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Calcium in PDB 6bcg: I-Ltri A28G Bound to Cognate Substrate (Pre-Cleavage Complex)

Protein crystallography data

The structure of I-Ltri A28G Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bcg 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) 35.76 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.859, 65.942, 169.734, 89.99, 90.03, 90.24
R / Rfree (%) 26.3 / 30.7

Calcium Binding Sites:

The binding sites of Calcium atom in the I-Ltri A28G Bound to Cognate Substrate (Pre-Cleavage Complex) (pdb code 6bcg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the I-Ltri A28G Bound to Cognate Substrate (Pre-Cleavage Complex), PDB code: 6bcg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6bcg

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Calcium binding site 1 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:77.2
occ:1.00
 OE1 D:GLU184 2.4 65.2 1.0
OP1 E:DA17 2.6 72.5 1.0
CD D:GLU184 3.4 64.8 1.0
OP1 F:DC15 3.6 82.1 1.0
P E:DA17 3.8 93.1 1.0
OE2 D:GLU184 3.9 69.7 1.0
O3' F:DC15 4.0 85.2 1.0
OP2 E:DA17 4.0 76.5 1.0
C4' F:DC15 4.1 80.2 1.0
O D:GLY28 4.2 54.8 1.0
OE1 D:GLN211 4.4 62.8 1.0
C5' E:DA17 4.5 68.8 1.0
O E:HOH101 4.5 60.3 1.0
O4' F:DC15 4.6 90.0 1.0
CG D:GLU184 4.6 53.7 1.0
O5' E:DA17 4.7 71.5 1.0
C3' F:DC15 4.7 71.3 1.0
OP2 F:DG16 4.7 0.1 1.0
P F:DC15 4.9 98.4 1.0
C4' E:DA17 4.9 66.8 1.0
O3' E:DT16 5.0 75.9 1.0

Calcium binding site 2 out of 8 in 6bcg

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Calcium binding site 2 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:73.5
occ:1.00
 O D:GLY183 2.5 64.1 1.0
OE2 D:GLU184 2.6 69.7 1.0
OE2 D:GLU29 2.6 62.4 1.0
OP2 F:DG16 2.9 0.1 1.0
OP2 E:DA17 3.0 76.5 1.0
OE1 D:GLU29 3.1 78.6 1.0
CD D:GLU29 3.2 66.1 1.0
C D:GLY183 3.3 58.1 1.0
CD D:GLU184 3.7 64.8 1.0
OP1 E:DT16 3.9 76.8 1.0
N D:GLU184 4.1 54.4 1.0
CA D:GLY183 4.1 58.1 1.0
P E:DA17 4.2 93.1 1.0
CA D:GLU184 4.2 61.1 1.0
P F:DG16 4.3 0.3 1.0
O3' E:DT16 4.4 75.9 1.0
CG D:GLU29 4.5 63.4 1.0
OE1 D:GLU184 4.5 65.2 1.0
CG D:GLU184 4.6 53.7 1.0
C4' E:DT16 4.7 77.3 1.0
C3' E:DT16 4.8 74.5 1.0
OP1 F:DG16 4.8 0.0 1.0
OP1 E:DA17 4.9 72.5 1.0
C5' E:DT16 4.9 83.9 1.0
CB D:GLU184 4.9 61.7 1.0

