Sodium in PDB 8vnk: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S, PDB code: 8vnk 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)	43.07 / 1.61
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.06, 114.06, 88.02, 90, 90, 120
R / Rfree (%)	18.2 / 19.4

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S (pdb code 8vnk). 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 MN2+ For 160S, PDB code: 8vnk:
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 MN2+ 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 MN2+ For 160S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:16.0 occ:0.60 MN C:MN501 0.1 15.8 0.4 OD1 B:ASN319 2.2 18.4 1.0 OP3 C:DG414 2.2 16.6 0.4 O B:HOH595 2.2 21.5 1.0 OP1 C:DG414 2.3 17.4 0.6 O B:HOH520 2.3 16.8 1.0 O B:HOH541 2.3 23.1 1.0 O3' C:DA413 2.5 17.3 0.8 O3' C:DA413 2.5 17.2 0.2 P C:DG414 2.8 17.5 0.6 CG B:ASN319 3.3 16.8 1.0 P C:DG414 3.5 15.4 0.4 O5' C:DG414 3.7 17.3 0.6 C3' C:DA413 3.7 18.0 0.8 C3' C:DA413 3.7 17.9 0.2 OP1 C:DG414 3.9 18.1 0.4 O B:ASN319 3.9 16.8 1.0 ND2 B:ASN319 3.9 16.8 1.0 O5' C:DG414 4.0 17.3 0.4 N B:HIS298 4.0 16.7 1.0 C4' C:DA413 4.1 19.6 0.8 OP2 C:DG414 4.1 19.9 0.6 C4' C:DA413 4.1 19.5 0.2 O C:HOH641 4.1 26.9 1.0 OG B:SER297 4.2 18.4 1.0 C B:ASN319 4.3 18.0 1.0 O B:HIS298 4.3 17.4 1.0 C2' C:DA413 4.3 17.8 0.8 C2' C:DA413 4.3 18.0 0.2 CB B:ASN319 4.5 15.8 1.0 CA B:SER297 4.6 16.2 1.0 OD1 B:ASN323 4.6 16.1 1.0 CA B:ASN319 4.7 16.3 1.0 ND1 B:HIS301 4.7 19.8 1.0 CB B:HIS298 4.7 15.9 1.0 OP2 C:DG414 4.7 21.8 0.4 C5' C:DA413 4.7 17.6 0.8 C B:SER297 4.7 16.6 1.0 CA B:HIS298 4.8 16.5 1.0 C5' C:DA413 4.8 17.8 0.2 CE1 B:HIS301 4.9 19.3 1.0 CB B:SER297 4.9 17.2 1.0 C B:HIS298 4.9 15.8 1.0 N B:LYS320 4.9 15.2 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 MN2+ 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 MN2+ For 160S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:15.6 occ:0.55 MN D:MN601 0.1 15.5 0.5 OD1 A:ASN119 2.2 16.5 1.0 O A:HOH716 2.2 14.9 1.0 O3' D:DA513 2.3 17.2 0.8 OP3 D:DG514 2.3 15.9 0.5 O3' D:DA513 2.3 17.4 0.2 O A:HOH803 2.3 19.3 1.0 OP1 D:DG514 2.4 15.8 0.6 O A:HOH736 2.4 21.2 1.0 P D:DG514 2.8 17.8 0.6 CG A:ASN119 3.3 14.0 1.0 C3' D:DA513 3.5 19.6 0.8 C3' D:DA513 3.6 19.1 0.2 P D:DG514 3.6 14.1 0.5 O5' D:DG514 3.7 14.5 0.6 O A:ASN119 3.8 16.1 1.0 C4' D:DA513 3.9 20.2 0.8 ND2 A:ASN119 3.9 15.8 1.0 OP2 D:DG514 4.0 18.4 0.5 C4' D:DA513 4.0 19.9 0.2 O5' D:DG514 4.0 15.6 0.5 OP2 D:DG514 4.0 18.4 0.6 C2' D:DA513 4.1 17.1 0.8 N A:HIS98 4.1 15.0 1.0 C2' D:DA513 4.2 17.2 0.2 C A:ASN119 4.2 16.4 1.0 O D:HOH741 4.2 28.4 1.0 OG A:SER97 4.3 17.2 1.0 O A:HIS98 4.4 17.7 1.0 OD1 A:ASN123 4.4 17.0 1.0 CB A:ASN119 4.5 14.4 1.0 C5' D:DA513 4.6 18.3 0.8 CA A:ASN119 4.6 16.4 1.0 CA A:SER97 4.6 14.9 1.0 C5' D:DA513 4.7 18.4 0.2 ND1 A:HIS101 4.7 20.4 1.0 N A:LYS120 4.8 15.7 1.0 C A:SER97 4.8 13.9 1.0 OP1 D:DG514 4.8 20.7 0.5 CB A:HIS98 4.9 15.3 1.0 CA A:HIS98 4.9 16.4 1.0 CE1 A:HIS101 4.9 20.4 1.0

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