Magnesium in PDB 8vnt: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S, PDB code: 8vnt 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)	33.02 / 1.62
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.129, 114.129, 88.74, 90, 90, 120
R / Rfree (%)	17.7 / 19.8

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S (pdb code 8vnt). 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S, PDB code: 8vnt:
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 PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S


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 PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:20.5 occ:1.00 O A:HOH717 2.1 19.0 1.0 OP3 d:DG514 2.2 24.6 0.6 O d:HOH618 2.2 24.8 1.0 O3' D:DA513 2.2 25.0 1.0 O A:HOH765 2.2 22.6 1.0 OD1 A:ASN119 2.2 21.0 1.0 O d:HOH601 2.4 24.9 0.4 P d:DG514 3.3 19.6 0.6 CG A:ASN119 3.4 18.3 1.0 C3' D:DA513 3.5 25.1 1.0 OP2 d:DG514 3.7 25.0 0.6 O5' d:DG514 3.9 16.4 0.6 O A:ASN119 3.9 17.5 1.0 C4' D:DA513 3.9 23.4 1.0 ND2 A:ASN119 4.0 18.7 1.0 OP2 d:DG514 4.0 29.4 0.4 C2' D:DA513 4.1 20.6 1.0 O d:HOH606 4.1 32.6 1.0 N A:HIS98 4.1 17.5 1.0 C A:ASN119 4.3 19.2 1.0 OG A:SER97 4.4 22.5 1.0 OD1 A:ASN123 4.4 19.4 1.0 C5' D:DA513 4.5 21.9 1.0 O A:HIS98 4.5 22.2 1.0 CB A:ASN119 4.6 15.2 1.0 OP1 d:DG514 4.6 23.0 0.6 CA A:SER97 4.6 17.9 1.0 O A:HOH773 4.7 27.6 1.0 CA A:ASN119 4.7 18.1 1.0 ND1 A:HIS101 4.8 23.3 1.0 C A:SER97 4.9 16.5 1.0 CB A:HIS98 4.9 16.7 1.0 N A:LYS120 4.9 16.2 1.0 CA A:HIS98 5.0 17.0 1.0

Magnesium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S


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 PH6.0 (K+ Mes) with 500 Um MG2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:19.2 occ:1.00 OP3 c:DG414 2.0 22.6 0.8 OD1 B:ASN319 2.1 20.2 1.0 O B:HOH591 2.1 22.5 0.2 O B:HOH567 2.2 22.4 1.0 O B:HOH521 2.2 19.4 1.0 O3' C:DA413 2.2 21.4 1.0 O B:HOH612 2.3 24.8 1.0 P c:DG414 3.2 21.5 0.8 CG B:ASN319 3.2 18.6 1.0 C3' C:DA413 3.5 21.2 1.0 OP1 c:DG414 3.6 23.0 0.8 O5' c:DG414 3.8 19.8 0.8 ND2 B:ASN319 3.8 16.9 1.0 O B:ASN319 3.8 18.5 1.0 C4' C:DA413 4.0 20.5 1.0 N B:HIS298 4.1 18.4 1.0 O c:HOH615 4.1 30.4 1.0 C2' C:DA413 4.2 19.5 1.0 C B:ASN319 4.3 19.3 1.0 OG B:SER297 4.3 21.3 1.0 OP1 c:DG414 4.3 24.6 0.2 O B:HIS298 4.4 21.3 1.0 CB B:ASN319 4.5 17.3 1.0 OP2 c:DG414 4.5 24.1 0.8 OD1 B:ASN323 4.6 18.6 1.0 CA B:SER297 4.6 19.1 1.0 CA B:ASN319 4.7 17.6 1.0 C5' C:DA413 4.7 20.2 1.0 ND1 B:HIS301 4.7 21.4 1.0 C B:SER297 4.8 20.5 1.0 CB B:HIS298 4.9 15.9 1.0 CA B:HIS298 4.9 17.5 1.0 N B:LYS320 4.9 16.2 1.0 CB B:SER297 5.0 19.5 1.0 O B:HOH581 5.0 26.9 1.0 CE1 B:HIS301 5.0 23.3 1.0

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