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Potassium in PDB 7qqq: SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate

Protein crystallography data

The structure of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate, PDB code: 7qqq was solved by M.Pacesa, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.99, 67.91, 187.819, 90, 111.22, 90
R / Rfree (%) 18.9 / 23.5

Other elements in 7qqq:

The structure of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Potassium atom in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate (pdb code 7qqq). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 13 binding sites of Potassium where determined in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate, PDB code: 7qqq:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 13 in 7qqq

Go back to Potassium Binding Sites List in 7qqq
Potassium binding site 1 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:64.9
occ:1.00
 O4 A:U66 2.8 60.6 1.0
OP2 A:A65 2.8 46.6 1.0
OG1 B:THR1102 2.9 56.7 1.0
O A:HOH219 3.1 44.9 1.0
O A:HOH249 3.4 62.0 1.0
CG2 B:THR1102 3.6 41.1 1.0
C4 A:U66 3.7 50.4 1.0
CB B:THR1102 3.8 48.0 1.0
C5 A:U66 3.9 49.3 1.0
P A:A65 4.2 43.0 1.0
N4 A:C67 4.4 46.0 1.0
OP1 A:U64 4.4 44.0 1.0
OP1 A:A65 4.7 43.5 1.0
O B:VAL1100 4.7 46.1 1.0
O5' A:A65 4.8 48.4 1.0
N7 A:A65 4.8 59.3 1.0
OP2 A:U64 4.9 46.7 1.0
N3 A:U66 5.0 51.2 1.0
N B:THR1102 5.0 37.7 1.0

Potassium binding site 2 out of 13 in 7qqq

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Potassium binding site 2 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:81.6
occ:1.00
 O B:HOH1545 2.8 66.4 1.0
O A:HOH231 2.8 59.4 1.0
O B:GLN1350 2.8 51.7 1.0
O A:HOH209 2.9 62.6 1.0
O4' A:A68 3.1 66.6 1.0
C1' A:A68 3.6 66.1 1.0
C B:GLN1350 4.0 51.3 1.0
C4' A:A68 4.2 60.8 1.0
O B:SER1351 4.3 48.7 1.0
OG1 B:THR1098 4.3 49.3 1.0
N9 A:A68 4.3 61.3 1.0
O5' A:A68 4.4 45.2 1.0
N B:THR1098 4.5 45.1 1.0
C B:SER1351 4.5 49.1 1.0
CG2 B:THR1098 4.6 46.3 1.0
C8 A:A68 4.6 60.9 1.0
CG1 B:VAL1095 4.7 38.9 1.0
CB B:GLN1350 4.7 52.7 1.0
OP2 A:A68 4.7 52.0 1.0
CA B:GLN1350 4.7 52.6 1.0
OP1 A:A68 4.8 54.9 1.0
N B:GLN1350 4.8 52.4 1.0
C2' A:A68 4.8 63.1 1.0
O2' A:A68 4.8 52.9 1.0
P A:A68 4.9 49.6 1.0
C5' A:A68 4.9 45.5 1.0
N B:SER1351 4.9 49.4 1.0
CA B:SER1351 4.9 46.8 1.0
CB B:THR1098 5.0 48.8 1.0

Potassium binding site 3 out of 13 in 7qqq

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Potassium binding site 3 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:125.8
occ:1.00
 O A:HOH202 2.9 85.3 1.0
O A:HOH262 2.9 91.0 1.0
O A:HOH220 3.1 91.4 1.0
N7 A:G27 3.2 63.1 1.0
O A:HOH221 3.4 75.5 1.0
O A:HOH269 3.5 67.7 1.0
C8 A:G27 3.8 63.8 1.0
C5 A:G27 4.4 60.5 1.0
N7 A:A26 4.6 52.8 1.0
OP2 A:G27 4.6 73.2 1.0
O6 A:G27 4.9 76.4 1.0
C8 A:A26 5.0 45.8 1.0

