Calcium 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:

Sodium

(Na)

4 atoms

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

Calcium binding site 1 out of 2 in the I-Crei(D20N)/Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of I-Crei(D20N)/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:11.5 occ:1.00 OP1 D:DG565 2.3 11.9 1.0 O B:GLY319 2.3 11.8 1.0 OP1 C:DA514 2.3 9.5 1.0 OD1 A:ASN20 2.4 11.8 1.0 O C:HOH1007 2.5 11.8 1.0 O C:HOH1004 2.5 14.5 1.0 O D:HOH1035 2.6 14.2 1.0 CG A:ASN20 3.5 11.8 1.0 C B:GLY319 3.5 10.4 1.0 P C:DA514 3.7 8.7 1.0 P D:DG565 3.8 11.6 1.0 O3' C:DG513 3.9 9.9 1.0 C4' C:DA514 4.2 10.6 1.0 CB A:ASN20 4.2 9.9 1.0 C5' C:DA514 4.3 10.1 1.0 CA B:ASN320 4.3 9.7 1.0 N B:ASN320 4.4 9.8 1.0 O3' D:DC564 4.4 10.5 1.0 C5' D:DG565 4.4 9.9 1.0 O B:HOH1006 4.4 12.7 1.0 O5' C:DA514 4.5 8.9 1.0 O3' C:DA514 4.5 9.4 1.0 CA B:GLY319 4.5 11.9 1.0 NE2 A:GLN47 4.5 11.3 1.0 O5' D:DG565 4.5 11.6 1.0 ND2 A:ASN20 4.5 11.4 1.0 OD1 B:ASN320 4.6 12.1 1.0 O B:HOH1227 4.7 24.8 1.0 CB B:ASN320 4.7 9.8 1.0 OP2 D:DG565 4.7 14.1 1.0 OP2 C:DA514 4.9 10.8 1.0 C3' C:DA514 4.9 10.2 1.0 O B:HOH1072 4.9 15.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of I-Crei(D20N)/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:10.4 occ:1.00 OP1 C:DG515 2.2 10.4 1.0 O A:GLY19 2.3 10.9 1.0 OP1 D:DC564 2.4 11.0 1.0 OD1 B:ASN320 2.4 12.1 1.0 O C:HOH1008 2.4 10.9 1.0 O D:HOH1013 2.5 14.6 1.0 O D:HOH1035 2.6 14.2 1.0 CG B:ASN320 3.5 10.6 1.0 C A:GLY19 3.5 10.1 1.0 P C:DG515 3.7 11.2 1.0 P D:DC564 3.7 10.0 1.0 O3' D:DA563 3.9 10.0 1.0 O3' C:DA514 4.2 9.4 1.0 CB B:ASN320 4.3 9.8 1.0 CA A:ASN20 4.4 9.6 1.0 N A:ASN20 4.4 9.8 1.0 C5' D:DC564 4.4 9.9 1.0 C5' C:DG515 4.4 10.1 1.0 O A:HOH1002 4.4 11.7 1.0 C4' D:DC564 4.5 9.8 1.0 ND2 B:ASN320 4.5 10.6 1.0 O5' D:DC564 4.5 11.2 1.0 CA A:GLY19 4.5 9.8 1.0 O5' C:DG515 4.5 10.5 1.0 NE2 B:GLN347 4.5 8.2 1.0 O3' D:DC564 4.6 10.5 1.0 O A:HOH1118 4.7 26.2 1.0 OP2 C:DG515 4.7 10.9 1.0 OD1 A:ASN20 4.7 11.8 1.0 CB A:ASN20 4.8 9.9 1.0 OP1 D:DG565 4.8 11.9 1.0 OP2 D:DC564 4.8 9.6 1.0 O A:HOH1062 4.9 14.9 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