Magnesium in PDB 8vmu: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 320S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 320S, PDB code: 8vmu 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 / 1.52
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 (%)	18.5 / 19.4

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 320S 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 320S (pdb code 8vmu). 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 320S, PDB code: 8vmu:
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 320S


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 320S within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:15.4 occ:0.70 NA C:NA502 0.0 15.4 0.3 O C:HOH637 2.1 21.4 1.0 O B:HOH567 2.1 19.8 1.0 OD1 B:ASN319 2.1 16.9 1.0 OP3 C:DG414 2.1 17.7 0.7 O B:HOH515 2.2 16.3 1.0 O3' C:DA413 2.3 17.2 0.3 O3' C:DA413 2.3 17.2 0.7 OP1 C:DG414 2.3 17.9 0.3 P C:DG414 2.9 13.1 0.3 CG B:ASN319 3.3 15.8 1.0 P C:DG414 3.4 19.6 0.7 C3' C:DA413 3.6 17.4 0.3 C3' C:DA413 3.6 17.4 0.7 O B:ASN319 3.8 14.5 1.0 O5' C:DG414 3.8 15.1 0.3 ND2 B:ASN319 3.9 15.1 1.0 OP1 C:DG414 3.9 18.9 0.7 O5' C:DG414 4.0 16.4 0.7 C4' C:DA413 4.0 16.8 0.3 C4' C:DA413 4.0 16.8 0.7 N B:HIS298 4.1 14.5 1.0 OP2 C:DG414 4.1 19.5 0.3 O C:HOH636 4.1 23.4 1.0 OG B:SER297 4.2 17.9 1.0 C B:ASN319 4.2 16.1 1.0 C2' C:DA413 4.2 16.6 0.3 C2' C:DA413 4.2 16.6 0.7 O B:HIS298 4.3 17.5 1.0 OD1 B:ASN323 4.4 16.0 1.0 CB B:ASN319 4.5 14.5 1.0 CA B:SER297 4.6 15.5 1.0 CA B:ASN319 4.6 13.7 1.0 OP2 C:DG414 4.6 21.5 0.7 ND1 B:HIS301 4.7 19.7 1.0 C5' C:DA413 4.7 15.2 0.3 C5' C:DA413 4.7 15.2 0.7 C B:SER297 4.8 14.7 1.0 CB B:HIS298 4.8 14.8 1.0 CA B:HIS298 4.8 14.5 1.0 N B:LYS320 4.9 13.9 1.0 CE1 B:HIS301 4.9 19.0 1.0 CB B:SER297 4.9 16.2 1.0 O B:HOH501 4.9 20.5 0.2 C B:HIS298 5.0 14.5 1.0

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 320S


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 320S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:17.0 occ:0.60 NA D:NA602 0.0 17.1 0.4 O A:HOH713 2.1 15.4 1.0 O A:HOH747 2.1 21.3 1.0 OD1 A:ASN119 2.2 16.4 1.0 O A:HOH811 2.2 20.3 1.0 O3' D:DA513 2.3 16.7 0.6 OP3 D:DG514 2.3 17.4 0.6 O3' D:DA513 2.3 16.5 0.4 OP1 D:DG514 2.4 17.1 0.4 P D:DG514 2.9 14.6 0.4 CG A:ASN119 3.3 14.8 1.0 P D:DG514 3.5 19.6 0.6 C3' D:DA513 3.5 18.5 0.6 C3' D:DA513 3.6 18.5 0.4 O A:ASN119 3.8 13.7 1.0 O5' D:DG514 3.9 14.2 0.4 OP2 D:DG514 3.9 18.1 0.6 C4' D:DA513 3.9 17.8 0.4 C4' D:DA513 4.0 17.9 0.6 ND2 A:ASN119 4.0 14.7 1.0 O5' D:DG514 4.0 14.5 0.6 N A:HIS98 4.0 13.4 1.0 OP2 D:DG514 4.1 19.5 0.4 C A:ASN119 4.2 16.2 1.0 O D:HOH731 4.2 29.0 1.0 C2' D:DA513 4.2 16.5 0.6 OG A:SER97 4.2 17.5 1.0 C2' D:DA513 4.3 16.7 0.4 O A:HIS98 4.3 18.3 1.0 OD1 A:ASN123 4.4 16.6 1.0 CB A:ASN119 4.5 12.5 1.0 CA A:SER97 4.6 15.0 1.0 C5' D:DA513 4.6 17.3 0.6 C5' D:DA513 4.6 17.4 0.4 CA A:ASN119 4.6 14.8 1.0 ND1 A:HIS101 4.7 19.0 1.0 C A:SER97 4.7 14.0 1.0 CB A:HIS98 4.8 14.8 1.0 CA A:HIS98 4.8 15.0 1.0 OP1 D:DG514 4.8 21.6 0.6 N A:LYS120 4.9 12.8 1.0 O A:HOH786 4.9 21.9 1.0 CE1 A:HIS101 4.9 17.7 1.0 CB A:SER97 4.9 16.6 1.0 C A:HIS98 5.0 15.4 1.0

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