Potassium binding site 4 out of 13 in 7qqq

Go back to Potassium Binding Sites List in 7qqq
Potassium binding site 4 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1401

b:116.2
occ:1.00
 O B:HOH1556 2.8 72.1 1.0
OE2 B:GLU57 3.3 84.7 1.0
O B:HOH1554 3.4 91.8 1.0
O A:HOH249 3.5 62.0 1.0
O B:HOH1600 3.6 75.9 1.0
NE2 B:GLN1101 4.2 55.8 1.0
CD B:GLU57 4.2 74.4 1.0
O B:HOH1560 4.3 62.0 1.0
OE1 B:GLU57 4.7 80.7 1.0
O B:HOH1501 4.8 54.2 1.0
O B:HOH1621 4.9 76.7 1.0

Potassium binding site 5 out of 13 in 7qqq

Go back to Potassium Binding Sites List in 7qqq
Potassium binding site 5 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1402

b:91.1
occ:1.00
 O B:THR624 2.8 67.7 1.0
O B:TYR656 2.8 51.8 1.0
O B:PHE626 3.3 58.8 1.0
O B:LEU623 3.5 58.5 1.0
C B:THR624 3.6 60.9 1.0
OP1 C:DC8 3.8 73.8 1.0
C B:PHE626 3.9 59.6 1.0
C B:TYR656 3.9 47.8 1.0
CA B:THR624 3.9 59.4 1.0
CG2 B:THR657 4.3 52.7 1.0
N B:PHE626 4.3 64.1 1.0
C B:LEU623 4.4 49.1 1.0
N B:GLU627 4.4 61.5 1.0
CA B:GLU627 4.5 62.4 1.0
CB B:GLU627 4.5 69.5 1.0
N B:TYR656 4.6 62.9 1.0
N B:LEU625 4.6 57.2 1.0
CA B:THR657 4.6 46.3 1.0
N B:THR624 4.6 57.4 1.0
N B:THR657 4.7 49.4 1.0
C B:LEU625 4.7 59.1 1.0
CA B:PHE626 4.7 58.7 1.0
CG B:GLU627 4.8 83.2 1.0
CA B:TYR656 4.9 50.7 1.0
CB B:ARG655 4.9 69.2 1.0
C5' C:DC8 5.0 60.4 1.0

Potassium binding site 6 out of 13 in 7qqq

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Potassium binding site 6 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1403

b:94.6
occ:1.00
 O B:ALA367 2.8 58.5 1.0
O B:GLY365 2.9 86.0 1.0
O B:TYR362 2.9 60.3 1.0
O B:GLY361 3.4 68.8 1.0
N B:ALA367 3.5 82.0 1.0
C B:TYR362 3.6 64.4 1.0
C B:GLY365 3.6 82.2 1.0
C B:ALA367 3.7 60.5 1.0
C B:GLY366 3.8 85.4 1.0
NZ B:LYS401 3.9 46.3 1.0
CA B:GLY366 3.9 87.1 1.0
CA B:TYR362 4.0 73.3 1.0
N B:GLY366 4.1 84.4 1.0
CA B:ALA367 4.2 71.0 1.0
C B:GLY361 4.4 69.8 1.0
N B:ILE363 4.5 61.9 1.0
OP1 A:U22 4.5 48.5 1.0
O B:GLY366 4.5 83.4 1.0
N B:GLY365 4.6 73.2 1.0
C B:ILE363 4.6 69.8 1.0
O B:ILE363 4.7 73.3 1.0
CA B:GLY365 4.7 76.8 1.0
N B:TYR362 4.7 71.0 1.0
N B:SER368 4.8 55.3 1.0
CA B:ILE363 4.9 63.3 1.0
CB B:ALA367 4.9 72.2 1.0
N B:ASP364 5.0 70.8 1.0

Potassium binding site 7 out of 13 in 7qqq

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Potassium binding site 7 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1404

b:110.1
occ:1.00
 O B:PHE643 2.8 96.8 1.0
O B:ALA640 2.8 96.2 1.0
C B:PHE643 3.9 91.8 1.0
C B:ALA640 4.0 87.6 1.0
CA B:HIS641 4.2 76.0 1.0
C B:HIS641 4.4 77.5 1.0
O B:HIS641 4.4 80.0 1.0
OD1 B:ASP645 4.5 147.1 1.0
CA B:ASP644 4.5 107.7 1.0
N B:HIS641 4.5 81.7 1.0
N B:ASP644 4.7 97.6 1.0
N B:PHE643 4.7 78.4 1.0
C B:ASP644 4.9 111.8 1.0
CA B:PHE643 5.0 84.5 1.0
N B:ASP645 5.0 115.6 1.0