Calcium binding site 3 out of 8 in 6bcg

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Calcium binding site 3 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:75.8
occ:1.00
 OE1 A:GLU184 2.2 72.6 1.0
OP2 B:DA17 2.4 62.2 1.0
CD A:GLU184 2.5 65.7 1.0
OE2 A:GLU184 2.5 68.3 1.0
OP1 C:DC15 2.8 81.1 1.0
O A:GLY28 3.3 53.8 1.0
CG A:GLU184 3.6 59.3 1.0
P B:DA17 3.7 78.2 1.0
OE1 A:GLN211 3.9 75.5 1.0
C4' C:DC15 3.9 77.3 1.0
O3' C:DC15 4.2 73.4 1.0
OP1 B:DA17 4.2 69.5 1.0
P C:DC15 4.2 85.8 1.0
C A:GLY28 4.2 53.1 1.0
CA A:GLY28 4.4 53.7 1.0
C5' C:DC15 4.5 79.7 1.0
C3' C:DC15 4.6 71.1 1.0
O5' B:DA17 4.6 69.2 1.0
O3' B:DT16 4.8 75.2 1.0
C5' B:DA17 4.8 61.2 1.0
CD A:GLN211 4.9 74.6 1.0
O4' C:DC15 4.9 86.7 1.0
CB A:GLU184 4.9 66.0 1.0
O5' C:DC15 4.9 84.3 1.0
O3' C:DA14 4.9 83.1 1.0
NE2 A:GLN211 5.0 75.4 1.0

Calcium binding site 4 out of 8 in 6bcg

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Calcium binding site 4 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:76.7
occ:1.00
 OE2 A:GLU29 2.2 73.4 1.0
OP2 C:DG16 2.4 96.3 1.0
OE1 A:GLU29 2.6 74.0 1.0
CD A:GLU29 2.7 69.9 1.0
O A:GLY183 2.8 63.5 1.0
C A:GLY183 3.5 62.7 1.0
OE2 A:GLU184 3.5 68.3 1.0
OP1 B:DT16 3.7 83.8 1.0
O3' B:DT16 3.8 75.2 1.0
C4' B:DT16 3.9 92.2 1.0
P C:DG16 3.9 89.2 1.0
CA A:GLY183 4.0 61.0 1.0
C3' B:DT16 4.1 75.5 1.0
CG A:GLU29 4.1 67.8 1.0
N A:GLU184 4.3 59.8 1.0
CG A:GLU184 4.3 59.3 1.0
OP2 B:DA17 4.3 62.2 1.0
C5' B:DT16 4.3 94.5 1.0
CD A:GLU184 4.3 65.7 1.0
CA A:GLU184 4.5 63.8 1.0
O3' C:DC15 4.6 73.4 1.0
P B:DA17 4.7 78.2 1.0
CB A:GLU29 4.7 63.7 1.0
OP1 C:DG16 4.7 73.6 1.0
O5' C:DG16 4.7 75.6 1.0
CB A:GLU184 5.0 66.0 1.0

Calcium binding site 5 out of 8 in 6bcg

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Calcium binding site 5 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:79.1
occ:1.00
 OE1 G:GLU184 2.5 55.2 1.0
OP2 H:DA17 2.5 78.4 1.0
OP1 H:DA17 2.7 96.3 1.0
P H:DA17 3.3 90.0 1.0
CD G:GLU184 3.4 53.7 1.0
O3' I:DC15 3.5 81.9 1.0
OE2 G:GLU184 3.5 59.1 1.0
OP2 I:DG16 3.7 0.1 1.0
OP1 I:DC15 3.9 93.6 1.0
P I:DG16 4.1 98.4 1.0
C4' I:DC15 4.4 88.1 1.0
O5' H:DA17 4.4 77.5 1.0
O G:GLY28 4.4 49.7 1.0
C5' H:DA17 4.5 67.9 1.0
O3' H:DT16 4.5 80.2 1.0
OE1 G:GLN211 4.6 67.8 1.0
C3' I:DC15 4.6 76.4 1.0
OP1 I:DG16 4.6 99.9 1.0
CG G:GLU184 4.8 55.0 1.0
CA G:CA402 4.9 75.6 1.0

Calcium binding site 6 out of 8 in 6bcg

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Calcium binding site 6 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca402

