Magnesium in PDB 8vnc: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 320S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 320S, PDB code: 8vnc 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)	47.79 / 1.62
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 / 18.8

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 320S 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 320S (pdb code 8vnc). 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 320S, PDB code: 8vnc:
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 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 PH8.0 (Tris) with 500 Um MG2+ For 320S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:14.1 occ:1.00 O A:HOH737 2.0 16.4 1.0 OD1 A:ASN119 2.0 14.7 1.0 O A:HOH718 2.0 15.3 1.0 O A:HOH797 2.1 15.2 1.0 O3' D:DA513 2.2 16.6 1.0 CG A:ASN119 3.1 15.3 1.0 P d:DG514 3.3 17.0 1.0 C3' D:DA513 3.5 16.9 1.0 OP2 d:DG514 3.7 17.0 1.0 ND2 A:ASN119 3.7 15.7 1.0 O A:ASN119 3.8 15.1 1.0 O5' d:DG514 3.8 15.9 1.0 C4' D:DA513 4.0 16.8 1.0 O d:HOH610 4.1 18.6 1.0 N A:HIS98 4.1 15.3 1.0 C2' D:DA513 4.1 17.3 1.0 C A:ASN119 4.2 14.9 1.0 OG A:SER97 4.2 17.5 1.0 O A:HIS98 4.4 16.8 1.0 CB A:ASN119 4.4 14.1 1.0 OD1 A:ASN123 4.4 16.4 1.0 ND1 A:HIS101 4.5 19.2 1.0 CA A:ASN119 4.6 15.2 1.0 OP1 d:DG514 4.6 18.8 1.0 CA A:SER97 4.6 14.6 1.0 CE1 A:HIS101 4.8 18.8 1.0 C5' D:DA513 4.8 15.5 1.0 N A:LYS120 4.8 13.7 1.0 C A:SER97 4.8 14.1 1.0 CB A:HIS98 4.9 14.2 1.0 CA A:HIS98 4.9 14.8 1.0 CB A:SER97 5.0 16.5 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 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 PH8.0 (Tris) with 500 Um MG2+ For 320S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:14.3 occ:1.00 OD1 B:ASN319 2.0 14.9 1.0 O B:HOH601 2.0 14.4 1.0 O B:HOH554 2.0 15.6 1.0 O B:HOH515 2.1 15.1 1.0 O3' C:DA413 2.2 17.1 1.0 CG B:ASN319 3.1 16.7 1.0 P c:DG414 3.3 16.7 1.0 C3' C:DA413 3.5 16.4 1.0 OP1 c:DG414 3.7 17.9 1.0 ND2 B:ASN319 3.7 15.3 1.0 O5' c:DG414 3.8 15.8 1.0 O B:ASN319 3.8 15.6 1.0 C4' C:DA413 4.0 15.8 1.0 C2' C:DA413 4.1 17.1 1.0 N B:HIS298 4.2 16.1 1.0 OG B:SER297 4.2 17.1 1.0 O c:HOH512 4.2 19.1 1.0 C B:ASN319 4.2 16.1 1.0 O B:HIS298 4.3 16.9 1.0 CB B:ASN319 4.4 14.9 1.0 OD1 B:ASN323 4.4 15.3 1.0 ND1 B:HIS301 4.5 17.3 1.0 OP2 c:DG414 4.6 18.1 1.0 CA B:ASN319 4.6 16.1 1.0 CA B:SER297 4.7 15.8 1.0 C5' C:DA413 4.8 16.0 1.0 CE1 B:HIS301 4.8 19.5 1.0 C B:SER297 4.9 16.5 1.0 N B:LYS320 4.9 13.6 1.0 CB B:HIS298 4.9 15.4 1.0 CB B:SER297 4.9 16.1 1.0 CA B:HIS298 5.0 14.5 1.0

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