Magnesium in PDB 8vmv: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S, PDB code: 8vmv 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)	42.93 / 1.59
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.58, 113.58, 87.99, 90, 90, 120
R / Rfree (%)	17.9 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S (pdb code 8vmv). 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 600S, PDB code: 8vmv:
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 PH7.0 (K+ Mes) with 500 Um MG2+ For 600S


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 PH7.0 (K+ Mes) with 500 Um MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ d:Mg601 b:14.4 occ:0.90 NA d:NA602 0.0 14.1 0.1 O A:HOH761 2.0 16.5 1.0 OD1 A:ASN119 2.1 14.3 1.0 OP1 d:DG514 2.1 15.0 0.1 O A:HOH720 2.1 13.4 1.0 OP3 d:DG514 2.1 15.4 0.9 O d:HOH715 2.1 17.2 1.0 O3' D:DA513 2.2 17.1 0.9 O3' D:DA513 2.3 16.4 0.1 P d:DG514 2.6 35.0 0.1 CG A:ASN119 3.2 14.4 1.0 P d:DG514 3.3 15.0 0.9 C3' D:DA513 3.5 17.9 0.9 O5' d:DG514 3.6 16.5 0.1 C3' D:DA513 3.6 17.7 0.1 OP2 d:DG514 3.6 17.4 0.9 OP2 d:DG514 3.7 16.4 0.1 ND2 A:ASN119 3.8 14.8 1.0 O5' d:DG514 3.8 13.7 0.9 O A:ASN119 3.8 13.5 1.0 C4' D:DA513 4.0 16.8 0.9 C4' D:DA513 4.0 16.7 0.1 N A:HIS98 4.1 13.4 1.0 C2' D:DA513 4.1 14.7 0.9 O d:HOH707 4.1 21.8 1.0 C2' D:DA513 4.2 15.0 0.1 C A:ASN119 4.2 13.9 1.0 OG A:SER97 4.2 16.6 1.0 O A:HIS98 4.3 16.4 1.0 CB A:ASN119 4.4 12.1 1.0 OD1 A:ASN123 4.4 15.2 1.0 OP1 d:DG514 4.5 18.3 0.9 CA A:SER97 4.6 12.6 1.0 ND1 A:HIS101 4.6 18.2 1.0 CA A:ASN119 4.6 14.3 1.0 C5' D:DA513 4.7 15.6 0.9 C A:SER97 4.8 12.6 1.0 C5' D:DA513 4.8 16.2 0.1 CE1 A:HIS101 4.8 17.2 1.0 N A:LYS120 4.9 11.8 1.0 CB A:HIS98 4.9 13.9 1.0 CA A:HIS98 4.9 13.7 1.0 CB A:SER97 4.9 14.4 1.0 O A:HOH781 4.9 20.9 1.0 C5' d:DG514 5.0 15.5 0.1

Magnesium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S


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 PH7.0 (K+ Mes) with 500 Um MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:13.8 occ:1.00 O B:HOH561 2.1 15.1 1.0 O c:HOH514 2.1 16.2 1.0 OP3 c:DG414 2.1 15.8 1.0 OD1 B:ASN319 2.1 16.1 1.0 O3' C:DA413 2.2 17.3 1.0 O B:HOH518 2.2 14.8 1.0 CG B:ASN319 3.2 14.2 1.0 P c:DG414 3.3 16.9 1.0 C3' C:DA413 3.5 15.5 1.0 OP1 c:DG414 3.5 16.7 1.0 ND2 B:ASN319 3.8 12.8 1.0 O5' c:DG414 3.8 15.5 1.0 O B:ASN319 3.9 14.1 1.0 C4' C:DA413 4.0 15.0 1.0 N B:HIS298 4.1 13.9 1.0 O c:HOH510 4.1 19.5 1.0 C2' C:DA413 4.1 14.3 1.0 OG B:SER297 4.2 15.7 1.0 C B:ASN319 4.2 14.0 1.0 O B:HIS298 4.3 15.8 1.0 OP2 c:DG414 4.4 18.2 1.0 CB B:ASN319 4.4 14.6 1.0 OD1 B:ASN323 4.5 14.9 1.0 ND1 B:HIS301 4.5 16.1 1.0 CA B:SER297 4.6 14.6 1.0 CA B:ASN319 4.6 15.2 1.0 C5' C:DA413 4.7 13.8 1.0 C B:SER297 4.8 15.8 1.0 CE1 B:HIS301 4.8 18.9 1.0 CB B:HIS298 4.8 12.9 1.0 CA B:HIS298 4.9 12.9 1.0 N B:LYS320 4.9 12.2 1.0 CB B:SER297 4.9 13.8 1.0

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