Magnesium in PDB 8vnb: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 240S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 240S, PDB code: 8vnb 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 / 1.72
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 (%)	17.7 / 19.7

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 240S also contains other interesting chemical elements:

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 240S (pdb code 8vnb). 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 240S, PDB code: 8vnb:
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 240S


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 240S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:15.2 occ:1.00 O A:HOH743 2.0 15.1 1.0 OD1 A:ASN119 2.1 15.4 1.0 O A:HOH717 2.1 15.8 1.0 O A:HOH800 2.1 16.1 1.0 O3' D:DA513 2.2 17.0 1.0 CG A:ASN119 3.1 15.6 1.0 P d:DG514 3.3 18.4 1.0 C3' D:DA513 3.5 17.5 1.0 ND2 A:ASN119 3.7 15.4 1.0 OP2 d:DG514 3.7 18.1 1.0 O A:ASN119 3.8 14.7 1.0 O5' d:DG514 3.8 16.8 1.0 C4' D:DA513 4.0 17.1 1.0 C2' D:DA513 4.1 16.5 1.0 N A:HIS98 4.1 16.0 1.0 O d:HOH612 4.2 20.5 1.0 OG A:SER97 4.2 16.6 1.0 C A:ASN119 4.2 14.7 1.0 O A:HIS98 4.3 17.2 1.0 CB A:ASN119 4.4 13.5 1.0 OD1 A:ASN123 4.4 17.4 1.0 OP1 d:DG514 4.5 19.7 1.0 ND1 A:HIS101 4.6 19.0 1.0 CA A:ASN119 4.6 14.5 1.0 CA A:SER97 4.6 15.9 1.0 C5' D:DA513 4.8 16.9 1.0 C A:SER97 4.8 14.2 1.0 CE1 A:HIS101 4.8 17.7 1.0 N A:LYS120 4.8 13.2 1.0 CB A:SER97 4.9 16.0 1.0 CA A:HIS98 4.9 16.0 1.0 CB A:HIS98 4.9 15.7 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 240S


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 240S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:15.3 occ:1.00 O B:HOH570 2.0 14.3 1.0 OD1 B:ASN319 2.1 15.9 1.0 O B:HOH595 2.1 15.7 1.0 O3' C:DA413 2.1 17.8 1.0 O B:HOH534 2.1 16.2 1.0 CG B:ASN319 3.2 16.3 1.0 P c:DG414 3.3 17.2 1.0 C3' C:DA413 3.4 16.1 1.0 OP1 c:DG414 3.7 19.6 1.0 ND2 B:ASN319 3.7 15.4 1.0 O5' c:DG414 3.8 16.7 1.0 O B:ASN319 3.8 15.9 1.0 C4' C:DA413 4.0 16.4 1.0 C2' C:DA413 4.1 16.7 1.0 N B:HIS298 4.1 15.3 1.0 OG B:SER297 4.1 17.0 1.0 O c:HOH512 4.2 19.3 1.0 C B:ASN319 4.2 16.5 1.0 O B:HIS298 4.3 15.9 1.0 CB B:ASN319 4.4 15.9 1.0 ND1 B:HIS301 4.5 17.1 1.0 OD1 B:ASN323 4.5 15.6 1.0 OP2 c:DG414 4.5 19.8 1.0 CA B:ASN319 4.6 15.8 1.0 CA B:SER297 4.6 17.0 1.0 CE1 B:HIS301 4.7 20.8 1.0 C5' C:DA413 4.8 17.0 1.0 C B:SER297 4.8 18.0 1.0 CB B:SER297 4.9 16.4 1.0 CB B:HIS298 4.9 15.8 1.0 N B:LYS320 4.9 13.7 1.0 CA B:HIS298 4.9 13.9 1.0

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