Sodium in PDB 1cz0: Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion

The structure of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion, PDB code: 1cz0 was solved by E.A.Galburt, B.Chevalier, M.S.Jurica, K.E.Flick, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.866, 113.866, 89.040, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 21.6

The structure of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion (pdb code 1cz0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion, PDB code: 1cz0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Na606 b:9.8 occ:1.00 O B:HOH725 2.3 19.2 1.0 OD1 B:ASN319 2.3 15.5 1.0 O B:HOH724 2.4 20.1 1.0 O B:HOH723 2.5 12.9 1.0 OP1 C:DG414 2.6 18.6 1.0 O3' C:DA413 2.6 21.9 1.0 P C:DG414 3.1 19.1 1.0 CG B:ASN319 3.4 16.6 1.0 O B:ASN319 3.7 16.1 1.0 C3' C:DA413 3.8 20.9 1.0 N B:HIS298 3.9 14.3 1.0 O5' C:DG414 4.0 18.4 1.0 OG B:SER297 4.0 19.7 1.0 ND2 B:ASN319 4.0 14.3 1.0 C4' C:DA413 4.2 20.1 1.0 C B:ASN319 4.2 15.9 1.0 O B:HIS298 4.3 14.6 1.0 OP2 C:DG414 4.4 18.0 1.0 C2' C:DA413 4.4 19.4 1.0 O C:HOH369 4.5 32.6 1.0 CA B:SER297 4.6 17.4 1.0 CB B:HIS298 4.6 14.9 1.0 CB B:ASN319 4.6 14.9 1.0 CA B:HIS298 4.7 13.4 1.0 CA B:ASN319 4.7 14.4 1.0 C B:SER297 4.7 17.4 1.0 OD1 B:ASN323 4.7 14.5 1.0 ND1 B:HIS301 4.7 12.7 1.0 CE1 B:HIS301 4.8 12.0 1.0 CB B:SER297 4.8 16.4 1.0 N B:LYS320 4.8 16.4 1.0 C5' C:DA413 4.8 17.9 1.0 C B:HIS298 4.9 15.6 1.0

Sodium binding site 2 out of 2 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Na605 b:12.5 occ:1.00 O A:HOH737 2.2 17.4 1.0 O A:HOH738 2.3 22.2 1.0 OD1 A:ASN119 2.4 13.5 1.0 OP1 D:DG514 2.6 18.5 1.0 O3' D:DA513 2.7 19.8 1.0 O A:HOH740 2.8 31.5 1.0 P D:DG514 3.2 17.1 1.0 CG A:ASN119 3.5 11.3 1.0 O A:ASN119 3.6 14.3 1.0 N A:HIS98 3.9 12.4 1.0 C3' D:DA513 4.0 19.3 1.0 O5' D:DG514 4.0 18.0 1.0 OG A:SER97 4.0 13.1 1.0 ND2 A:ASN119 4.1 13.4 1.0 C A:ASN119 4.1 14.1 1.0 O A:HIS98 4.2 17.1 1.0 C4' D:DA513 4.3 18.5 1.0 OP2 D:DG514 4.4 17.7 1.0 CA A:SER97 4.5 12.1 1.0 OD1 A:ASN123 4.5 17.7 1.0 CB A:HIS98 4.6 13.8 1.0 C A:SER97 4.6 12.8 1.0 C2' D:DA513 4.6 17.7 1.0 CA A:HIS98 4.6 14.5 1.0 CB A:ASN119 4.7 9.1 1.0 CA A:ASN119 4.7 10.7 1.0 C A:HIS98 4.8 17.6 1.0 ND1 A:HIS101 4.8 14.4 1.0 N A:LYS120 4.8 13.4 1.0 CB A:SER97 4.9 10.4 1.0 C5' D:DA513 4.9 19.3 1.0 CE1 A:HIS101 5.0 15.6 1.0

E.A.Galburt, B.Chevalier, W.Tang, M.S.Jurica, K.E.Flick, R.J.Monnat Jr., B.L.Stoddard. A Novel Endonuclease Mechanism Directly Visualized For I-Ppoi. Nat.Struct.Biol. V. 6 1096 1999.
ISSN: ISSN 1072-8368
PubMed: 10581547
DOI: 10.1038/70027