Sodium in PDB 8vnj: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S, PDB code: 8vnj 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)	47.86 / 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 (%)	18.5 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S 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 120S (pdb code 8vnj). 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 120S, PDB code: 8vnj:
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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:16.8 occ:0.75 MN C:MN501 0.0 16.7 0.2 OD1 B:ASN319 2.2 18.2 1.0 O3' C:DA413 2.3 17.0 0.8 O B:HOH541 2.3 22.8 1.0 O B:HOH533 2.3 17.6 1.0 O B:HOH596 2.3 22.2 1.0 OP3 C:DG414 2.4 17.0 0.2 O3' C:DA413 2.4 17.0 0.2 OP1 C:DG414 2.5 17.1 0.8 P C:DG414 2.9 15.2 0.8 CG B:ASN319 3.4 17.2 1.0 C3' C:DA413 3.6 18.6 0.8 P C:DG414 3.6 15.7 0.2 C3' C:DA413 3.6 18.5 0.2 O5' C:DG414 3.8 17.1 0.8 O B:ASN319 3.8 15.8 1.0 C4' C:DA413 3.9 18.0 0.8 ND2 B:ASN319 4.0 16.9 1.0 N B:HIS298 4.0 15.8 1.0 C4' C:DA413 4.0 17.9 0.2 OP1 C:DG414 4.0 19.2 0.2 O5' C:DG414 4.0 18.1 0.2 OP2 C:DG414 4.1 18.7 0.8 O C:HOH639 4.2 27.5 1.0 OG B:SER297 4.2 19.0 1.0 C B:ASN319 4.2 17.4 1.0 C2' C:DA413 4.2 16.4 0.8 C2' C:DA413 4.3 16.5 0.2 O B:HIS298 4.3 17.3 1.0 CB B:ASN319 4.6 16.1 1.0 OD1 B:ASN323 4.6 15.4 1.0 CA B:SER297 4.6 16.5 1.0 C5' C:DA413 4.6 15.4 0.8 CA B:ASN319 4.7 17.1 1.0 C5' C:DA413 4.7 15.6 0.2 CB B:HIS298 4.7 16.3 1.0 C B:SER297 4.7 17.2 1.0 CA B:HIS298 4.7 16.9 1.0 ND1 B:HIS301 4.7 18.4 1.0 OP2 C:DG414 4.9 24.9 0.2 CB B:SER297 4.9 19.1 1.0 C B:HIS298 4.9 16.6 1.0 N B:LYS320 4.9 14.6 1.0 CE1 B:HIS301 4.9 21.4 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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:16.4 occ:0.75 MN D:MN601 0.0 16.4 0.2 OD1 A:ASN119 2.2 16.6 1.0 O A:HOH709 2.2 16.3 1.0 O3' D:DA513 2.3 17.0 0.8 O3' D:DA513 2.3 17.0 0.2 O A:HOH803 2.3 20.0 1.0 O A:HOH733 2.4 20.1 1.0 OP3 D:DG514 2.5 16.0 0.2 OP1 D:DG514 2.5 16.1 0.8 P D:DG514 2.9 15.4 0.8 CG A:ASN119 3.4 15.1 1.0 C3' D:DA513 3.5 19.8 0.8 C3' D:DA513 3.5 19.6 0.2 P D:DG514 3.7 15.6 0.2 O A:ASN119 3.8 15.4 1.0 C4' D:DA513 3.8 19.0 0.8 O5' D:DG514 3.9 15.4 0.8 C4' D:DA513 3.9 19.0 0.2 N A:HIS98 4.0 15.5 1.0 ND2 A:ASN119 4.0 16.3 1.0 O5' D:DG514 4.1 16.6 0.2 C2' D:DA513 4.1 16.8 0.8 OP2 D:DG514 4.2 18.5 0.8 OP2 D:DG514 4.2 18.7 0.2 C2' D:DA513 4.2 16.9 0.2 C A:ASN119 4.2 16.7 1.0 OG A:SER97 4.3 17.9 1.0 O A:HIS98 4.3 17.5 1.0 O D:HOH727 4.4 30.7 1.0 OD1 A:ASN123 4.4 17.6 1.0 C5' D:DA513 4.5 18.4 0.8 C5' D:DA513 4.6 18.4 0.2 CB A:ASN119 4.6 13.2 1.0 CA A:SER97 4.6 13.2 1.0 CA A:ASN119 4.7 16.2 1.0 ND1 A:HIS101 4.7 19.8 1.0 CB A:HIS98 4.7 16.9 1.0 C A:SER97 4.7 14.3 1.0 CA A:HIS98 4.8 17.3 1.0 N A:LYS120 4.9 14.9 1.0 CE1 A:HIS101 4.9 19.1 1.0 CB A:SER97 5.0 14.8 1.0 O A:HOH769 5.0 23.3 1.0 C A:HIS98 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.