Calcium in PDB 6bcn: I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex)

The structure of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bcn 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)	35.71 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.650, 64.020, 168.976, 89.93, 90.19, 93.64
R / Rfree (%)	23.7 / 27.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) (pdb code 6bcn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bcn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the I-Ltri E184D 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 I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:46.2 occ:1.00 OP1 D:DC15 2.3 33.6 1.0 O A:ALA28 2.3 24.8 1.0 OP2 B:DA17 2.3 30.1 1.0 OD2 A:ASP184 2.5 39.5 1.0 OD1 A:ASP184 2.9 37.1 1.0 CG A:ASP184 3.0 35.8 1.0 C A:ALA28 3.1 23.6 1.0 CA A:ALA28 3.3 28.5 1.0 CA A:CA403 3.7 56.2 1.0 P B:DA17 3.7 25.0 1.0 P D:DC15 3.8 30.6 1.0 OE1 A:GLU29 3.8 32.3 1.0 OE1 A:GLN211 3.9 30.7 1.0 CB A:ALA28 4.0 25.7 1.0 O5' B:DA17 4.2 42.5 1.0 C5' D:DC15 4.2 36.2 1.0 O A:ASP27 4.3 25.9 1.0 CB A:ASP184 4.3 32.4 1.0 N A:GLU29 4.4 25.4 1.0 C5' B:DA17 4.4 29.1 1.0 NE2 A:GLN211 4.5 30.7 1.0 C4' D:DC15 4.5 35.9 1.0 O3' D:DA14 4.5 28.7 1.0 O5' D:DC15 4.5 34.9 1.0 N A:ALA28 4.6 19.2 1.0 CD A:GLN211 4.6 31.6 1.0 O3' B:DT16 4.6 22.1 1.0 O A:HOH511 4.7 26.1 1.0 OP1 B:DA17 4.7 18.7 1.0 OP2 D:DC15 4.7 30.0 1.0 C A:ASP27 4.9 24.1 1.0 CA A:GLU29 5.0 28.8 1.0

Calcium binding site 2 out of 13 in the I-Ltri E184D 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 I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:36.6 occ:1.00 O A:GLY183 2.2 36.5 1.0 OP1 B:DT16 2.3 22.1 1.0 OP2 D:DG16 2.4 35.1 1.0 OE2 A:GLU29 2.4 33.3 1.0 C A:GLY183 3.1 28.4 1.0 CA A:GLY183 3.4 27.5 1.0 CD A:GLU29 3.5 28.9 1.0 P D:DG16 3.7 24.1 1.0 P B:DT16 3.7 35.0 1.0 CA A:CA403 3.9 56.2 1.0 O A:HOH513 4.0 30.4 1.0 OE1 A:GLU29 4.0 32.3 1.0 O A:ALA182 4.1 29.5 1.0 C5' B:DT16 4.2 30.4 1.0 O5' D:DG16 4.2 31.8 1.0 C4' B:DT16 4.2 30.2 1.0 OP1 D:DG16 4.3 24.1 1.0 O3' B:DA15 4.3 17.0 1.0 C5' D:DG16 4.4 35.0 1.0 N A:ASP184 4.4 26.8 1.0 NZ A:LYS274 4.4 30.4 1.0 O5' B:DT16 4.5 35.9 1.0 CG A:GLU29 4.5 30.4 1.0 N A:GLY183 4.6 21.6 1.0 OP2 B:DT16 4.7 37.5 1.0 C A:ALA182 4.8 27.9 1.0 OD1 A:ASP184 4.8 37.1 1.0 O3' D:DC15 4.8 26.1 1.0 CA A:ASP184 4.9 34.8 1.0

