Sodium in PDB 8vns: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 200 Mm MN2+ For 600S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 200 Mm MN2+ For 600S, PDB code: 8vns 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)	48.39 / 2.11
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.905, 117.905, 84.743, 90, 90, 120
R / Rfree (%)	22.2 / 25.2

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 200 Mm 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 200 Mm MN2+ For 600S (pdb code 8vns). 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 200 Mm MN2+ For 600S, PDB code: 8vns:
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 200 Mm 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 200 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:27.4 occ:0.30 MN C:MN501 0.0 27.3 0.7 OP2 c:DG414 1.9 28.4 0.3 O B:HOH501 2.0 31.8 1.0 O B:HOH506 2.0 34.0 1.0 O c:HOH503 2.0 32.2 1.0 OD1 B:ASN319 2.1 28.8 1.0 O3' C:DA413 2.1 29.1 0.3 O3' C:DA413 2.1 28.7 0.7 P c:DG414 2.5 36.3 0.3 CG B:ASN319 3.1 32.6 1.0 O5' c:DG414 3.4 30.4 0.3 P c:DG414 3.4 25.9 0.7 C3' C:DA413 3.4 33.2 0.3 C3' C:DA413 3.5 33.2 0.7 ND2 B:ASN319 3.6 36.5 1.0 OP1 c:DG414 3.7 32.6 0.7 OP1 c:DG414 3.8 33.3 0.3 O5' c:DG414 3.8 30.1 0.7 O B:ASN319 4.0 32.1 1.0 C4' C:DA413 4.0 36.1 0.3 C2' C:DA413 4.0 32.3 0.3 C2' C:DA413 4.1 32.3 0.7 C4' C:DA413 4.1 36.4 0.7 OG B:SER297 4.2 35.5 1.0 N B:HIS298 4.3 30.2 1.0 C B:ASN319 4.3 34.9 1.0 CB B:ASN319 4.5 26.5 1.0 O B:HIS298 4.5 32.5 1.0 OD1 B:ASN323 4.6 29.4 1.0 ND1 B:HIS301 4.7 27.0 1.0 CA B:ASN319 4.7 29.1 1.0 CA B:SER297 4.7 30.3 1.0 OP2 c:DG414 4.8 28.0 0.7 C5' C:DA413 4.8 33.7 0.3 C5' c:DG414 4.8 32.4 0.3 O B:HOH502 4.8 28.8 0.2 C5' C:DA413 4.9 33.8 0.7 CB B:SER297 4.9 35.4 1.0 C B:SER297 5.0 32.0 1.0 N B:LYS320 5.0 30.8 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 200 Mm 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 200 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:29.1 occ:0.20 MN D:MN601 0.0 29.0 0.8 O A:HOH702 2.0 28.9 1.0 O3' D:DA513 2.0 33.4 0.2 O3' D:DA513 2.1 33.6 0.8 OD1 A:ASN119 2.1 24.7 1.0 O D:HOH705 2.1 30.4 1.0 OP1 d:DG514 2.1 29.0 0.2 O A:HOH701 2.2 32.3 1.0 P d:DG514 2.6 33.5 0.2 CG A:ASN119 3.2 30.6 1.0 P d:DG514 3.4 27.2 0.8 C3' D:DA513 3.4 33.1 0.2 C3' D:DA513 3.4 33.1 0.8 O5' d:DG514 3.5 32.8 0.2 OP2 d:DG514 3.7 29.4 0.8 ND2 A:ASN119 3.8 24.1 1.0 O5' d:DG514 3.8 34.3 0.8 OP2 d:DG514 3.8 30.4 0.2 O A:ASN119 3.8 30.1 1.0 C4' D:DA513 3.9 37.0 0.2 C4' D:DA513 4.0 37.3 0.8 C2' D:DA513 4.0 33.0 0.8 C2' D:DA513 4.1 33.1 0.2 OG A:SER97 4.2 33.1 1.0 C A:ASN119 4.2 32.9 1.0 N A:HIS98 4.3 30.9 1.0 CB A:ASN119 4.4 27.6 1.0 O A:HIS98 4.5 27.7 1.0 OD1 A:ASN123 4.5 33.4 1.0 C5' D:DA513 4.5 35.9 0.2 C5' D:DA513 4.6 35.9 0.8 CA A:ASN119 4.6 26.1 1.0 OP1 d:DG514 4.7 30.6 0.8 CA A:SER97 4.7 29.8 1.0 ND1 A:HIS101 4.8 34.5 1.0 C5' d:DG514 4.8 32.2 0.2 CB A:SER97 4.9 27.4 1.0 N A:LYS120 4.9 22.2 1.0 C A:SER97 5.0 30.0 1.0

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