Calcium in PDB 6bcf: I-Ltri G183A Bound to Cognate Substrate (Pre-Cleavage Complex)

The structure of I-Ltri G183A Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bcf 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)	38.99 / 2.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.956, 66.770, 169.414, 90.12, 90.08, 90.06
R / Rfree (%)	23.9 / 30.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the I-Ltri G183A Bound to Cognate Substrate (Pre-Cleavage Complex) (pdb code 6bcf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the I-Ltri G183A Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bcf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:77.7 occ:1.00 O D:ALA28 2.6 58.2 1.0 OE1 D:GLU184 2.9 60.0 1.0 OE2 D:GLU184 2.9 57.6 1.0 CD D:GLU184 3.2 58.1 1.0 C D:ALA28 3.7 52.9 1.0 OP1 F:DC15 3.9 65.8 1.0 CA D:ALA28 4.4 53.7 1.0 OP1 E:DA17 4.4 82.8 1.0 CA D:CA403 4.5 30.0 1.0 CG D:GLU184 4.6 57.8 1.0 N D:GLU29 4.8 56.4 1.0 OE1 D:GLN211 4.9 84.2 1.0 NE2 D:GLN211 4.9 56.6 1.0 CG D:GLU29 5.0 62.8 1.0 CA D:GLU29 5.0 62.9 1.0

Calcium binding site 2 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:65.5 occ:1.00 OE1 D:GLU29 2.5 88.5 1.0 O D:ALA183 2.5 65.3 1.0 OE2 D:GLU29 2.7 72.3 1.0 OP1 E:DT16 2.7 66.2 1.0 CD D:GLU29 2.9 68.5 1.0 C D:ALA183 3.6 57.8 1.0 CA D:ALA183 4.0 59.6 1.0 P E:DT16 4.2 71.7 1.0 CG D:GLU29 4.4 62.8 1.0 OP1 F:DG16 4.6 62.4 1.0 CB D:ALA183 4.7 55.4 1.0 N D:GLU184 4.8 55.7 1.0 OP2 E:DT16 4.8 93.9 1.0 O3' E:DA15 4.9 62.7 1.0

Calcium binding site 3 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:30.0 occ:1.00 OP1 E:DA17 2.2 82.8 1.0 OE2 D:GLU184 2.6 57.6 1.0 OE2 D:GLU29 2.9 72.3 1.0 OP1 F:DG16 3.0 62.4 1.0 P F:DG16 3.5 59.2 1.0 P E:DA17 3.5 71.4 1.0 O3' F:DC15 3.5 65.3 1.0 OP2 F:DG16 3.7 68.3 1.0 CD D:GLU184 3.8 58.1 1.0 O3' E:DT16 3.8 77.8 1.0 CD D:GLU29 3.8 68.5 1.0 CG D:GLU29 3.9 62.8 1.0 CG D:GLU184 4.3 57.8 1.0 OP2 E:DA17 4.4 0.8 1.0 CA D:CA401 4.5 77.7 1.0 C5' E:DA17 4.5 77.5 1.0 O5' E:DA17 4.6 73.4 1.0 C3' F:DC15 4.7 59.7 1.0 OE1 D:GLU184 4.8 60.0 1.0 C4' F:DC15 4.9 69.1 1.0

Calcium binding site 4 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:73.5 occ:1.00 O A:ALA183 2.4 75.1 1.0 OE2 A:GLU29 2.5 68.7 1.0 OE1 A:GLU29 2.7 97.5 1.0 OP1 B:DT16 2.8 73.0 1.0 CD A:GLU29 2.9 72.2 1.0 C A:ALA183 3.5 61.2 1.0 CA A:ALA183 3.9 61.6 1.0 P B:DT16 4.2 87.7 1.0 CG A:GLU29 4.4 66.6 1.0 OP1 C:DG16 4.5 64.7 1.0 CB A:ALA183 4.6 60.1 1.0 N A:GLU184 4.7 58.3 1.0 CA B:CA101 4.9 30.0 1.0 OP2 B:DT16 4.9 0.7 1.0 O3' B:DA15 5.0 61.3 1.0

Calcium binding site 5 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:56.7 occ:1.00 O A:ALA28 2.6 57.2 1.0 OE1 A:GLU184 2.7 62.5 1.0 OE2 A:GLU184 2.9 55.3 1.0 CD A:GLU184 3.2 57.0 1.0 C A:ALA28 3.7 51.3 1.0 OP1 C:DC15 3.7 59.3 1.0 OP1 B:DA17 3.9 95.4 1.0 CA A:ALA28 4.4 53.8 1.0 CG A:GLU184 4.6 60.6 1.0 CA B:CA101 4.7 30.0 1.0 N A:GLU29 4.7 62.6 1.0 NE2 A:GLN211 4.8 64.4 1.0 CA A:GLU29 4.9 76.6 1.0