Potassium binding site 8 out of 13 in 7qqq

Go back to Potassium Binding Sites List in 7qqq
Potassium binding site 8 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1405

b:143.9
occ:1.00
 O B:GLY231 2.8 142.2 1.0
O B:LEU229 3.2 90.9 1.0
O B:ILE226 3.4 87.6 1.0
N B:GLY231 3.6 130.9 1.0
C B:GLY231 3.8 134.4 1.0
CA B:GLY231 4.1 133.4 1.0
C B:LEU229 4.3 90.7 1.0
O B:ALA227 4.3 89.8 1.0
CA B:PRO230 4.3 100.4 1.0
C B:PRO230 4.3 115.9 1.0
C B:ILE226 4.4 92.6 1.0
CA B:ALA227 4.5 95.7 1.0
CG2 B:ILE226 4.6 94.5 1.0
O B:GLU232 4.6 121.4 1.0
C B:ALA227 4.7 91.2 1.0
N B:PRO230 4.8 95.5 1.0
N B:ALA227 4.9 97.6 1.0

Potassium binding site 9 out of 13 in 7qqq

Go back to Potassium Binding Sites List in 7qqq
Potassium binding site 9 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1406

b:128.0
occ:1.00
 O B:HOH1622 2.9 59.9 1.0
O B:LYS111 3.0 80.8 1.0
O B:GLU108 3.4 75.5 1.0
O B:HOH1506 3.5 85.7 1.0
O B:HIS113 3.9 68.4 1.0
C B:LYS111 4.0 66.0 1.0
CB B:LYS111 4.4 47.6 1.0
C B:GLU108 4.6 73.8 1.0
CA B:LYS111 4.6 51.3 1.0
CG B:GLU108 4.7 79.3 1.0
C B:HIS113 4.8 60.1 1.0
N B:LYS111 4.8 51.8 1.0
C B:LYS112 4.9 67.3 1.0
N B:LYS112 5.0 64.7 1.0

Potassium binding site 10 out of 13 in 7qqq

Go back to Potassium Binding Sites List in 7qqq
Potassium binding site 10 out of 13 in the SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of SPCAS9 Bound to AAVS1 Off-TARGET4 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1407

b:72.4
occ:1.00
 O C:HOH206 2.8 77.0 1.0
OD1 B:ASN588 2.8 43.7 1.0
O B:ARG586 2.9 45.1 1.0
O B:GLU584 3.0 81.6 1.0
O B:HOH1624 3.2 86.8 1.0
CG B:ASN588 3.5 49.2 1.0
O B:HOH1584 3.6 64.6 1.0
O B:HOH1539 3.6 59.9 1.0
ND2 B:ASN588 3.7 58.6 1.0
O C:HOH204 3.9 80.2 1.0
C B:ARG586 4.1 46.4 1.0
C B:GLU584 4.2 79.0 1.0
N B:ARG586 4.4 58.0 1.0
N B:GLU584 4.5 66.9 1.0
N B:ASN588 4.6 41.8 1.0
CA B:GLU584 4.8 78.8 1.0
CB B:ASN588 4.8 47.8 1.0
C B:PHE587 4.9 46.4 1.0
CA B:ARG586 4.9 52.2 1.0
CB B:GLU584 4.9 92.6 1.0

Reference:

M.Pacesa, C.H.Lin, A.Clery, A.Saha, P.R.Arantes, K.Bargsten, M.J.Irby, F.H.Allain, G.Palermo, P.Cameron, P.D.Donohoue, M.Jinek. Structural Basis For CAS9 Off-Target Activity. Cell V. 185 4067 2022.
ISSN: ISSN 1097-4172
PubMed: 36306733
DOI: 10.1016/J.CELL.2022.09.026
Page generated: Mon Aug 12 20:35:30 2024

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