Calcium binding site 3 out of 13 in the I-Ltri E184D 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 I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:56.2 occ:1.00 OP2 D:DG16 2.4 35.1 1.0 OE1 A:GLU29 2.4 32.3 1.0 O3' B:DT16 2.5 22.1 1.0 O3' D:DC15 2.5 26.1 1.0 OD1 A:ASP184 2.6 37.1 1.0 OP2 B:DA17 3.0 30.1 1.0 P D:DG16 3.0 24.1 1.0 P B:DA17 3.1 25.0 1.0 CD A:GLU29 3.3 28.9 1.0 C3' B:DT16 3.3 26.0 1.0 OE2 A:GLU29 3.4 33.3 1.0 C3' D:DC15 3.5 31.7 1.0 C4' B:DT16 3.6 30.2 1.0 CG A:ASP184 3.7 35.8 1.0 CA A:CA401 3.7 46.2 1.0 O A:GLY183 3.7 36.5 1.0 CA A:CA402 3.9 36.6 1.0 C4' D:DC15 3.9 35.9 1.0 O5' D:DG16 3.9 31.8 1.0 O5' B:DA17 4.0 42.5 1.0 C A:GLY183 4.1 28.4 1.0 OP1 D:DG16 4.2 24.1 1.0 O A:ALA28 4.2 24.8 1.0 OP1 B:DA17 4.2 18.7 1.0 CA A:ASP184 4.3 34.8 1.0 CB A:ASP184 4.4 32.4 1.0 OD2 A:ASP184 4.5 39.5 1.0 N A:ASP184 4.5 26.8 1.0 O4' B:DT16 4.6 29.0 1.0 C5' D:DC15 4.6 36.2 1.0 C5' B:DT16 4.7 30.4 1.0 OP1 D:DC15 4.7 33.6 1.0 CG A:GLU29 4.7 30.4 1.0 C2' B:DT16 4.7 31.3 1.0 C A:ALA28 4.8 23.6 1.0 CA A:GLY183 4.9 27.5 1.0 C2' D:DC15 4.9 27.4 1.0 OP1 B:DT16 4.9 22.1 1.0

Calcium binding site 4 out of 13 in the I-Ltri E184D 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 4 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:43.9 occ:1.00 OP1 F:DC15 2.3 38.1 1.0 O C:HOH520 2.3 24.1 1.0 O C:ALA28 2.4 22.3 1.0 OP2 E:DA17 2.5 29.4 1.0 OD2 C:ASP184 2.7 33.2 1.0 OD1 C:ASP184 2.7 31.5 1.0 CG C:ASP184 2.9 32.4 1.0 C C:ALA28 3.2 24.9 1.0 O E:HOH204 3.4 26.2 1.0 CA C:ALA28 3.4 27.7 1.0 OE1 C:GLU29 3.5 44.1 1.0 P F:DC15 3.8 31.0 1.0 P E:DA17 3.8 28.5 1.0 OE1 C:GLN211 4.0 25.0 1.0 CB C:ALA28 4.0 26.1 1.0 CA C:CA402 4.0 50.0 1.0 C5' F:DC15 4.0 35.8 1.0 O5' E:DA17 4.2 37.9 1.0 CB C:ASP184 4.3 34.5 1.0 C4' F:DC15 4.4 36.1 1.0 N C:GLU29 4.4 28.7 1.0 O5' F:DC15 4.4 36.0 1.0 C5' E:DA17 4.5 32.2 1.0 O3' F:DA14 4.5 30.3 1.0 O C:ASP27 4.5 20.6 1.0 OP1 E:DA17 4.6 23.8 1.0 NE2 C:GLN211 4.7 31.8 1.0 CD C:GLN211 4.7 27.5 1.0 OP2 F:DC15 4.7 35.7 1.0 N C:ALA28 4.7 16.8 1.0 CD C:GLU29 4.8 35.5 1.0 O3' E:DT16 4.9 29.8 1.0 CA C:GLU29 4.9 33.3 1.0 O3' F:DC15 5.0 27.9 1.0 C3' F:DC15 5.0 34.8 1.0

Calcium binding site 5 out of 13 in the I-Ltri E184D 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 5 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:50.0 occ:1.00 OE1 C:GLU29 2.2 44.1 1.0 OP2 F:DG16 2.2 38.7 1.0 OE2 C:GLU29 2.5 40.0 1.0 CD C:GLU29 2.6 35.5 1.0 O3' F:DC15 2.9 27.9 1.0 OD1 C:ASP184 3.0 31.5 1.0 P F:DG16 3.0 30.7 1.0 O3' E:DT16 3.0 29.8 1.0 CA C:CA403 3.3 37.9 1.0 O C:GLY183 3.3 36.7 1.0 OP2 E:DA17 3.4 29.4 1.0 C3' E:DT16 3.5 34.1 1.0 P E:DA17 3.5 28.5 1.0 C4' E:DT16 3.5 35.4 1.0 C C:GLY183 3.8 30.1 1.0 O5' F:DG16 3.9 30.6 1.0 C3' F:DC15 4.0 34.8 1.0 CA C:CA401 4.0 43.9 1.0 CG C:ASP184 4.1 32.4 1.0 OP1 F:DG16 4.1 24.0 1.0 CG C:GLU29 4.1 27.9 1.0 C5' E:DT16 4.1 37.0 1.0 O5' E:DA17 4.2 37.9 1.0 OP1 E:DT16 4.3 32.8 1.0 N C:ASP184 4.4 30.9 1.0 CA C:GLY183 4.4 31.0 1.0 CA C:ASP184 4.5 32.1 1.0 C4' F:DC15 4.5 36.1 1.0 O C:ALA28 4.5 22.3 1.0 OP1 E:DA17 4.7 23.8 1.0 O4' E:DT16 4.8 35.0 1.0 CB C:ASP184 4.8 34.5 1.0 C C:ALA28 4.9 24.9 1.0 CB C:GLU29 4.9 32.5 1.0 C5' F:DG16 5.0 32.9 1.0 CA C:GLU29 5.0 33.3 1.0 C2' E:DT16 5.0 33.8 1.0