b:75.6
occ:1.00
 OE2 G:GLU29 2.4 59.1 1.0
OE2 G:GLU184 2.5 59.1 1.0
OE1 G:GLU29 2.6 64.1 1.0
CD G:GLU29 2.8 60.4 1.0
O G:GLY183 2.9 61.7 1.0
OP2 H:DA17 3.0 78.4 1.0
OP2 I:DG16 3.4 0.1 1.0
C G:GLY183 3.6 58.1 1.0
CD G:GLU184 3.7 53.7 1.0
P H:DA17 3.7 90.0 1.0
O3' H:DT16 3.9 80.2 1.0
C3' H:DT16 4.2 80.5 1.0
CA G:GLY183 4.3 55.8 1.0
N G:GLU184 4.3 57.0 1.0
CG G:GLU29 4.3 60.9 1.0
C4' H:DT16 4.3 80.5 1.0
OP1 H:DT16 4.3 69.9 1.0
OE1 G:GLU184 4.4 55.2 1.0
CA G:GLU184 4.5 57.1 1.0
CG G:GLU184 4.6 55.0 1.0
O5' H:DA17 4.6 77.5 1.0
P I:DG16 4.7 98.4 1.0
O G:GLY28 4.8 49.7 1.0
OP1 H:DA17 4.8 96.3 1.0
C5' H:DT16 4.8 87.1 1.0
CA G:CA401 4.9 79.1 1.0

Calcium binding site 7 out of 8 in 6bcg

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Calcium binding site 7 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:78.2
occ:1.00
 OP2 L:DG16 2.5 85.4 1.0
OP1 K:DT16 2.6 80.5 1.0
O J:GLY183 2.6 55.1 1.0
OE1 J:GLU29 2.6 71.7 1.0
CD J:GLU29 3.3 63.3 1.0
OE2 J:GLU29 3.4 57.3 1.0
C J:GLY183 3.7 53.7 1.0
C4' K:DT16 3.8 91.2 1.0
C5' K:DT16 3.8 96.3 1.0
P L:DG16 3.8 86.7 1.0
OE2 J:GLU184 3.9 60.6 1.0
P K:DT16 4.0 0.2 1.0
CA J:GLY183 4.3 56.5 1.0
C3' K:DT16 4.3 76.8 1.0
O3' K:DT16 4.4 84.5 1.0
OP1 L:DG16 4.4 69.9 1.0
O5' K:DT16 4.4 99.4 1.0
O5' L:DG16 4.6 70.4 1.0
C5' L:DG16 4.6 65.3 1.0
N J:GLU184 4.7 48.0 1.0
CG J:GLU29 4.7 61.4 1.0
O3' K:DA15 4.9 80.0 1.0
O3' L:DC15 4.9 72.6 1.0
OP2 K:DT16 4.9 94.4 1.0
O4' K:DT16 4.9 85.4 1.0
OP2 K:DA17 5.0 69.3 1.0

Calcium binding site 8 out of 8 in 6bcg

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Calcium binding site 8 out of 8 in the I-Ltri A28G 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 A28G Bound to Cognate Substrate (Pre-Cleavage Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca402

b:76.8
occ:1.00
 OE1 J:GLU184 2.3 57.0 1.0
OP2 K:DA17 2.3 69.3 1.0
OP1 L:DC15 3.0 76.8 1.0
CD J:GLU184 3.1 56.9 1.0
OE2 J:GLU184 3.3 60.6 1.0
O J:GLY28 3.5 51.2 1.0
P K:DA17 3.5 86.5 1.0
OE1 J:GLN211 3.9 68.0 1.0
OP1 K:DA17 3.9 96.8 1.0
C4' L:DC15 4.0 75.4 1.0
O3' L:DC15 4.1 72.6 1.0
P L:DC15 4.4 89.3 1.0
CG J:GLU184 4.4 55.2 1.0
O5' K:DA17 4.5 72.5 1.0
C5' L:DC15 4.5 83.9 1.0
O3' K:DT16 4.5 84.5 1.0
C J:GLY28 4.5 55.8 1.0
C3' L:DC15 4.6 68.9 1.0
C5' K:DA17 4.6 66.2 1.0
CD J:GLN211 4.8 69.7 1.0
O4' L:DC15 4.9 82.1 1.0
NE2 J:GLN211 4.9 72.6 1.0
O5' L:DC15 4.9 91.4 1.0
O3' L:DA14 4.9 77.2 1.0
CA J:GLY28 5.0 56.9 1.0

Reference:

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
Page generated: Mon Jul 15 16:49:10 2024

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