Sodium in PDB 1t9i: I-Crei(D20N)/Dna Complex

The structure of I-Crei(D20N)/Dna Complex, PDB code: 1t9i was solved by B.Chevalier, D.Sussman, C.Otis, D.Boudreau, M.Turmel, C.Lemieux, K.Stephens, R.J.Monnat Jr., B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.800, 67.310, 89.350, 90.00, 92.40, 90.00
R / Rfree (%)	19.4 / 21.1

The structure of I-Crei(D20N)/Dna Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the I-Crei(D20N)/Dna Complex (pdb code 1t9i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the I-Crei(D20N)/Dna Complex, PDB code: 1t9i:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of I-Crei(D20N)/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na806 b:46.5 occ:1.00 O C:HOH1178 2.2 22.5 1.0 O D:HOH1282 2.3 34.3 1.0 O D:HOH1164 2.4 36.7 1.0 O D:HOH1449 2.5 33.0 1.0 O D:HOH1269 2.5 51.3 1.0 O C:HOH1410 2.6 30.8 1.0 O D:HOH1586 4.2 37.2 1.0 N3 C:DA503 4.3 10.3 1.0 C2 C:DA503 4.6 10.0 1.0 O C:HOH1101 4.6 21.6 1.0 O4' D:DC574 4.8 26.8 1.0 O4' C:DA504 4.8 19.0 1.0 N3 D:DG573 4.9 30.8 1.0 O4' D:DG573 4.9 33.0 1.0 C4' C:DA504 4.9 15.3 1.0

Sodium binding site 2 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of I-Crei(D20N)/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na805 b:38.0 occ:1.00 O D:HOH1256 2.2 24.3 1.0 O C:HOH1464 2.4 38.4 1.0 O C:HOH1622 2.4 40.7 1.0 O C:HOH1582 2.4 44.3 1.0 O C:HOH1055 2.4 35.5 1.0 O D:HOH1563 2.5 45.6 1.0 O D:HOH1429 4.4 37.1 1.0 O C:HOH1221 4.4 23.2 1.0 N3 D:DA553 4.5 18.5 1.0 C2 D:DA553 4.6 19.4 1.0 O C:HOH1431 4.6 37.2 1.0 N2 D:DG552 4.6 16.1 1.0 O2 C:DC523 4.8 38.6 1.0 O4' C:DG524 4.8 41.7 1.0 O4' D:DA554 4.9 19.6 1.0 O4' C:DC523 4.9 40.1 1.0

Sodium binding site 3 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of I-Crei(D20N)/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:21.9 occ:1.00 O A:HOH1044 2.3 33.8 1.0 O A:HOH1273 2.3 33.4 1.0 O A:ASN136 2.4 10.2 1.0 O B:HOH1314 2.4 28.0 1.0 O A:HOH1576 2.4 55.3 1.0 O A:HOH1618 2.4 40.7 1.0 O A:ALA134 2.6 14.3 1.0 O A:HOH1247 3.2 31.6 1.0 C A:ASN136 3.6 11.0 1.0 C A:ALA134 3.7 11.9 1.0 C A:LEU135 4.1 11.4 1.0 O A:LEU135 4.2 12.3 1.0 CA A:ASP137 4.3 11.3 1.0 O B:HOH1487 4.3 43.3 1.0 O A:ALA133 4.3 12.1 1.0 N A:ASP137 4.4 11.3 1.0 N A:ASN136 4.4 11.1 1.0 N A:SER138 4.4 11.9 1.0 CA A:ALA134 4.5 12.5 1.0 OE1 B:GLN350 4.5 31.1 1.0 N A:LEU135 4.6 11.2 1.0 O A:HOH1421 4.6 38.3 1.0 CA A:ASN136 4.6 9.8 1.0 O A:HOH1235 4.6 29.7 1.0 CA A:LEU135 4.6 11.1 1.0 OD1 A:ASP137 4.7 16.3 1.0 C A:ASP137 4.9 10.8 1.0

Sodium binding site 4 out of 4 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of I-Crei(D20N)/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na803 b:20.1 occ:1.00 O B:HOH1218 2.3 29.8 1.0 O B:HOH1209 2.3 27.5 1.0 O B:HOH1610 2.4 40.7 1.0 O B:ASN436 2.4 12.8 1.0 O A:HOH1017 2.4 35.0 1.0 O B:HOH1277 2.5 22.1 1.0 O B:HOH1090 2.7 21.6 1.0 O B:ALA434 2.7 17.5 1.0 C B:ASN436 3.6 11.3 1.0 C B:ALA434 3.8 15.6 1.0 CA B:ASP437 4.2 12.5 1.0 O B:LEU435 4.3 14.2 1.0 N B:SER438 4.3 12.4 1.0 C B:LEU435 4.3 14.7 1.0 N B:ASP437 4.4 12.4 1.0 O B:ALA433 4.4 13.7 1.0 N B:ASN436 4.5 13.1 1.0 CA B:ALA434 4.6 14.0 1.0 OE1 A:GLN50 4.6 28.7 1.0 OD1 B:ASP437 4.7 16.5 1.0 CA B:ASN436 4.7 11.3 1.0 N B:LEU435 4.7 14.9 1.0 C B:ASP437 4.8 11.8 1.0 O B:HOH1213 4.8 23.4 1.0 NE2 A:GLN50 4.8 25.8 1.0 CA B:LEU435 4.8 13.6 1.0 O B:HOH1527 4.9 42.0 1.0

B.Chevalier, D.Sussman, C.Otis, A.J.Noel, M.Turmel, C.Lemieux, K.Stephens, R.J.Monnat Jr., B.L.Stoddard. Metal-Dependent Dna Cleavage Mechanism of the I-Crei Laglidadg Homing Endonuclease. Biochemistry V. 43 14015 2004.
ISSN: ISSN 0006-2960
PubMed: 15518550
DOI: 10.1021/BI048970C