Sodium in PDB 8vno: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 600S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 600S, PDB code: 8vno 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 / 1.70
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 / 19.3

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 600S 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 600S (pdb code 8vno). 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 600S, PDB code: 8vno:
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 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 MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ c:Na502 b:16.4 occ:0.10 MN c:MN501 0.0 16.2 0.9 OP2 c:DG414 2.0 18.0 0.1 OD1 B:ASN319 2.1 16.7 1.0 O B:HOH600 2.1 17.8 1.0 O B:HOH578 2.1 17.2 1.0 O B:HOH516 2.2 16.2 1.0 O3' C:DA413 2.4 17.9 0.9 O3' C:DA413 2.4 17.9 0.1 P c:DG414 2.6 18.8 0.1 CG B:ASN319 3.2 16.7 1.0 P c:DG414 3.3 17.7 0.9 C3' C:DA413 3.6 18.1 0.9 C3' C:DA413 3.7 18.1 0.1 OP1 c:DG414 3.7 18.9 0.9 O5' c:DG414 3.7 18.2 0.1 ND2 B:ASN319 3.8 16.8 1.0 OP1 c:DG414 3.8 19.0 0.1 O B:ASN319 3.9 16.5 1.0 O5' c:DG414 3.9 16.6 0.9 C4' C:DA413 4.1 18.1 0.9 C4' C:DA413 4.1 18.1 0.1 N B:HIS298 4.2 16.5 1.0 C2' C:DA413 4.2 17.2 0.9 O c:HOH614 4.2 22.1 1.0 OG B:SER297 4.2 17.3 1.0 C2' C:DA413 4.2 17.3 0.1 C B:ASN319 4.2 19.0 1.0 O B:HIS298 4.3 17.5 1.0 CB B:ASN319 4.5 19.1 1.0 OD1 B:ASN323 4.5 16.5 1.0 ND1 B:HIS301 4.5 18.9 1.0 OP2 c:DG414 4.6 19.4 0.9 CA B:ASN319 4.6 17.0 1.0 CA B:SER297 4.7 17.0 1.0 C5' C:DA413 4.8 17.9 0.9 C5' C:DA413 4.8 18.0 0.1 CE1 B:HIS301 4.8 24.4 1.0 CB B:HIS298 4.8 15.5 1.0 C B:SER297 4.9 16.9 1.0 C5' c:DG414 4.9 19.1 0.1 N B:LYS320 4.9 12.1 1.0 CA B:HIS298 4.9 15.6 1.0 CB B:SER297 5.0 18.0 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 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 MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ d:Na602 b:15.7 occ:0.10 MN d:MN601 0.0 15.4 0.9 OD1 A:ASN119 2.1 15.5 1.0 O A:HOH729 2.2 18.4 1.0 OP1 d:DG514 2.2 17.0 0.1 O A:HOH789 2.2 17.7 1.0 O A:HOH723 2.2 17.1 1.0 O3' D:DA513 2.3 18.4 0.1 O3' D:DA513 2.4 19.1 0.9 P d:DG514 2.8 16.7 0.1 CG A:ASN119 3.2 14.8 1.0 P d:DG514 3.4 16.6 0.9 C3' D:DA513 3.6 19.2 0.1 C3' D:DA513 3.6 19.6 0.9 OP2 d:DG514 3.7 18.2 0.9 ND2 A:ASN119 3.7 17.1 1.0 O5' d:DG514 3.8 17.5 0.1 O A:ASN119 3.8 15.7 1.0 O5' d:DG514 3.9 14.6 0.9 OP2 d:DG514 4.0 18.3 0.1 C4' D:DA513 4.0 18.3 0.9 C4' D:DA513 4.1 18.2 0.1 C2' D:DA513 4.1 17.2 0.9 N A:HIS98 4.1 15.7 1.0 C2' D:DA513 4.2 17.3 0.1 O d:HOH712 4.2 22.4 1.0 C A:ASN119 4.2 16.0 1.0 OG A:SER97 4.3 17.2 1.0 O A:HIS98 4.4 17.1 1.0 OD1 A:ASN123 4.4 17.8 1.0 CB A:ASN119 4.5 13.1 1.0 ND1 A:HIS101 4.6 18.3 1.0 CA A:ASN119 4.6 13.9 1.0 OP1 d:DG514 4.6 17.5 0.9 CA A:SER97 4.7 14.0 1.0 C5' D:DA513 4.7 17.5 0.9 C5' D:DA513 4.8 17.6 0.1 CE1 A:HIS101 4.8 17.8 1.0 C A:SER97 4.8 13.8 1.0 N A:LYS120 4.9 14.4 1.0 CB A:HIS98 4.9 15.7 1.0 CA A:HIS98 5.0 17.4 1.0 CB A:SER97 5.0 15.0 1.0

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