Sodium in PDB 8vnf: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 20S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 20S, PDB code: 8vnf 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 / 1.50
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 (%)	18.2 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 20S 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 20S (pdb code 8vnf). 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 20S, PDB code: 8vnf:
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 20S


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 20S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:16.7 occ:0.90 MN C:MN501 0.1 16.4 0.1 OD1 B:ASN319 2.3 18.4 1.0 O B:HOH597 2.3 23.0 1.0 OP3 C:DG414 2.3 17.6 0.1 O B:HOH538 2.4 16.1 1.0 O B:HOH526 2.4 19.6 1.0 O3' C:DA413 2.4 16.0 0.9 OP1 C:DG414 2.4 17.5 0.9 O3' C:DA413 2.5 16.2 0.1 P C:DG414 3.0 16.7 0.9 CG B:ASN319 3.4 15.3 1.0 P C:DG414 3.6 17.7 0.1 C3' C:DA413 3.7 16.7 0.9 C3' C:DA413 3.8 16.8 0.1 N B:HIS298 3.8 16.2 1.0 O B:ASN319 3.8 16.6 1.0 O5' C:DG414 3.9 17.0 0.9 OP1 C:DG414 3.9 18.3 0.1 ND2 B:ASN319 4.0 16.6 1.0 O5' C:DG414 4.1 17.6 0.1 C4' C:DA413 4.1 16.0 0.9 O C:HOH639 4.1 29.5 1.0 C4' C:DA413 4.2 16.2 0.1 OG B:SER297 4.2 19.2 1.0 OP2 C:DG414 4.2 18.2 0.9 O B:HIS298 4.2 17.8 1.0 C B:ASN319 4.3 16.2 1.0 C2' C:DA413 4.4 17.0 0.9 CA B:SER297 4.5 15.6 1.0 C2' C:DA413 4.5 17.0 0.1 CB B:HIS298 4.6 16.3 1.0 C B:SER297 4.6 15.9 1.0 CB B:ASN319 4.6 15.4 1.0 CA B:HIS298 4.6 14.6 1.0 OD1 B:ASN323 4.6 16.1 1.0 CA B:ASN319 4.7 16.4 1.0 C5' C:DA413 4.7 15.5 0.9 C B:HIS298 4.8 17.2 1.0 C5' C:DA413 4.8 15.8 0.1 ND1 B:HIS301 4.8 18.3 1.0 OP2 C:DG414 4.8 19.6 0.1 CB B:SER297 4.8 19.1 1.0 CE1 B:HIS301 4.9 17.8 1.0 N B:LYS320 5.0 14.5 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 20S


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 20S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:16.7 occ:0.90 MN D:MN601 0.0 16.8 0.1 O A:HOH737 2.2 16.7 1.0 OD1 A:ASN119 2.2 17.3 1.0 O3' D:DA513 2.4 16.1 0.9 O A:HOH811 2.4 21.2 1.0 O A:HOH701 2.4 18.9 1.0 O3' D:DA513 2.4 16.4 0.1 OP3 D:DG514 2.4 15.6 0.1 OP1 D:DG514 2.6 16.5 0.9 P D:DG514 3.1 16.3 0.9 CG A:ASN119 3.4 14.8 1.0 C3' D:DA513 3.6 17.6 0.9 C3' D:DA513 3.6 17.5 0.1 P D:DG514 3.7 15.4 0.1 O A:ASN119 3.8 15.6 1.0 C4' D:DA513 3.9 17.3 0.9 N A:HIS98 3.9 14.6 1.0 O5' D:DG514 3.9 16.4 0.9 C4' D:DA513 3.9 17.4 0.1 ND2 A:ASN119 4.0 15.4 1.0 OP2 D:DG514 4.0 18.1 0.1 OG A:SER97 4.1 17.8 1.0 O5' D:DG514 4.2 16.6 0.1 C A:ASN119 4.2 16.8 1.0 C2' D:DA513 4.3 16.7 0.9 OP2 D:DG514 4.3 18.4 0.9 O A:HIS98 4.3 17.5 1.0 C2' D:DA513 4.3 16.8 0.1 OD1 A:ASN123 4.5 17.6 1.0 CA A:SER97 4.5 14.3 1.0 C5' D:DA513 4.6 17.1 0.9 CB A:ASN119 4.6 14.1 1.0 C5' D:DA513 4.6 17.2 0.1 O D:HOH712 4.6 33.4 1.0 C A:SER97 4.7 15.5 1.0 CA A:ASN119 4.7 15.0 1.0 CB A:HIS98 4.7 16.4 1.0 CA A:HIS98 4.7 15.2 1.0 ND1 A:HIS101 4.8 19.4 1.0 CB A:SER97 4.8 17.2 1.0 N A:LYS120 4.9 14.2 1.0 C A:HIS98 4.9 15.8 1.0 OP1 D:DG514 4.9 17.5 0.1 CE1 A:HIS101 4.9 19.1 1.0 O A:HOH773 5.0 22.1 1.0

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