Sodium in PDB 8vnm: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 320S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 320S, PDB code: 8vnm 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 / 1.59
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 (%)	17.4 / 19

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 320S 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 320S (pdb code 8vnm). 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 320S, PDB code: 8vnm:
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 320S


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 320S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:15.5 occ:0.20 MN C:MN501 0.0 15.6 0.8 OP1 C:DG414 2.1 16.1 0.2 OD1 B:ASN319 2.1 16.4 1.0 O B:HOH600 2.2 18.3 1.0 O3' C:DA413 2.2 16.9 0.8 OP3 C:DG414 2.2 15.7 0.8 O B:HOH564 2.2 18.8 1.0 O3' C:DA413 2.2 16.6 0.2 O B:HOH519 2.3 15.7 1.0 P C:DG414 2.7 15.8 0.2 CG B:ASN319 3.2 16.1 1.0 P C:DG414 3.4 15.6 0.8 C3' C:DA413 3.5 15.5 0.8 C3' C:DA413 3.5 15.7 0.2 O5' C:DG414 3.6 16.1 0.2 OP1 C:DG414 3.6 15.5 0.8 ND2 B:ASN319 3.8 15.6 1.0 O5' C:DG414 3.9 15.2 0.8 O B:ASN319 3.9 15.4 1.0 OP2 C:DG414 4.0 16.8 0.2 C4' C:DA413 4.0 16.6 0.2 O C:HOH634 4.0 22.7 1.0 C4' C:DA413 4.0 16.7 0.8 N B:HIS298 4.1 14.8 1.0 C2' C:DA413 4.1 15.9 0.2 C2' C:DA413 4.2 16.0 0.8 C B:ASN319 4.2 15.4 1.0 OG B:SER297 4.3 16.8 1.0 O B:HIS298 4.3 16.0 1.0 CB B:ASN319 4.5 16.1 1.0 OD1 B:ASN323 4.5 16.0 1.0 ND1 B:HIS301 4.6 18.2 1.0 OP2 C:DG414 4.6 18.3 0.8 CA B:ASN319 4.6 15.1 1.0 CA B:SER297 4.7 16.0 1.0 C5' C:DA413 4.7 16.5 0.2 C5' C:DA413 4.7 16.4 0.8 C B:SER297 4.8 15.9 1.0 CB B:HIS298 4.8 14.4 1.0 CE1 B:HIS301 4.9 20.9 1.0 CA B:HIS298 4.9 14.0 1.0 N B:LYS320 4.9 13.0 1.0 C5' C:DG414 4.9 17.1 0.2 O B:HOH501 5.0 18.1 0.1 CB B:SER297 5.0 14.8 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 320S


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 320S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:14.4 occ:0.20 MN D:MN601 0.0 14.3 0.8 OD1 A:ASN119 2.1 14.0 1.0 OP1 D:DG514 2.1 15.7 0.2 O3' D:DA513 2.2 17.7 0.8 O A:HOH713 2.2 14.3 1.0 O A:HOH796 2.2 17.4 1.0 O A:HOH748 2.2 19.2 1.0 OP3 D:DG514 2.2 15.5 0.8 O3' D:DA513 2.3 17.3 0.2 P D:DG514 2.7 17.6 0.2 CG A:ASN119 3.2 13.7 1.0 P D:DG514 3.4 14.0 0.8 C3' D:DA513 3.5 16.9 0.8 C3' D:DA513 3.5 16.8 0.2 O5' D:DG514 3.6 15.6 0.2 OP2 D:DG514 3.7 15.1 0.8 ND2 A:ASN119 3.8 15.4 1.0 O A:ASN119 3.8 15.1 1.0 O5' D:DG514 3.9 12.1 0.8 OP2 D:DG514 4.0 17.4 0.2 C4' D:DA513 4.0 17.2 0.2 C4' D:DA513 4.1 17.3 0.8 C2' D:DA513 4.1 15.7 0.2 O D:HOH732 4.1 22.3 1.0 C2' D:DA513 4.1 15.6 0.8 N A:HIS98 4.1 14.6 1.0 C A:ASN119 4.2 15.2 1.0 OG A:SER97 4.2 17.3 1.0 O A:HIS98 4.4 18.5 1.0 CB A:ASN119 4.5 13.1 1.0 OD1 A:ASN123 4.5 16.6 1.0 ND1 A:HIS101 4.6 20.2 1.0 OP1 D:DG514 4.6 16.6 0.8 CA A:ASN119 4.6 14.9 1.0 CA A:SER97 4.6 13.5 1.0 C5' D:DA513 4.7 16.0 0.2 C5' D:DA513 4.8 15.8 0.8 C A:SER97 4.8 13.1 1.0 N A:LYS120 4.9 13.3 1.0 CE1 A:HIS101 4.9 20.0 1.0 CB A:HIS98 4.9 15.0 1.0 CA A:HIS98 4.9 15.6 1.0 C5' D:DG514 5.0 15.9 0.2 CB A:SER97 5.0 15.3 1.0 O A:HOH701 5.0 16.9 0.1

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