Sodium in PDB 8vnq: Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S, PDB code: 8vnq 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)	48.20 / 1.93
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.646, 114.646, 89.057, 90, 90, 120
R / Rfree (%)	19.3 / 21

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S (pdb code 8vnq). 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 H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S, PDB code: 8vnq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:25.1 occ:1.00 OD1 B:ASN319 2.2 23.9 1.0 O B:HOH536 2.4 25.1 1.0 O B:HOH505 2.4 22.7 1.0 O B:HOH566 2.4 26.2 1.0 OP1 C:DG414 2.5 25.3 1.0 O3' C:DA413 2.6 24.1 1.0 P C:DG414 3.2 25.7 1.0 CG B:ASN319 3.4 25.7 1.0 O B:ASN319 3.7 22.8 1.0 C3' C:DA413 3.9 23.0 1.0 OG B:SER297 3.9 28.0 1.0 ND2 B:ASN319 4.0 22.9 1.0 N B:ALA298 4.0 26.5 1.0 O5' C:DG414 4.0 26.6 1.0 C4' C:DA413 4.2 21.2 1.0 C B:ASN319 4.2 23.4 1.0 O C:HOH631 4.2 33.1 1.0 O B:ALA298 4.3 22.3 1.0 OP2 C:DG414 4.4 24.2 1.0 C2' C:DA413 4.5 23.9 1.0 CA B:SER297 4.5 25.5 1.0 CB B:ASN319 4.5 25.4 1.0 OD1 B:ASN323 4.6 21.6 1.0 CA B:ASN319 4.6 23.4 1.0 C B:SER297 4.7 27.5 1.0 CB B:SER297 4.7 24.9 1.0 C5' C:DA413 4.8 25.2 1.0 CA B:ALA298 4.8 23.8 1.0 C B:ALA298 4.9 25.0 1.0 CB B:ALA298 4.9 24.8 1.0 ND1 B:HIS301 4.9 23.6 1.0 N B:LYS320 4.9 21.2 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:22.3 occ:1.00 O A:HOH750 2.2 22.5 1.0 OD1 A:ASN119 2.3 19.9 1.0 O A:HOH702 2.4 23.1 1.0 OP1 D:DG514 2.5 21.3 1.0 O3' D:DA513 2.6 21.5 1.0 O A:HOH789 2.6 25.4 1.0 P D:DG514 3.1 22.8 1.0 CG A:ASN119 3.4 19.8 1.0 O A:ASN119 3.8 21.9 1.0 C3' D:DA513 3.8 23.6 1.0 N A:ALA98 3.9 20.8 1.0 O5' D:DG514 4.0 19.2 1.0 ND2 A:ASN119 4.0 20.1 1.0 C4' D:DA513 4.1 24.9 1.0 OG A:SER97 4.2 22.3 1.0 C A:ASN119 4.2 19.8 1.0 O A:ALA98 4.3 23.6 1.0 OP2 D:DG514 4.3 21.3 1.0 C2' D:DA513 4.5 21.6 1.0 CA A:SER97 4.5 19.6 1.0 OD1 A:ASN123 4.6 22.3 1.0 C A:SER97 4.6 20.9 1.0 CB A:ASN119 4.6 18.6 1.0 CA A:ALA98 4.7 25.1 1.0 CA A:ASN119 4.7 20.3 1.0 CB A:ALA98 4.7 22.6 1.0 C5' D:DA513 4.7 24.2 1.0 CB A:SER97 4.8 19.3 1.0 C A:ALA98 4.9 22.3 1.0 N A:LYS120 4.9 19.4 1.0 ND1 A:HIS101 4.9 25.0 1.0

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