Sodium in PDB 8vn2: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 320S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 320S, PDB code: 8vn2 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 / 1.63
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 (%)	17.6 / 19.2

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 320S 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 320S (pdb code 8vn2). 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 320S, PDB code: 8vn2:
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 320S


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 320S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:14.2 occ:0.40 MG C:MG501 0.0 14.1 0.6 OP3 C:DG414 2.0 14.9 0.6 OD1 B:ASN319 2.2 15.5 1.0 O B:HOH528 2.2 13.3 1.0 O B:HOH606 2.3 19.4 1.0 O B:HOH518 2.3 18.2 1.0 O3' C:DA413 2.4 14.4 0.4 O3' C:DA413 2.4 14.5 0.6 OP1 C:DG414 2.5 15.1 0.4 P C:DG414 3.0 13.6 0.4 P C:DG414 3.3 20.6 0.6 CG B:ASN319 3.4 12.8 1.0 C3' C:DA413 3.6 15.1 0.4 C3' C:DA413 3.6 15.1 0.6 OP1 C:DG414 3.7 20.5 0.6 O B:ASN319 3.8 12.8 1.0 O5' C:DG414 3.9 17.3 0.4 O5' C:DG414 3.9 16.8 0.6 C4' C:DA413 4.0 14.3 0.4 ND2 B:ASN319 4.0 12.4 1.0 N B:HIS298 4.0 13.0 1.0 C4' C:DA413 4.0 14.3 0.6 C B:ASN319 4.2 12.0 1.0 OP2 C:DG414 4.2 15.2 0.4 OG B:SER297 4.2 14.5 1.0 O C:HOH642 4.2 27.4 1.0 C2' C:DA413 4.3 13.3 0.4 C2' C:DA413 4.3 13.3 0.6 O B:HIS298 4.4 12.9 1.0 OD1 B:ASN323 4.5 12.7 1.0 OP2 C:DG414 4.5 26.3 0.6 CB B:ASN319 4.6 12.9 1.0 CA B:SER297 4.6 12.4 1.0 C5' C:DA413 4.7 12.9 0.4 CA B:ASN319 4.7 13.9 1.0 ND1 B:HIS301 4.7 16.9 1.0 C5' C:DA413 4.7 12.9 0.6 CB B:HIS298 4.7 12.6 1.0 C B:SER297 4.8 13.2 1.0 CA B:HIS298 4.8 14.4 1.0 CE1 B:HIS301 4.9 16.8 1.0 N B:LYS320 4.9 9.9 1.0 CB B:SER297 4.9 14.0 1.0 C B:HIS298 5.0 13.7 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 320S


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 320S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:14.9 occ:0.60 MG D:MG601 0.1 14.8 0.4 OP3 D:DG514 2.2 13.6 0.4 O A:HOH712 2.2 12.2 1.0 OD1 A:ASN119 2.2 13.7 1.0 O3' D:DA513 2.3 13.6 0.6 O3' D:DA513 2.3 13.6 0.4 O A:HOH810 2.3 17.9 1.0 O A:HOH738 2.3 18.9 1.0 OP1 D:DG514 2.6 12.4 0.6 P D:DG514 3.0 14.0 0.6 CG A:ASN119 3.4 12.4 1.0 P D:DG514 3.4 16.3 0.4 C3' D:DA513 3.5 15.0 0.6 C3' D:DA513 3.5 14.9 0.4 O A:ASN119 3.8 11.7 1.0 OP2 D:DG514 3.8 16.0 0.4 O5' D:DG514 3.9 12.4 0.6 C4' D:DA513 3.9 14.1 0.6 C4' D:DA513 3.9 14.1 0.4 O5' D:DG514 4.0 16.0 0.4 N A:HIS98 4.0 12.1 1.0 ND2 A:ASN119 4.0 12.5 1.0 C2' D:DA513 4.2 13.6 0.6 C2' D:DA513 4.2 13.6 0.4 OP2 D:DG514 4.2 15.9 0.6 C A:ASN119 4.2 11.8 1.0 OG A:SER97 4.3 13.7 1.0 OD1 A:ASN123 4.4 14.3 1.0 O A:HIS98 4.4 14.1 1.0 O D:HOH745 4.5 29.8 1.0 C5' D:DA513 4.6 14.4 0.6 CA A:SER97 4.6 11.1 1.0 CB A:ASN119 4.6 10.1 1.0 C5' D:DA513 4.6 14.4 0.4 OP1 D:DG514 4.7 22.8 0.4 CA A:ASN119 4.7 12.0 1.0 ND1 A:HIS101 4.7 16.4 1.0 C A:SER97 4.7 9.8 1.0 CB A:HIS98 4.8 12.4 1.0 CA A:HIS98 4.8 13.5 1.0 O A:HOH778 4.9 21.2 1.0 N A:LYS120 4.9 10.3 1.0 CE1 A:HIS101 5.0 16.2 1.0 CB A:SER97 5.0 11.6 1.0

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