Calcium binding site 6 out of 13 in the I-Ltri E184D 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 6 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:37.9 occ:1.00 OE2 C:GLU29 2.2 40.0 1.0 O C:GLY183 2.2 36.7 1.0 OP1 E:DT16 2.5 32.8 1.0 OP2 F:DG16 2.5 38.7 1.0 C C:GLY183 3.1 30.1 1.0 O F:HOH109 3.1 25.6 1.0 CA C:GLY183 3.3 31.0 1.0 CA C:CA402 3.3 50.0 1.0 CD C:GLU29 3.3 35.5 1.0 P F:DG16 3.9 30.7 1.0 P E:DT16 3.9 29.3 1.0 O C:ALA182 3.9 27.6 1.0 OE1 C:GLU29 4.1 44.1 1.0 C5' E:DT16 4.2 37.0 1.0 CG C:GLU29 4.3 27.9 1.0 N C:ASP184 4.3 30.9 1.0 O5' F:DG16 4.4 30.6 1.0 N C:GLY183 4.4 25.5 1.0 C5' F:DG16 4.6 32.9 1.0 C4' E:DT16 4.6 35.4 1.0 O5' E:DT16 4.6 39.4 1.0 C C:ALA182 4.6 27.6 1.0 OP1 F:DG16 4.6 24.0 1.0 O3' E:DA15 4.6 25.5 1.0 OP2 E:DT16 4.7 41.9 1.0 OD1 C:ASP184 4.9 31.5 1.0 CA C:ASP184 5.0 32.1 1.0 CE C:LYS274 5.0 23.4 1.0 O3' F:DC15 5.0 27.9 1.0

Calcium binding site 7 out of 13 in the I-Ltri E184D 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 7 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:51.5 occ:1.00 OP1 I:DC15 2.3 39.4 1.0 O G:ALA28 2.4 39.1 1.0 OP2 H:DA17 2.4 41.8 1.0 OD2 G:ASP184 2.6 37.5 1.0 OD1 G:ASP184 2.9 47.3 1.0 CG G:ASP184 3.0 43.1 1.0 C G:ALA28 3.2 37.2 1.0 CA G:ALA28 3.5 38.1 1.0 CA G:CA402 3.5 58.2 1.0 P H:DA17 3.8 37.2 1.0 P I:DC15 3.8 36.4 1.0 OE1 G:GLU29 3.9 49.0 1.0 NE2 G:GLN211 4.0 35.5 1.0 CB G:ALA28 4.1 35.1 1.0 O5' H:DA17 4.2 39.8 1.0 O G:ASP27 4.3 28.9 1.0 OE1 G:GLN211 4.3 48.9 1.0 C5' I:DC15 4.3 38.6 1.0 C5' H:DA17 4.4 38.5 1.0 CB G:ASP184 4.4 42.9 1.0 O3' I:DA14 4.4 36.8 1.0 N G:GLU29 4.5 39.2 1.0 CD G:GLN211 4.6 37.5 1.0 O5' I:DC15 4.6 38.3 1.0 C4' I:DC15 4.6 38.0 1.0 N G:ALA28 4.7 24.6 1.0 OP1 H:DA17 4.7 31.9 1.0 OP2 I:DC15 4.7 34.7 1.0 O3' H:DT16 4.8 36.5 1.0 C G:ASP27 4.9 29.0 1.0

Calcium binding site 8 out of 13 in the I-Ltri E184D 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 8 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca402 b:58.2 occ:1.00 O3' I:DC15 2.4 27.8 1.0 OD1 G:ASP184 2.5 47.3 1.0 OP2 I:DG16 2.5 40.7 1.0 OP2 H:DA17 2.5 41.8 1.0 OE1 G:GLU29 2.7 49.0 1.0 O3' H:DT16 2.8 36.5 1.0 P I:DG16 3.0 34.3 1.0 P H:DA17 3.2 37.2 1.0 C3' I:DC15 3.3 36.0 1.0 CG G:ASP184 3.5 43.1 1.0 CA G:CA401 3.5 51.5 1.0 C4' I:DC15 3.6 38.0 1.0 CD G:GLU29 3.6 46.4 1.0 O G:GLY183 3.7 56.0 1.0 OE2 G:GLU29 3.8 54.5 1.0 C3' H:DT16 3.8 31.9 1.0 O5' I:DG16 3.8 43.1 1.0 CA G:ASP184 4.1 40.5 1.0 C G:GLY183 4.1 49.2 1.0 CB G:ASP184 4.1 42.9 1.0 O5' H:DA17 4.2 39.8 1.0 C4' H:DT16 4.2 31.0 1.0 OP1 I:DG16 4.2 30.9 1.0 O G:ALA28 4.2 39.1 1.0 C5' I:DC15 4.3 38.6 1.0 OP1 H:DA17 4.3 31.9 1.0 OD2 G:ASP184 4.3 37.5 1.0 OP1 I:DC15 4.3 39.4 1.0 N G:ASP184 4.3 39.8 1.0 C2' I:DC15 4.7 44.2 1.0 O4' I:DC15 4.8 38.5 1.0 C G:ALA28 4.8 37.2 1.0 CA G:GLY183 4.9 48.8 1.0

