Calcium in PDB 6bce: Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex)

The structure of Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bce was solved by C.Brown, K.Zhang, T.A.Mcmurrough, G.B.Gloor, D.R.Edgell, M.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.50 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.261, 42.752, 103.380, 90.00, 109.22, 90.00
R / Rfree (%)	20.1 / 22.5

The binding sites of Calcium atom in the Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex) (pdb code 6bce). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bce:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:24.8 occ:1.00 O A:ALA28 2.4 18.9 1.0 OP1 C:DC15 2.4 23.3 1.0 O A:HOH531 2.4 21.1 1.0 O C:HOH133 2.4 25.4 1.0 OP2 B:DA17 2.4 21.6 1.0 OE2 A:GLU184 2.5 21.3 1.0 C A:ALA28 3.4 22.1 1.0 CD A:GLU184 3.5 21.2 1.0 P B:DA17 3.6 25.1 1.0 P C:DC15 3.8 26.9 1.0 OE1 A:GLU184 3.8 26.4 1.0 CA A:ALA28 3.9 19.4 1.0 CA A:CA403 3.9 32.3 1.0 O5' B:DA17 4.0 21.7 1.0 C5' B:DA17 4.0 22.1 1.0 O B:HOH119 4.1 32.9 1.0 OE1 A:GLU29 4.2 26.1 1.0 NE2 A:GLN211 4.3 23.5 1.0 O A:HOH534 4.3 33.8 1.0 OP1 B:DA17 4.3 24.9 1.0 OE1 A:GLN211 4.3 23.6 1.0 O A:ASP27 4.4 19.5 1.0 O3' C:DA14 4.4 28.5 1.0 C5' C:DC15 4.5 23.5 1.0 N A:GLU29 4.6 17.6 1.0 OP2 C:DC15 4.6 26.3 1.0 CD A:GLN211 4.7 23.9 1.0 O5' C:DC15 4.7 25.1 1.0 C4' C:DC15 4.8 22.7 1.0 O3' B:DT16 4.8 22.6 1.0 CB A:ALA28 4.8 19.1 1.0 CG A:GLU184 4.8 19.6 1.0 C4' B:DA17 4.9 23.8 1.0 CA A:GLU29 5.0 18.4 1.0

Calcium binding site 2 out of 3 in the Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:25.4 occ:1.00 OP2 C:DG16 2.4 22.2 1.0 O A:HOH573 2.4 25.8 1.0 OE2 A:GLU29 2.4 24.2 1.0 O A:GLY183 2.4 22.6 1.0 OP1 B:DT16 2.4 22.1 1.0 O A:HOH658 2.4 25.0 1.0 C A:GLY183 3.5 22.0 1.0 CD A:GLU29 3.5 26.7 1.0 P C:DG16 3.6 25.1 1.0 CA A:GLY183 3.8 19.2 1.0 O C:HOH118 3.8 36.4 1.0 P B:DT16 3.9 23.7 1.0 CA A:CA403 3.9 32.3 1.0 O5' C:DG16 4.1 23.1 1.0 OE1 A:GLU29 4.1 26.1 1.0 C5' C:DG16 4.1 21.4 1.0 C4' B:DT16 4.2 26.6 1.0 OP1 C:DG16 4.3 27.0 1.0 C5' B:DT16 4.3 20.9 1.0 O A:HOH517 4.3 26.9 1.0 O A:ALA182 4.4 22.3 1.0 O3' B:DA15 4.4 27.7 1.0 O5' B:DT16 4.6 23.3 1.0 CG A:GLU29 4.6 16.3 1.0 N A:GLU184 4.6 21.4 1.0 O3' C:DC15 4.8 22.2 1.0 OP2 B:DT16 4.9 23.9 1.0 OE1 A:GLU184 4.9 26.4 1.0 C4' C:DG16 4.9 24.4 1.0 N A:GLY183 5.0 19.1 1.0

Calcium binding site 3 out of 3 in the Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wild-Type I-Ltri Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:32.3 occ:1.00 OE1 A:GLU29 2.2 26.1 1.0 OE1 A:GLU184 2.2 26.4 1.0 OP2 C:DG16 2.4 22.2 1.0 OP2 B:DA17 2.4 21.6 1.0 O3' C:DC15 2.7 22.2 1.0 O3' B:DT16 2.7 22.6 1.0 CD A:GLU29 3.0 26.7 1.0 P C:DG16 3.1 25.1 1.0 P B:DA17 3.2 25.1 1.0 OE2 A:GLU29 3.2 24.2 1.0 CD A:GLU184 3.3 21.2 1.0 C3' C:DC15 3.6 21.7 1.0 C3' B:DT16 3.6 21.3 1.0 OE2 A:GLU184 3.7 21.3 1.0 O A:GLY183 3.8 22.6 1.0 O5' C:DG16 3.9 23.1 1.0 CA A:CA402 3.9 25.4 1.0 CA A:CA401 3.9 24.8 1.0 C4' C:DC15 4.0 22.7 1.0 O A:ALA28 4.0 18.9 1.0 C4' B:DT16 4.1 26.6 1.0 O5' B:DA17 4.1 21.7 1.0 OP1 B:DA17 4.3 24.9 1.0 C A:GLY183 4.3 22.0 1.0 OP1 C:DG16 4.4 27.0 1.0 CG A:GLU29 4.5 16.3 1.0 CG A:GLU184 4.5 19.6 1.0 C A:ALA28 4.5 22.1 1.0 C5' C:DC15 4.6 23.5 1.0 CA A:GLU184 4.7 19.8 1.0 OP1 C:DC15 4.8 23.3 1.0 N A:GLU184 4.8 21.4 1.0 CB A:ALA28 4.9 19.1 1.0 CA A:GLU29 5.0 18.4 1.0

T.A.Mcmurrough, C.M.Brown, K.Zhang, G.Hausner, M.S.Junop, G.B.Gloor, D.R.Edgell. Active Site Residue Identity Regulates Cleavage Preference of Laglidadg Homing Endonucleases. Nucleic Acids Res. V. 46 11990 2018.
ISSN: ESSN 1362-4962
PubMed: 30357419
DOI: 10.1093/NAR/GKY976