Magnesium in PDB 8vmy: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S, PDB code: 8vmy 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)	47.84 / 1.53
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.88, 113.88, 88.22, 90, 90, 120
R / Rfree (%)	18 / 18.9

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 20S (pdb code 8vmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S, PDB code: 8vmy:

Magnesium binding site 1 out of 1 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S


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 PH6.0 (K+ Mes) with 500 Um MG2+ For 20S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:13.0 occ:0.05 NA D:NA602 0.0 12.8 0.9 OP3 D:DG514 2.2 12.6 0.1 O A:HOH723 2.3 13.6 1.0 OD1 A:ASN119 2.3 12.7 1.0 O A:HOH763 2.4 14.9 1.0 O A:HOH810 2.4 17.5 1.0 O3' D:DA513 2.4 12.1 0.9 O3' D:DA513 2.4 12.3 0.1 OP1 D:DG514 2.6 11.5 0.9 P D:DG514 3.1 12.8 0.9 CG A:ASN119 3.4 11.2 1.0 P D:DG514 3.6 11.9 0.1 C3' D:DA513 3.6 13.2 0.1 C3' D:DA513 3.7 13.1 0.9 O A:ASN119 3.7 11.9 1.0 N A:HIS98 3.8 11.4 1.0 O5' D:DG514 4.0 12.7 0.9 C4' D:DA513 4.0 13.4 0.1 C4' D:DA513 4.0 13.4 0.9 OP2 D:DG514 4.0 14.1 0.1 ND2 A:ASN119 4.1 11.9 1.0 C A:ASN119 4.2 13.8 1.0 O5' D:DG514 4.2 12.9 0.1 O A:HIS98 4.2 13.1 1.0 OG A:SER97 4.3 13.7 1.0 OP2 D:DG514 4.3 14.2 0.9 C2' D:DA513 4.3 12.5 0.1 C2' D:DA513 4.4 12.4 0.9 OD1 A:ASN123 4.5 13.6 1.0 CA A:SER97 4.5 11.2 1.0 C A:SER97 4.6 11.1 1.0 CB A:HIS98 4.6 14.1 1.0 CB A:ASN119 4.6 10.5 1.0 CA A:HIS98 4.6 13.3 1.0 C5' D:DA513 4.6 12.5 0.1 C5' D:DA513 4.6 12.4 0.9 CA A:ASN119 4.7 12.4 1.0 O D:HOH748 4.7 28.5 1.0 OP1 D:DG514 4.7 13.4 0.1 ND1 A:HIS101 4.8 15.2 1.0 C A:HIS98 4.8 11.7 1.0 N A:LYS120 4.9 10.3 1.0 CB A:SER97 4.9 11.7 1.0 CE1 A:HIS101 5.0 15.5 1.0 O A:HOH771 5.0 19.0 1.0

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