Magnesium in PDB 8vnd: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 600S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 600S, PDB code: 8vnd 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 / 1.60
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 / 19.2

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 600S 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 600S (pdb code 8vnd). 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 600S, PDB code: 8vnd:
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 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 PH8.0 (Tris) with 500 Um MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:13.4 occ:1.00 O A:HOH759 2.0 14.7 1.0 OD1 A:ASN119 2.0 14.1 1.0 O A:HOH722 2.1 14.7 1.0 O D:HOH735 2.1 15.8 1.0 O3' D:DA513 2.1 15.7 1.0 CG A:ASN119 3.1 14.7 1.0 P d:DG514 3.3 15.1 1.0 C3' D:DA513 3.4 15.4 1.0 OP2 d:DG514 3.6 16.6 1.0 ND2 A:ASN119 3.7 15.4 1.0 O5' d:DG514 3.8 14.5 1.0 O A:ASN119 3.8 14.5 1.0 C4' D:DA513 4.0 16.5 1.0 C2' D:DA513 4.0 14.9 1.0 O d:HOH611 4.1 18.5 1.0 N A:HIS98 4.1 14.2 1.0 C A:ASN119 4.2 15.1 1.0 OG A:SER97 4.2 16.6 1.0 O A:HIS98 4.3 16.5 1.0 CB A:ASN119 4.4 13.0 1.0 OD1 A:ASN123 4.4 16.3 1.0 OP1 d:DG514 4.5 17.4 1.0 ND1 A:HIS101 4.5 18.6 1.0 CA A:ASN119 4.6 13.7 1.0 CA A:SER97 4.6 14.3 1.0 C5' D:DA513 4.7 15.1 1.0 CE1 A:HIS101 4.8 18.3 1.0 C A:SER97 4.8 13.4 1.0 N A:LYS120 4.8 14.4 1.0 CB A:HIS98 4.9 12.6 1.0 CA A:HIS98 4.9 13.5 1.0 CB A:SER97 4.9 14.4 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 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 PH8.0 (Tris) with 500 Um MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:14.2 occ:1.00 OD1 B:ASN319 2.0 15.7 1.0 O C:HOH625 2.0 14.7 1.0 O B:HOH569 2.1 15.2 1.0 O3' C:DA413 2.1 15.4 1.0 O B:HOH515 2.1 14.1 1.0 CG B:ASN319 3.1 16.3 1.0 P c:DG414 3.3 15.0 1.0 C3' C:DA413 3.4 15.3 1.0 OP1 c:DG414 3.6 17.5 1.0 ND2 B:ASN319 3.7 14.9 1.0 O5' c:DG414 3.8 14.7 1.0 O B:ASN319 3.8 14.6 1.0 C4' C:DA413 4.0 13.6 1.0 C2' C:DA413 4.0 14.9 1.0 O c:HOH508 4.1 18.6 1.0 N B:HIS298 4.1 14.7 1.0 OG B:SER297 4.2 15.3 1.0 C B:ASN319 4.2 16.0 1.0 O B:HIS298 4.3 16.1 1.0 CB B:ASN319 4.4 14.9 1.0 OD1 B:ASN323 4.5 14.3 1.0 OP2 c:DG414 4.5 16.8 1.0 ND1 B:HIS301 4.5 16.3 1.0 CA B:ASN319 4.6 14.2 1.0 CA B:SER297 4.6 14.9 1.0 C5' C:DA413 4.7 15.5 1.0 CE1 B:HIS301 4.8 19.4 1.0 C B:SER297 4.8 15.9 1.0 N B:LYS320 4.9 13.8 1.0 CB B:HIS298 4.9 14.8 1.0 CA B:HIS298 4.9 13.3 1.0 CB B:SER297 4.9 14.7 1.0

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