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Potassium in PDB 7qr8: SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate

Protein crystallography data

The structure of SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate, PDB code: 7qr8 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) 48.12 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.278, 68.029, 186.741, 90, 110.74, 90
R / Rfree (%) 22.2 / 25

Other elements in 7qr8:

The structure of SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate (pdb code 7qr8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the SPCAS9 Bound to Ptprc Off-TARGET1 Dna Substrate, PDB code: 7qr8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 7qr8

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Potassium binding site 1 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:123.6
occ:1.00
 O4 A:U8 3.0 95.0 1.0
O6 C:DG11 3.0 80.4 1.0
O C:HOH207 3.0 72.9 1.0
O4 C:DT12 3.5 84.1 1.0
C6 C:DG11 3.9 76.5 1.0
N7 C:DG11 4.1 69.7 1.0
C4 A:U8 4.1 98.0 1.0
C5 C:DG11 4.4 72.1 1.0
N4 A:C9 4.5 89.5 1.0
C4 C:DT12 4.6 85.4 1.0
N3 A:U8 4.6 99.7 1.0
O4 C:DT10 4.8 73.5 1.0

Potassium binding site 2 out of 10 in 7qr8

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Potassium binding site 2 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:61.4
occ:1.00
 OP2 A:A65 2.8 57.0 1.0
O4 A:U66 2.8 61.1 1.0
O B:HOH1578 2.8 54.2 1.0
O A:HOH219 2.8 74.6 1.0
O A:HOH210 2.8 44.2 1.0
OG1 B:THR1102 2.9 58.7 1.0
CG2 B:THR1102 3.5 39.6 1.0
C4 A:U66 3.6 55.4 1.0
C5 A:U66 3.8 55.2 1.0
CB B:THR1102 3.8 48.3 1.0
O B:HOH1583 4.1 56.3 1.0
P A:A65 4.2 54.7 1.0
OP1 A:U64 4.3 46.1 1.0
N4 A:C67 4.6 48.7 1.0
K B:K1401 4.6 103.8 1.0
N7 A:A65 4.7 56.1 1.0
OP2 A:U64 4.7 44.2 1.0
O5' A:A65 4.7 45.6 1.0
OP1 A:A65 4.8 49.8 1.0
P A:U64 4.9 47.4 1.0
O B:VAL1100 4.9 44.3 1.0
O B:HOH1541 4.9 62.1 1.0
N3 A:U66 4.9 57.5 1.0
CA B:THR1102 5.0 49.5 1.0

Potassium binding site 3 out of 10 in 7qr8

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Potassium binding site 3 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:67.4
occ:1.00
 O B:GLN1350 2.7 59.4 1.0
O B:HOH1568 2.8 62.9 1.0
O4' A:A68 2.9 58.9 1.0
C1' A:A68 3.5 60.7 1.0
C B:GLN1350 3.8 53.0 1.0
O B:SER1351 4.0 54.9 1.0
N9 A:A68 4.0 52.3 1.0
C B:SER1351 4.0 57.5 1.0
C4' A:A68 4.1 54.3 1.0
O5' A:A68 4.1 46.1 1.0
C8 A:A68 4.1 59.9 1.0
OP1 A:A68 4.2 58.9 1.0
CA B:SER1351 4.4 50.1 1.0
N B:ILE1352 4.5 52.4 1.0
P A:A68 4.5 46.9 1.0
OG1 B:THR1098 4.5 60.0 1.0
OP2 A:A68 4.6 61.5 1.0
N B:SER1351 4.6 53.1 1.0
C5' A:A68 4.6 51.6 1.0
CG1 B:VAL1095 4.7 46.1 1.0
CA B:ILE1352 4.7 50.4 1.0
C2' A:A68 4.8 56.5 1.0
CA B:GLN1350 4.8 49.5 1.0
N B:THR1098 5.0 47.6 1.0
CB B:GLN1350 5.0 52.3 1.0
N B:GLN1350 5.0 44.7 1.0

