Atomistry » Calcium » PDB 6b40-6bgp » 6bcg
Atomistry »
  Calcium »
    PDB 6b40-6bgp »
      6bcg »

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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Go back to Calcium Binding Sites List in 6bcg
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy