Sodium in PDB 8vn3: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 600S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 600S, PDB code: 8vn3 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 (%)	17.9 / 19.3

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 600S 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 600S (pdb code 8vn3). 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 600S, PDB code: 8vn3:
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 600S


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 600S within 5.0Å range: probe atom residue distance (Å) B Occ c:Na502 b:14.3 occ:0.30 MG c:MG501 0.1 14.1 0.7 OD1 B:ASN319 2.1 15.3 1.0 O B:HOH612 2.2 18.4 1.0 O B:HOH563 2.2 19.1 1.0 OP2 c:DG414 2.2 17.1 0.3 O3' C:DA413 2.2 15.7 0.3 O B:HOH519 2.3 13.1 1.0 O3' C:DA413 2.3 16.3 0.7 P c:DG414 2.7 17.1 0.3 P c:DG414 3.1 17.9 0.7 CG B:ASN319 3.3 13.5 1.0 OP1 c:DG414 3.5 17.3 0.7 C3' C:DA413 3.6 15.8 0.7 C3' C:DA413 3.6 15.7 0.3 O5' c:DG414 3.7 18.8 0.3 O5' c:DG414 3.7 13.5 0.7 O B:ASN319 3.8 12.5 1.0 OP1 c:DG414 3.9 18.0 0.3 ND2 B:ASN319 3.9 12.3 1.0 N B:HIS298 4.0 13.2 1.0 C4' C:DA413 4.0 13.2 0.7 C4' C:DA413 4.1 13.2 0.3 O c:HOH615 4.2 26.4 1.0 OG B:SER297 4.2 15.0 1.0 C2' C:DA413 4.2 12.2 0.7 C B:ASN319 4.3 13.9 1.0 C2' C:DA413 4.3 12.4 0.3 O B:HIS298 4.3 15.0 1.0 OP2 c:DG414 4.4 22.9 0.7 CB B:ASN319 4.5 11.2 1.0 CA B:SER297 4.5 13.1 1.0 OD1 B:ASN323 4.6 12.6 1.0 CA B:ASN319 4.7 12.3 1.0 O c:HOH601 4.7 19.0 0.2 ND1 B:HIS301 4.7 17.2 1.0 C B:SER297 4.7 13.5 1.0 C5' C:DA413 4.7 13.4 0.7 CB B:HIS298 4.7 11.7 1.0 C5' C:DA413 4.8 13.4 0.3 CA B:HIS298 4.8 12.3 1.0 CB B:SER297 4.9 13.7 1.0 CE1 B:HIS301 4.9 18.0 1.0 N B:LYS320 4.9 11.1 1.0 C B:HIS298 5.0 11.7 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 600S


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 600S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:14.1 occ:0.35 MG D:MG601 0.1 13.9 0.7 O A:HOH715 2.1 12.8 1.0 O3' D:DA513 2.2 15.6 0.7 O3' D:DA513 2.2 15.6 0.3 OD1 A:ASN119 2.2 13.7 1.0 O A:HOH808 2.3 19.4 1.0 O A:HOH777 2.3 18.0 1.0 OP1 d:DG514 2.6 14.0 0.3 P d:DG514 2.9 17.0 0.3 P d:DG514 3.3 17.2 0.6 CG A:ASN119 3.4 13.1 1.0 C3' D:DA513 3.4 16.7 0.3 C3' D:DA513 3.4 16.7 0.7 OP2 d:DG514 3.7 16.6 0.6 O5' d:DG514 3.7 16.4 0.3 C4' D:DA513 3.8 14.5 0.3 C4' D:DA513 3.8 14.5 0.7 O A:ASN119 3.8 11.6 1.0 O5' d:DG514 3.8 15.5 0.6 ND2 A:ASN119 4.0 12.6 1.0 C2' D:DA513 4.1 15.2 0.7 C2' D:DA513 4.1 15.2 0.3 N A:HIS98 4.1 12.2 1.0 OP2 d:DG514 4.1 17.1 0.3 C A:ASN119 4.2 12.2 1.0 O d:HOH609 4.2 29.2 1.0 OD1 A:ASN123 4.4 13.4 1.0 OG A:SER97 4.4 15.9 1.0 C5' D:DA513 4.5 14.3 0.3 O A:HIS98 4.5 14.8 1.0 CB A:ASN119 4.5 9.8 1.0 C5' D:DA513 4.5 14.3 0.7 OP1 d:DG514 4.6 23.9 0.6 CA A:SER97 4.6 10.2 1.0 CA A:ASN119 4.7 12.0 1.0 ND1 A:HIS101 4.7 15.8 1.0 C A:SER97 4.8 10.3 1.0 N A:LYS120 4.8 11.6 1.0 O A:HOH780 4.8 21.5 1.0 CB A:HIS98 4.9 12.5 1.0 CA A:HIS98 4.9 12.4 1.0 CE1 A:HIS101 5.0 16.4 1.0

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