Calcium binding site 9 out of 13 in the I-Ltri E184D 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 9 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca401 b:42.2 occ:1.00 OP1 L:DC15 2.3 45.7 1.0 O J:ALA28 2.4 37.9 1.0 OP2 K:DA17 2.4 36.6 1.0 OD2 J:ASP184 2.6 46.2 1.0 O L:HOH103 2.8 30.1 1.0 OD1 J:ASP184 3.0 52.0 1.0 CG J:ASP184 3.1 44.6 1.0 C J:ALA28 3.2 39.8 1.0 CA J:ALA28 3.4 39.7 1.0 P L:DC15 3.8 38.0 1.0 P K:DA17 3.8 36.1 1.0 CA J:CA402 3.8 57.9 1.0 OE1 J:GLN211 4.0 41.3 1.0 OE1 J:GLU29 4.0 47.7 1.0 CB J:ALA28 4.1 40.5 1.0 O5' K:DA17 4.2 37.3 1.0 O J:ASP27 4.3 29.8 1.0 C5' K:DA17 4.3 37.6 1.0 C5' L:DC15 4.4 41.6 1.0 CB J:ASP184 4.4 44.9 1.0 NE2 J:GLN211 4.5 43.5 1.0 N J:GLU29 4.5 42.6 1.0 O3' L:DA14 4.5 35.3 1.0 CD J:GLN211 4.6 40.7 1.0 N J:ALA28 4.6 31.3 1.0 OP2 L:DC15 4.6 39.8 1.0 O5' L:DC15 4.6 41.5 1.0 OP1 K:DA17 4.7 32.4 1.0 C4' L:DC15 4.7 41.1 1.0 O3' K:DT16 4.8 37.0 1.0 C J:ASP27 4.9 33.6 1.0

Calcium binding site 10 out of 13 in the I-Ltri E184D 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 10 of I-Ltri E184D Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca402 b:57.9 occ:1.00 OP2 L:DG16 2.5 48.7 1.0 OE1 J:GLU29 2.5 47.7 1.0 O3' L:DC15 2.5 31.4 1.0 OD1 J:ASP184 2.6 52.0 1.0 O3' K:DT16 2.7 37.0 1.0 OP2 K:DA17 2.8 36.6 1.0 P L:DG16 3.0 40.3 1.0 P K:DA17 3.3 36.1 1.0 CD J:GLU29 3.4 45.8 1.0 CA J:CA403 3.4 47.7 1.0 OE2 J:GLU29 3.5 42.3 1.0 C3' L:DC15 3.5 39.6 1.0 O J:GLY183 3.5 56.4 1.0 CG J:ASP184 3.6 44.6 1.0 C3' K:DT16 3.6 39.2 1.0 CA J:CA401 3.8 42.2 1.0 C4' L:DC15 3.8 41.1 1.0 O5' L:DG16 3.9 39.2 1.0 C J:GLY183 3.9 50.3 1.0 C4' K:DT16 3.9 37.4 1.0 CA J:ASP184 4.1 44.9 1.0 CB J:ASP184 4.2 44.9 1.0 O5' K:DA17 4.2 37.3 1.0 OP1 L:DG16 4.2 43.8 1.0 N J:ASP184 4.3 39.4 1.0 O J:ALA28 4.3 37.9 1.0 OP1 K:DA17 4.4 32.4 1.0 OD2 J:ASP184 4.4 46.2 1.0 C5' L:DC15 4.6 41.6 1.0 OP1 L:DC15 4.6 45.7 1.0 CA J:GLY183 4.7 51.2 1.0 C J:ALA28 4.8 39.8 1.0 CG J:GLU29 4.8 46.3 1.0 C2' L:DC15 4.9 40.2 1.0 O4' K:DT16 4.9 40.1 1.0 C5' K:DT16 4.9 38.7 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