Calcium in PDB 1g9y: Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium

The structure of Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium, PDB code: 1g9y was solved by B.Chevalier, R.J.Monnat, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.99 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.200, 67.800, 88.300, 90.00, 91.60, 90.00
R / Rfree (%)	20.7 / 26

The binding sites of Calcium atom in the Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium (pdb code 1g9y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium, PDB code: 1g9y:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca803 b:38.6 occ:1.00 OD1 B:ASP220 2.2 23.2 1.0 OP2 C:DG415 2.3 20.2 0.5 OD1 A:ASP20 2.4 25.0 1.0 OP2 D:DG515 2.6 15.5 0.5 O3' C:DC414 2.7 17.2 0.5 O3' D:DA514 2.9 15.1 0.5 P C:DG415 3.1 21.4 0.5 P D:DG515 3.3 18.4 0.5 CG B:ASP220 3.5 21.4 1.0 CA B:CA802 3.5 23.5 1.0 CA A:CA801 3.6 27.5 1.0 CG A:ASP20 3.7 28.4 1.0 C3' C:DC414 3.8 25.0 0.5 O B:GLY219 3.8 26.6 1.0 O A:GLY19 3.8 24.8 1.0 C3' D:DA514 3.9 16.3 0.5 O5' C:DG415 4.0 21.4 0.5 CA B:ASP220 4.2 20.3 1.0 C B:GLY219 4.2 23.3 1.0 C4' C:DC414 4.2 24.6 0.5 C A:GLY19 4.2 25.6 1.0 C4' D:DA514 4.2 16.7 0.5 OP1 C:DG415 4.3 24.7 0.5 O5' D:DG515 4.3 14.3 0.5 OD2 B:ASP220 4.3 20.8 1.0 CA A:ASP20 4.4 22.0 1.0 CB B:ASP220 4.4 20.9 1.0 N B:ASP220 4.4 22.3 1.0 OP1 D:DG515 4.5 19.4 0.5 OD2 A:ASP20 4.5 32.6 1.0 N A:ASP20 4.5 24.1 1.0 CB A:ASP20 4.6 27.4 1.0 OP1 C:DC414 4.6 11.6 0.5 O D:HOH4 4.7 19.1 1.0 OP1 D:DA514 4.9 39.6 0.5 O C:HOH806 4.9 27.5 1.0

Calcium binding site 2 out of 3 in the Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:27.5 occ:1.00 OP1 D:DA514 2.3 39.6 0.5 O B:GLY219 2.3 26.6 1.0 OP2 C:DG415 2.3 20.2 0.5 O B:HOH803 2.5 18.8 1.0 O C:HOH805 2.5 22.7 1.0 OD2 A:ASP20 2.6 32.6 1.0 OD1 A:ASP20 2.6 25.0 1.0 CG A:ASP20 3.0 28.4 1.0 C B:GLY219 3.4 23.3 1.0 P D:DA514 3.6 31.9 0.5 CA C:CA803 3.6 38.6 1.0 P C:DG415 3.7 21.4 0.5 O3' D:DG513 3.9 29.7 0.5 CA B:GLY219 4.0 20.5 1.0 O B:HOH816 4.0 28.5 1.0 NE2 A:GLN47 4.2 21.1 1.0 O B:ASP218 4.2 24.4 1.0 C5' C:DG415 4.2 19.2 0.5 O5' C:DG415 4.3 21.4 0.5 OE1 A:GLN47 4.4 28.5 1.0 CB A:ASP20 4.4 27.4 1.0 C5' D:DA514 4.4 20.8 0.5 N B:ASP220 4.5 22.3 1.0 OP1 C:DG415 4.5 24.7 0.5 C4' D:DA514 4.6 16.7 0.5 O5' D:DA514 4.6 33.4 0.5 OP2 D:DA514 4.6 37.0 0.5 CD A:GLN47 4.7 23.0 1.0 O3' C:DC414 4.8 17.2 0.5 CA B:ASP220 4.9 20.3 1.0 OD1 B:ASP220 4.9 23.2 1.0 N B:GLY219 5.0 19.5 1.0 C B:ASP218 5.0 23.4 1.0

Calcium binding site 3 out of 3 in the Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Homing Endonuclease I-Crei / Dna Substrate Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:23.5 occ:1.00 OP2 D:DG515 2.2 15.5 0.5 O A:GLY19 2.3 24.8 1.0 OP1 C:DC414 2.3 11.6 0.5 OD2 B:ASP220 2.4 20.8 1.0 O A:HOH804 2.4 18.5 1.0 OD1 B:ASP220 2.6 23.2 1.0 O D:HOH24 2.7 26.1 1.0 CG B:ASP220 2.9 21.4 1.0 C A:GLY19 3.3 25.6 1.0 CA C:CA803 3.5 38.6 1.0 P D:DG515 3.6 18.4 0.5 P C:DC414 3.7 14.2 0.5 CA A:GLY19 3.9 25.4 1.0 O3' C:DA413 4.1 19.3 0.5 O A:HOH815 4.1 25.5 1.0 O A:ASP18 4.1 21.0 1.0 NE2 B:GLN247 4.2 18.5 1.0 O5' D:DG515 4.3 14.3 0.5 CB B:ASP220 4.4 20.9 1.0 OP1 D:DG515 4.4 19.4 0.5 OE1 B:GLN247 4.4 20.0 1.0 N A:ASP20 4.5 24.1 1.0 C5' D:DG515 4.6 21.8 0.5 OP2 C:DC414 4.6 13.5 0.5 C5' C:DC414 4.7 24.0 0.5 C4' C:DC414 4.7 24.6 0.5 O3' D:DA514 4.7 15.1 0.5 O5' C:DC414 4.7 11.4 0.5 CD B:GLN247 4.7 17.3 1.0 CA A:ASP20 4.9 22.0 1.0 OD1 A:ASP20 4.9 25.0 1.0 N A:GLY19 4.9 19.5 1.0 C A:ASP18 4.9 22.5 1.0 O3' C:DC414 5.0 17.2 0.5

B.S.Chevalier, R.J.Monnat Jr., B.L.Stoddard. The Homing Endonuclease I-Crei Uses Three Metals, One of Which Is Shared Between the Two Active Sites. Nat.Struct.Biol. V. 8 312 2001.
ISSN: ISSN 1072-8368
PubMed: 11276249
DOI: 10.1038/86181