Sodium in PDB 8vnl: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 240S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 240S, PDB code: 8vnl 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)	37.33 / 1.64
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 (%)	17.9 / 18.8

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 240S 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 240S (pdb code 8vnl). 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 240S, PDB code: 8vnl:
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 240S


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 240S within 5.0Å range: probe atom residue distance (Å) B Occ c:Na502 b:15.3 occ:0.40 MN c:MN501 0.1 15.2 0.6 OD1 B:ASN319 2.2 15.5 1.0 O B:HOH611 2.2 18.9 1.0 OP2 c:DG414 2.2 15.3 0.4 O3' C:DA413 2.2 17.2 0.6 O B:HOH564 2.3 20.4 1.0 O3' C:DA413 2.3 14.8 0.4 O B:HOH528 2.3 15.6 1.0 P c:DG414 2.8 14.2 0.4 CG B:ASN319 3.3 14.1 1.0 P c:DG414 3.3 14.8 0.6 C3' C:DA413 3.6 16.0 0.6 OP1 c:DG414 3.6 15.9 0.6 C3' C:DA413 3.6 16.0 0.4 O5' c:DG414 3.7 14.3 0.4 ND2 B:ASN319 3.8 14.5 1.0 O5' c:DG414 3.9 15.1 0.6 O B:ASN319 3.9 15.5 1.0 C4' C:DA413 4.0 17.1 0.4 N B:HIS298 4.0 15.0 1.0 OP1 c:DG414 4.1 14.7 0.4 O c:HOH607 4.1 24.7 1.0 C4' C:DA413 4.2 17.2 0.6 C2' C:DA413 4.2 15.9 0.4 OG B:SER297 4.2 17.0 1.0 C B:ASN319 4.3 16.4 1.0 O B:HIS298 4.3 15.4 1.0 C2' C:DA413 4.3 16.1 0.6 CB B:ASN319 4.5 13.3 1.0 OP2 c:DG414 4.5 15.0 0.6 CA B:SER297 4.6 15.4 1.0 OD1 B:ASN323 4.6 16.6 1.0 ND1 B:HIS301 4.6 18.8 1.0 CA B:ASN319 4.7 16.2 1.0 C5' C:DA413 4.7 17.1 0.4 CB B:HIS298 4.7 13.8 1.0 C B:SER297 4.7 15.6 1.0 CA B:HIS298 4.8 15.6 1.0 C5' C:DA413 4.8 17.1 0.6 CE1 B:HIS301 4.9 23.7 1.0 CB B:SER297 4.9 15.7 1.0 C B:HIS298 4.9 14.6 1.0 N B:LYS320 5.0 13.3 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 240S


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 240S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:14.7 occ:0.35 MN D:MN601 0.1 14.4 0.7 O3' D:DA513 2.0 18.8 0.7 OD1 A:ASN119 2.1 13.9 1.0 O A:HOH713 2.2 15.4 1.0 O3' D:DA513 2.2 14.3 0.3 O A:HOH810 2.2 17.5 1.0 O A:HOH757 2.3 19.8 1.0 OP1 d:DG514 2.4 14.5 0.3 P d:DG514 2.9 16.3 0.3 CG A:ASN119 3.3 13.6 1.0 C3' D:DA513 3.4 17.2 0.7 P d:DG514 3.4 12.6 0.7 C3' D:DA513 3.4 16.7 0.3 O5' d:DG514 3.7 14.2 0.3 OP2 d:DG514 3.7 14.7 0.7 O A:ASN119 3.8 16.0 1.0 C4' D:DA513 3.8 17.0 0.3 ND2 A:ASN119 3.9 16.1 1.0 O5' d:DG514 3.9 13.7 0.7 C4' D:DA513 4.0 17.4 0.7 C2' D:DA513 4.1 15.7 0.3 C2' D:DA513 4.1 16.5 0.7 OP2 d:DG514 4.1 15.3 0.3 O d:HOH606 4.2 25.2 1.0 N A:HIS98 4.2 13.4 1.0 C A:ASN119 4.2 14.8 1.0 OG A:SER97 4.4 17.1 1.0 OD1 A:ASN123 4.4 16.3 1.0 O A:HIS98 4.4 16.3 1.0 CB A:ASN119 4.5 13.3 1.0 C5' D:DA513 4.6 17.4 0.3 ND1 A:HIS101 4.6 20.1 1.0 CA A:ASN119 4.6 16.2 1.0 C5' D:DA513 4.6 17.4 0.7 OP1 d:DG514 4.7 14.3 0.7 CA A:SER97 4.7 13.9 1.0 N A:LYS120 4.8 13.2 1.0 CE1 A:HIS101 4.9 19.7 1.0 C A:SER97 4.9 11.8 1.0 CB A:HIS98 4.9 13.4 1.0 CA A:HIS98 5.0 13.9 1.0

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