Sodium in PDB 8vnn: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 480S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 480S, PDB code: 8vnn 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 / 1.79
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 (%)	17.7 / 19.5

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 480S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Manganese	(Mn)	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 MN2+ For 480S (pdb code 8vnn). 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 480S, PDB code: 8vnn:
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 480S


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 480S within 5.0Å range: probe atom residue distance (Å) B Occ c:Na502 b:16.5 occ:0.20 MN c:MN501 0.0 16.2 0.8 O c:HOH615 2.0 17.4 1.0 OD1 B:ASN319 2.1 15.2 1.0 O B:HOH585 2.1 17.6 1.0 OP2 c:DG414 2.2 17.9 0.2 O B:HOH527 2.2 17.9 1.0 O3' C:DA413 2.3 18.1 0.2 O3' C:DA413 2.3 18.3 0.8 P c:DG414 2.7 20.9 0.2 CG B:ASN319 3.2 16.3 1.0 P c:DG414 3.3 17.6 0.8 C3' C:DA413 3.6 17.4 0.2 O5' c:DG414 3.6 18.6 0.2 OP1 c:DG414 3.6 17.6 0.8 C3' C:DA413 3.6 17.4 0.8 O5' c:DG414 3.8 18.0 0.8 ND2 B:ASN319 3.8 16.5 1.0 O B:ASN319 3.8 18.2 1.0 C4' C:DA413 4.0 18.1 0.2 OP1 c:DG414 4.0 18.5 0.2 N B:HIS298 4.1 18.1 1.0 O c:HOH611 4.1 24.7 1.0 C4' C:DA413 4.2 18.1 0.8 C2' C:DA413 4.2 17.2 0.2 OG B:SER297 4.2 17.8 1.0 C B:ASN319 4.2 16.4 1.0 C2' C:DA413 4.3 17.3 0.8 O B:HIS298 4.3 15.7 1.0 CB B:ASN319 4.4 16.0 1.0 ND1 B:HIS301 4.5 16.8 1.0 OD1 B:ASN323 4.6 16.0 1.0 OP2 c:DG414 4.6 18.6 0.8 CA B:ASN319 4.6 15.8 1.0 CA B:SER297 4.7 18.0 1.0 C5' C:DA413 4.7 19.2 0.2 CE1 B:HIS301 4.8 23.0 1.0 C B:SER297 4.8 17.4 1.0 C5' C:DA413 4.8 19.3 0.8 CB B:HIS298 4.8 14.3 1.0 CA B:HIS298 4.9 16.9 1.0 N B:LYS320 4.9 14.7 1.0 CB B:SER297 4.9 16.6 1.0 O B:HOH501 4.9 18.5 0.1

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 480S


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 480S within 5.0Å range: probe atom residue distance (Å) B Occ d:Na602 b:15.1 occ:0.20 MN d:MN601 0.0 14.8 0.8 OD1 A:ASN119 2.1 13.5 1.0 OP1 d:DG514 2.1 16.9 0.2 O D:HOH731 2.1 18.0 1.0 O A:HOH727 2.2 18.1 1.0 O A:HOH706 2.2 16.5 1.0 O3' D:DA513 2.3 18.1 0.2 O3' D:DA513 2.4 18.3 0.8 P d:DG514 2.6 19.2 0.2 CG A:ASN119 3.2 14.6 1.0 P d:DG514 3.3 15.7 0.8 C3' D:DA513 3.5 18.2 0.2 C3' D:DA513 3.6 18.2 0.8 O5' d:DG514 3.6 18.2 0.2 ND2 A:ASN119 3.7 16.1 1.0 OP2 d:DG514 3.7 18.1 0.8 O A:ASN119 3.8 17.6 1.0 O5' d:DG514 3.8 14.6 0.8 OP2 d:DG514 3.8 17.9 0.2 C4' D:DA513 4.0 19.5 0.2 C4' D:DA513 4.0 19.6 0.8 C2' D:DA513 4.1 17.6 0.2 C A:ASN119 4.2 15.8 1.0 C2' D:DA513 4.2 17.8 0.8 N A:HIS98 4.2 14.6 1.0 OG A:SER97 4.2 17.1 1.0 O d:HOH709 4.2 25.5 1.0 O A:HIS98 4.4 17.8 1.0 CB A:ASN119 4.4 11.6 1.0 OD1 A:ASN123 4.4 17.0 1.0 CA A:ASN119 4.6 15.2 1.0 ND1 A:HIS101 4.6 20.9 1.0 OP1 d:DG514 4.6 16.9 0.8 CA A:SER97 4.6 16.5 1.0 C5' D:DA513 4.7 18.1 0.8 C5' D:DA513 4.7 18.2 0.2 N A:LYS120 4.8 16.0 1.0 C A:SER97 4.9 14.8 1.0 CE1 A:HIS101 4.9 21.0 1.0 CB A:SER97 4.9 14.7 1.0 O A:HOH703 5.0 16.7 0.1 CB A:HIS98 5.0 14.2 1.0 C5' d:DG514 5.0 17.8 0.2 CA A:HIS98 5.0 17.8 1.0

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