Potassium binding site 4 out of 10 in 7qr8

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Potassium binding site 4 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1401

b:103.8
occ:1.00
 O B:HOH1541 2.8 62.1 1.0
OE2 B:GLU57 3.2 66.4 1.0
OE1 B:GLU57 3.4 59.0 1.0
O B:HOH1578 3.4 54.2 1.0
CD B:GLU57 3.5 57.0 1.0
OP1 A:U64 4.0 46.1 1.0
OG1 B:THR1102 4.1 58.7 1.0
O B:THR1102 4.2 55.0 1.0
O B:HOH1583 4.3 56.3 1.0
CG B:GLU57 4.5 51.0 1.0
K A:K104 4.6 61.4 1.0
O B:HOH1551 4.6 46.4 1.0
O B:HOH1522 4.6 74.6 1.0
OP2 A:A65 4.7 57.0 1.0
C B:THR1102 4.9 50.4 1.0
N B:THR1102 5.0 49.3 1.0

Potassium binding site 5 out of 10 in 7qr8

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Potassium binding site 5 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1402

b:71.0
occ:1.00
 O B:TYR656 2.8 70.5 1.0
O B:PHE626 2.8 69.0 1.0
O B:THR624 3.0 59.4 1.0
O B:LEU623 3.1 68.4 1.0
O B:HOH1542 3.2 60.8 1.0
C B:PHE626 3.5 62.2 1.0
O C:HOH204 3.5 72.7 1.0
C B:THR624 3.6 61.0 1.0
CA B:THR624 3.9 61.3 1.0
C B:TYR656 4.0 68.4 1.0
CG B:ARG655 4.0 87.5 1.0
N B:PHE626 4.0 66.3 1.0
C B:LEU623 4.1 63.2 1.0
N B:GLU627 4.2 59.8 1.0
CA B:PHE626 4.3 60.5 1.0
CG2 B:THR657 4.3 66.2 1.0
N B:TYR656 4.4 76.2 1.0
C B:LEU625 4.4 65.0 1.0
N B:THR624 4.5 64.0 1.0
CA B:GLU627 4.5 66.7 1.0
N B:LEU625 4.5 58.5 1.0
CB B:GLU627 4.7 61.9 1.0
CD B:ARG655 4.7 81.9 1.0
OE1 B:GLU627 4.8 76.0 1.0
O B:LEU625 4.8 66.3 1.0
CA B:TYR656 4.8 66.6 1.0
N B:THR657 4.9 68.6 1.0
CA B:THR657 5.0 68.7 1.0

Potassium binding site 6 out of 10 in 7qr8

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Potassium binding site 6 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1403

b:91.7
occ:1.00
 O B:TYR362 3.0 62.7 1.0
O B:ALA367 3.0 64.9 1.0
O B:GLY365 3.1 61.0 1.0
O B:GLY361 3.3 65.5 1.0
C B:TYR362 3.6 65.5 1.0
N B:ALA367 3.8 73.2 1.0
C B:GLY365 3.8 62.0 1.0
NZ B:LYS401 3.8 58.9 1.0
O B:ILE363 3.9 66.5 1.0
CA B:GLY366 4.0 61.5 1.0
C B:GLY366 4.0 70.0 1.0
C B:ALA367 4.0 64.0 1.0
O B:HOH1506 4.2 58.3 1.0
N B:GLY366 4.2 58.5 1.0
CA B:TYR362 4.2 70.7 1.0
OP1 A:U22 4.3 52.5 1.0
C B:ILE363 4.3 66.1 1.0
N B:ILE363 4.3 68.5 1.0
C B:GLY361 4.4 67.6 1.0
CA B:ALA367 4.5 66.4 1.0
CA B:ILE363 4.6 67.4 1.0
N B:GLY365 4.7 69.5 1.0
O B:GLY366 4.7 67.3 1.0
N B:TYR362 4.8 74.1 1.0
CA B:GLY365 4.9 65.1 1.0
N B:ASP364 5.0 65.0 1.0
C B:ASP364 5.0 68.6 1.0

