Magnesium in PDB 8vna: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 160S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 160S, PDB code: 8vna 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)	37.20 / 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 (%)	18.2 / 19.7

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 160S 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 160S (pdb code 8vna). 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 160S, PDB code: 8vna:
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 160S


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 160S within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:16.3 occ:0.95 NA C:NA502 0.0 16.4 0.1 OP3 C:DG414 2.0 17.7 0.9 O C:HOH646 2.1 19.1 1.0 OD1 B:ASN319 2.1 18.4 1.0 O3' C:DA413 2.1 18.9 0.1 O B:HOH522 2.1 16.7 1.0 O B:HOH559 2.1 18.8 1.0 O3' C:DA413 2.2 19.1 0.9 OP1 C:DG414 2.3 17.6 0.1 P C:DG414 2.7 12.3 0.1 CG B:ASN319 3.2 17.5 1.0 P C:DG414 3.3 19.7 0.9 C3' C:DA413 3.4 16.7 0.1 C3' C:DA413 3.5 16.4 0.9 O5' C:DG414 3.6 17.8 0.1 OP1 C:DG414 3.7 18.2 0.9 O B:ASN319 3.8 15.9 1.0 O5' C:DG414 3.8 17.7 0.9 ND2 B:ASN319 3.8 16.2 1.0 C4' C:DA413 3.9 16.9 0.1 OP2 C:DG414 3.9 18.2 0.1 C4' C:DA413 4.0 16.8 0.9 N B:HIS298 4.1 15.5 1.0 C2' C:DA413 4.1 17.0 0.1 O C:HOH631 4.1 21.1 1.0 C2' C:DA413 4.1 17.1 0.9 OG B:SER297 4.2 18.1 1.0 C B:ASN319 4.2 17.4 1.0 O B:HIS298 4.3 18.7 1.0 OD1 B:ASN323 4.5 17.0 1.0 CB B:ASN319 4.5 15.7 1.0 OP2 C:DG414 4.5 23.7 0.9 ND1 B:HIS301 4.6 18.8 1.0 CA B:ASN319 4.6 15.7 1.0 CA B:SER297 4.6 16.1 1.0 C5' C:DA413 4.6 17.9 0.1 C5' C:DA413 4.7 18.0 0.9 C B:SER297 4.8 17.4 1.0 CB B:HIS298 4.8 15.9 1.0 CE1 B:HIS301 4.8 20.7 1.0 CA B:HIS298 4.9 14.7 1.0 N B:LYS320 4.9 14.9 1.0 CB B:SER297 4.9 17.0 1.0 C5' C:DG414 5.0 18.2 0.1 C B:HIS298 5.0 15.2 1.0

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 160S


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 160S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:16.7 occ:0.70 NA D:NA602 0.0 16.8 0.3 O A:HOH748 2.0 20.7 1.0 OP3 D:DG514 2.0 17.2 0.7 OD1 A:ASN119 2.1 16.9 1.0 O A:HOH708 2.2 17.4 1.0 O3' D:DA513 2.2 19.5 0.3 O D:HOH751 2.2 20.1 1.0 O3' D:DA513 2.3 19.5 0.7 OP1 D:DG514 2.4 16.5 0.3 P D:DG514 2.8 17.8 0.3 CG A:ASN119 3.3 16.3 1.0 P D:DG514 3.3 17.6 0.7 C3' D:DA513 3.4 19.0 0.3 C3' D:DA513 3.5 19.0 0.7 O5' D:DG514 3.7 18.6 0.3 OP2 D:DG514 3.7 18.9 0.7 O A:ASN119 3.8 15.3 1.0 O5' D:DG514 3.8 14.6 0.7 ND2 A:ASN119 3.9 15.8 1.0 C4' D:DA513 3.9 18.6 0.3 C4' D:DA513 4.0 18.7 0.7 N A:HIS98 4.1 14.8 1.0 OP2 D:DG514 4.1 20.0 0.3 C2' D:DA513 4.1 17.1 0.3 C2' D:DA513 4.1 17.1 0.7 OG A:SER97 4.2 18.9 1.0 C A:ASN119 4.2 15.4 1.0 O D:HOH740 4.2 24.4 1.0 O A:HIS98 4.3 19.2 1.0 OD1 A:ASN123 4.4 17.8 1.0 CB A:ASN119 4.5 15.5 1.0 OP1 D:DG514 4.5 21.6 0.7 CA A:ASN119 4.6 16.5 1.0 CA A:SER97 4.6 15.5 1.0 ND1 A:HIS101 4.6 20.4 1.0 C5' D:DA513 4.6 17.0 0.3 C5' D:DA513 4.7 16.9 0.7 C A:SER97 4.8 14.9 1.0 CB A:HIS98 4.8 16.2 1.0 CA A:HIS98 4.8 14.7 1.0 CE1 A:HIS101 4.8 19.7 1.0 N A:LYS120 4.9 14.0 1.0 CB A:SER97 4.9 17.2 1.0 O A:HOH784 5.0 23.4 1.0 C A:HIS98 5.0 16.8 1.0

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