Sodium in PDB 8vn1: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S, PDB code: 8vn1 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)	47.84 / 1.79
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.88, 113.88, 88.22, 90, 90, 120
R / Rfree (%)	17.8 / 20

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S (pdb code 8vn1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S, PDB code: 8vn1:
Jump to Sodium binding site number: 1; 2;

Sodium 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 160S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:15.0 occ:0.70 MG C:MG501 0.1 14.8 0.3 OP3 C:DG414 2.1 15.4 0.3 OD1 B:ASN319 2.2 13.9 1.0 O B:HOH808 2.2 22.5 1.0 O B:HOH728 2.3 16.1 1.0 O B:HOH745 2.3 17.1 1.0 O3' C:DA413 2.4 14.8 0.7 O3' C:DA413 2.4 14.8 0.3 OP1 C:DG414 2.5 16.8 0.7 P C:DG414 3.0 16.2 0.7 CG B:ASN319 3.3 14.6 1.0 P C:DG414 3.4 18.7 0.3 C3' C:DA413 3.6 13.1 0.7 C3' C:DA413 3.7 13.1 0.3 O B:ASN319 3.7 13.9 1.0 OP1 C:DG414 3.8 15.5 0.3 O5' C:DG414 3.9 14.7 0.7 N B:HIS298 3.9 12.0 1.0 O5' C:DG414 4.0 17.5 0.3 ND2 B:ASN319 4.0 13.4 1.0 C4' C:DA413 4.0 14.1 0.7 C4' C:DA413 4.1 14.1 0.3 O C:HOH641 4.2 29.7 1.0 C B:ASN319 4.2 13.6 1.0 OP2 C:DG414 4.2 16.4 0.7 OG B:SER297 4.2 14.6 1.0 O B:HIS298 4.3 13.9 1.0 C2' C:DA413 4.3 13.2 0.7 C2' C:DA413 4.4 13.3 0.3 OD1 B:ASN323 4.5 11.7 1.0 CB B:ASN319 4.5 13.5 1.0 CA B:SER297 4.6 13.7 1.0 CA B:ASN319 4.6 13.5 1.0 OP2 C:DG414 4.7 21.3 0.3 C5' C:DA413 4.7 12.3 0.7 CB B:HIS298 4.7 13.1 1.0 ND1 B:HIS301 4.7 12.4 1.0 C5' C:DA413 4.7 12.4 0.3 C B:SER297 4.7 13.2 1.0 CA B:HIS298 4.7 11.6 1.0 C B:HIS298 4.9 14.0 1.0 CE1 B:HIS301 4.9 17.7 1.0 N B:LYS320 4.9 10.5 1.0 CB B:SER297 4.9 14.6 1.0

Sodium 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 160S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 160S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:14.5 occ:0.70 MG D:MG601 0.0 14.3 0.3 OP3 D:DG514 2.2 13.2 0.3 OD1 A:ASN119 2.2 12.7 1.0 O A:HOH755 2.3 17.3 1.0 O A:HOH707 2.3 14.0 1.0 O3' D:DA513 2.3 13.4 0.7 O3' D:DA513 2.3 13.4 0.3 O A:HOH814 2.4 20.0 1.0 OP1 D:DG514 2.5 13.2 0.7 P D:DG514 3.0 13.9 0.7 CG A:ASN119 3.4 11.7 1.0 P D:DG514 3.5 18.6 0.3 C3' D:DA513 3.6 14.6 0.7 C3' D:DA513 3.6 14.6 0.3 O A:ASN119 3.8 12.5 1.0 O5' D:DG514 3.9 15.5 0.7 N A:HIS98 3.9 10.6 1.0 OP2 D:DG514 3.9 15.8 0.3 C4' D:DA513 3.9 15.1 0.7 C4' D:DA513 4.0 15.1 0.3 O5' D:DG514 4.0 16.1 0.3 ND2 A:ASN119 4.0 13.5 1.0 OP2 D:DG514 4.2 15.5 0.7 OG A:SER97 4.2 12.1 1.0 C A:ASN119 4.2 13.0 1.0 C2' D:DA513 4.3 14.9 0.3 C2' D:DA513 4.3 15.0 0.7 O A:HIS98 4.3 13.5 1.0 OD1 A:ASN123 4.5 12.5 1.0 CA A:SER97 4.5 11.5 1.0 O D:HOH709 4.6 31.0 1.0 CB A:ASN119 4.6 8.1 1.0 C5' D:DA513 4.6 15.4 0.7 C5' D:DA513 4.6 15.4 0.3 C A:SER97 4.6 11.1 1.0 CA A:ASN119 4.7 12.5 1.0 CB A:HIS98 4.7 14.4 1.0 OP1 D:DG514 4.7 19.7 0.3 CA A:HIS98 4.7 13.6 1.0 ND1 A:HIS101 4.8 16.9 1.0 CB A:SER97 4.9 9.2 1.0 C A:HIS98 4.9 13.1 1.0 N A:LYS120 4.9 12.7 1.0 O A:HOH796 5.0 19.7 1.0 CE1 A:HIS101 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.