Potassium binding site 7 out of 10 in 7qr8

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Potassium binding site 7 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1404

b:102.0
occ:1.00
 O B:GLU232 2.9 100.2 1.0
O B:LEU229 3.0 96.4 1.0
O B:ILE226 3.2 91.9 1.0
C B:LEU229 3.9 95.8 1.0
C B:GLU232 4.0 100.2 1.0
CA B:PRO230 4.1 97.7 1.0
C B:ILE226 4.1 93.1 1.0
N B:GLU232 4.2 102.0 1.0
CA B:ALA227 4.3 96.3 1.0
CG2 B:ILE226 4.3 94.2 1.0
N B:GLY231 4.3 103.3 1.0
N B:PRO230 4.4 91.3 1.0
C B:PRO230 4.5 101.6 1.0
N B:ALA227 4.6 92.5 1.0
C B:ALA227 4.7 98.6 1.0
CA B:GLU232 4.7 97.1 1.0
O B:ALA227 4.8 102.6 1.0
N B:LEU229 4.8 90.8 1.0
CA B:LEU229 4.9 95.5 1.0

Potassium binding site 8 out of 10 in 7qr8

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Potassium binding site 8 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1405

b:113.2
occ:1.00
 O B:HOH1598 2.8 76.0 1.0
O B:GLU108 2.9 64.7 1.0
O B:HOH1552 2.9 64.9 1.0
O B:LYS111 3.0 72.7 1.0
C B:GLU108 4.0 64.8 1.0
C B:LYS111 4.1 61.5 1.0
CG B:GLU108 4.2 69.4 1.0
O B:HIS113 4.4 61.5 1.0
CB B:LYS111 4.6 63.4 1.0
O B:GLU109 4.6 73.1 1.0
CA B:LYS111 4.7 58.0 1.0
N B:LYS111 4.7 68.9 1.0
CA B:GLU108 4.8 62.2 1.0
C B:GLU109 4.9 67.4 1.0
N B:GLU109 4.9 67.9 1.0
CA B:GLU109 4.9 64.8 1.0
OE2 B:GLU108 5.0 79.5 1.0

Potassium binding site 9 out of 10 in 7qr8

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Potassium binding site 9 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1406

b:119.5
occ:1.00
 OD1 B:ASN588 2.8 79.1 1.0
O B:GLU584 3.3 92.1 1.0
O B:ARG586 3.4 88.9 1.0
CG B:ASN588 3.8 79.8 1.0
ND2 B:ASN588 4.1 81.7 1.0
C B:GLU584 4.4 93.5 1.0
C B:ARG586 4.5 85.3 1.0
N B:ARG586 4.6 87.8 1.0
N B:GLU584 4.8 95.5 1.0
CG B:ARG586 4.9 85.5 1.0
N B:ASN588 5.0 75.5 1.0
CB B:ASP585 5.0 95.8 1.0

Potassium binding site 10 out of 10 in 7qr8

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Potassium binding site 10 out of 10 in the SPCAS9 Bound to Ptprc Off-TARGET1 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 Ptprc Off-TARGET1 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:96.4
occ:1.00
 O C:HOH211 2.2 57.5 1.0
O6 C:DG3 3.0 54.4 1.0
O C:HOH205 3.0 74.8 1.0
C6 C:DG3 4.0 50.9 1.0
O6 C:DG2 4.0 56.1 1.0
N7 C:DG3 4.2 55.3 1.0
N4 A:C18 4.3 48.7 1.0
O6 C:DG4 4.5 49.5 1.0
C5 C:DG3 4.5 52.1 1.0
C6 C:DG2 4.5 54.8 1.0
N7 C:DG2 4.7 53.3 1.0
C5 C:DG2 4.8 55.3 1.0
O C:HOH201 5.0 76.8 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 20:45:53 2024

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