:HIS298 4.7 15.8 1.0 ND1 B:HIS301 4.7 18.2 1.0 C B:HIS298 4.8 15.4 1.0 CE1 B:HIS301 4.9 19.4 1.0 CB B:SER297 4.9 17.5 1.0 N B:LYS320 4.9 13.9 1.0 OP2 C:DG414 4.9 20.7 0.1

Magnesium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 10S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:16.9 occ:0.15 NA D:NA602 0.0 17.0 0.8 OD1 A:ASN119 2.3 17.2 1.0 O A:HOH747 2.3 21.4 1.0 O A:HOH803 2.3 22.1 1.0 O A:HOH719 2.3 16.7 1.0 O3' D:DA513 2.4 15.6 0.8 O3' D:DA513 2.4 15.8 0.1 OP3 D:DG514 2.4 16.3 0.1 OP1 D:DG514 2.6 16.9 0.8 P D:DG514 3.0 16.4 0.8 CG A:ASN119 3.4 15.5 1.0 C3' D:DA513 3.6 17.2 0.8 C3' D:DA513 3.7 17.1 0.1 P D:DG514 3.7 17.3 0.1 O A:ASN119 3.7 14.9 1.0 N A:HIS98 3.9 15.0 1.0 O5' D:DG514 3.9 15.7 0.8 C4' D:DA513 4.0 16.6 0.8 C4' D:DA513 4.0 16.7 0.1 ND2 A:ASN119 4.1 15.9 1.0 O5' D:DG514 4.1 16.6 0.1 OP2 D:DG514 4.2 19.2 0.1 OG A:SER97 4.2 17.9 1.0 C A:ASN119 4.2 16.3 1.0 O A:HIS98 4.2 17.5 1.0 OP2 D:DG514 4.3 18.8 0.8 C2' D:DA513 4.3 16.0 0.8 C2' D:DA513 4.3 16.1 0.1 CA A:SER97 4.5 15.1 1.0 OD1 A:ASN123 4.5 17.5 1.0 O D:HOH721 4.5 34.0 1.0 CB A:ASN119 4.6 13.1 1.0 C A:SER97 4.6 14.5 1.0 CB A:HIS98 4.6 17.1 1.0 CA A:HIS98 4.6 16.0 1.0 CA A:ASN119 4.7 15.0 1.0 C5' D:DA513 4.7 16.4 0.8 C5' D:DA513 4.7 16.6 0.1 ND1 A:HIS101 4.7 18.5 1.0 C A:HIS98 4.8 16.4 1.0 CB A:SER97 4.9 16.4 1.0 N A:LYS120 4.9 13.8 1.0 CE1 A:HIS101 4.9 18.2 1.0 OP1 D:DG514 4.9 18.6 0.1 O A:HOH767 5.0 24.2 1.0

C.Chang, Y.Gao. Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.