Calcium binding site 6 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:30.0 occ:1.00 OP1 B:DA17 2.2 95.4 1.0 OE2 A:GLU184 2.7 55.3 1.0 OE2 A:GLU29 2.7 68.7 1.0 P B:DA17 3.0 81.6 1.0 OP1 C:DG16 3.1 64.7 1.0 O3' B:DT16 3.2 66.9 1.0 OP2 C:DG16 3.6 85.0 1.0 CD A:GLU29 3.6 72.2 1.0 P C:DG16 3.7 67.4 1.0 OP2 B:DA17 3.7 63.8 1.0 CG A:GLU29 3.8 66.6 1.0 CD A:GLU184 3.8 57.0 1.0 O3' C:DC15 3.9 67.0 1.0 CG A:GLU184 4.3 60.6 1.0 O5' B:DA17 4.3 63.4 1.0 C3' B:DT16 4.4 58.1 1.0 C5' B:DA17 4.5 65.0 1.0 CA A:CA402 4.7 56.7 1.0 C4' B:DT16 4.8 62.2 1.0 OE1 A:GLU29 4.8 97.5 1.0 CA A:CA401 4.9 73.5 1.0 OE1 A:GLU184 4.9 62.5 1.0 CB A:GLU29 5.0 76.8 1.0

Calcium binding site 7 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:90.5 occ:1.00 OE1 G:GLU184 2.5 68.1 1.0 O G:ALA28 2.6 69.5 1.0 OE2 G:GLU184 3.0 64.4 1.0 CD G:GLU184 3.1 64.3 1.0 C G:ALA28 3.7 60.4 1.0 OP1 I:DC15 3.9 74.4 1.0 CA G:ALA28 4.2 61.1 1.0 OE1 G:GLN211 4.3 87.8 1.0 CG G:GLU184 4.6 62.9 1.0 NE2 G:GLN211 4.6 67.4 1.0 O G:ASP27 4.7 55.2 1.0 CA H:CA101 4.8 30.0 1.0 N G:GLU29 4.8 61.4 1.0 OP1 H:DA17 4.9 1.0 1.0 OP2 H:DA17 4.9 0.3 1.0 CD G:GLN211 4.9 72.3 1.0

Calcium binding site 8 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca402 b:63.9 occ:1.00 O G:ALA183 2.3 61.0 1.0 OE1 G:GLU29 2.6 78.9 1.0 OE2 G:GLU29 2.8 70.3 1.0 OP1 H:DT16 2.9 69.7 1.0 CD G:GLU29 3.1 68.7 1.0 C G:ALA183 3.4 56.6 1.0 CA G:ALA183 3.9 60.9 1.0 P H:DT16 4.3 81.1 1.0 CG G:GLU29 4.6 63.9 1.0 N G:GLU184 4.6 53.1 1.0 O G:ALA182 4.7 52.9 1.0 CB G:ALA183 4.7 57.9 1.0 OP1 I:DG16 4.8 73.0 1.0 CA G:GLU184 4.9 61.8 1.0

Calcium binding site 9 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca101 b:30.0 occ:1.00 OE2 G:GLU184 2.4 64.4 1.0 OP2 H:DA17 2.5 0.3 1.0 OP1 H:DA17 2.7 1.0 1.0 OP1 I:DG16 2.8 73.0 1.0 P H:DA17 3.0 94.5 1.0 OE2 G:GLU29 3.1 70.3 1.0 P I:DG16 3.2 61.1 1.0 O3' I:DC15 3.3 81.4 1.0 OP2 I:DG16 3.5 65.2 1.0 CD G:GLU184 3.6 64.3 1.0 O3' H:DT16 3.7 79.4 1.0 CD G:GLU29 4.1 68.7 1.0 CG G:GLU184 4.2 62.9 1.0 CG G:GLU29 4.2 63.9 1.0 O5' H:DA17 4.5 68.1 1.0 C3' I:DC15 4.5 65.6 1.0 OE1 G:GLU184 4.6 68.1 1.0 CA G:CA401 4.8 90.5 1.0 O5' I:DG16 4.8 65.7 1.0 C4' I:DC15 4.8 75.6 1.0 C3' H:DT16 4.9 67.1 1.0

Calcium binding site 10 out of 12 in the I-Ltri G183A 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 G183A Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca401 b:72.8 occ:1.00 O J:ALA183 2.4 60.8 1.0 OE2 J:GLU29 2.7 76.0 1.0 OE1 J:GLU29 2.8 71.1 1.0 OP1 K:DT16 2.8 78.4 1.0 CD J:GLU29 3.0 73.4 1.0 C J:ALA183 3.5 57.7 1.0 CA J:ALA183 4.1 61.2 1.0 P K:DT16 4.3 92.1 1.0 CG J:GLU29 4.5 65.4 1.0 OP1 L:DG16 4.5 74.5 1.0 N J:GLU184 4.7 55.4 1.0 CB J:ALA183 4.8 56.2 1.0 O J:ALA182 4.9 51.0 1.0 O3' K:DA15 5.0 71.2 1.0 OP2 K:DT16 5.0 0.1 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