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Potassium in PDB 7qqx: SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate

Protein crystallography data

The structure of SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate, PDB code: 7qqx 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) 48.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.534, 67.378, 188.387, 90, 110.9, 90
R / Rfree (%) 18.2 / 21.6

Other elements in 7qqx:

The structure of SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate (pdb code 7qqx). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the SPCAS9 Bound to Fancf Off-TARGET5 Dna Substrate, PDB code: 7qqx:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 7qqx

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Potassium binding site 1 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:53.8
occ:1.00
 OP2 A:A65 2.7 46.7 1.0
O4 A:U66 2.9 55.5 1.0
OG1 B:THR1102 2.9 49.9 1.0
O B:HOH1677 3.0 49.2 1.0
O A:HOH310 3.0 46.7 1.0
O A:HOH222 3.0 44.9 1.0
O A:HOH306 3.1 61.4 1.0
C4 A:U66 3.6 52.7 1.0
C5 A:U66 3.8 47.1 1.0
CG2 B:THR1102 3.9 45.1 1.0
CB B:THR1102 4.0 48.0 1.0
P A:A65 4.1 41.1 1.0
O B:HOH1720 4.2 56.0 1.0
OP1 A:U64 4.3 46.0 1.0
N7 A:A65 4.5 47.1 1.0
N4 A:C67 4.5 40.1 1.0
O5' A:A65 4.6 43.0 1.0
OP1 A:A65 4.7 41.3 1.0
O A:HOH216 4.7 53.9 1.0
O A:HOH226 4.8 48.6 1.0
C8 A:A65 4.8 48.8 1.0
O B:VAL1100 4.9 43.2 1.0
OP2 A:U64 4.9 42.3 1.0
N3 A:U66 5.0 51.8 1.0
O B:HOH1714 5.0 58.0 1.0

Potassium binding site 2 out of 9 in 7qqx

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Potassium binding site 2 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:62.5
occ:1.00
 O B:GLN1350 2.7 41.0 1.0
O A:HOH264 2.8 51.8 1.0
O B:HOH1804 2.8 104.4 1.0
O A:HOH253 2.8 41.4 1.0
O B:HOH1602 2.8 49.1 1.0
O4' A:A68 3.0 53.4 1.0
O B:HOH1737 3.4 53.2 1.0
C1' A:A68 3.5 55.9 1.0
C B:GLN1350 3.8 42.9 1.0
C4' A:A68 4.1 50.1 1.0
O B:SER1351 4.2 47.4 1.0
N9 A:A68 4.3 53.8 1.0
O A:HOH249 4.3 46.1 1.0
OG1 B:THR1098 4.3 39.6 1.0
O5' A:A68 4.4 45.0 1.0
C B:SER1351 4.4 43.6 1.0
OP1 A:A68 4.5 48.0 1.0
C8 A:A68 4.6 54.1 1.0
CB B:GLN1350 4.6 43.9 1.0
CA B:GLN1350 4.6 46.8 1.0
OP2 A:A68 4.7 53.1 1.0
N B:THR1098 4.7 40.5 1.0
P A:A68 4.7 50.3 1.0
N B:GLN1350 4.7 50.2 1.0
CG1 B:VAL1095 4.8 37.2 1.0
N B:SER1351 4.8 41.7 1.0
C2' A:A68 4.8 60.4 1.0
C5' A:A68 4.8 44.6 1.0
CA B:SER1351 4.8 41.8 1.0
CG2 B:THR1098 4.9 36.2 1.0
O2' A:A68 4.9 63.4 1.0
N B:ILE1352 4.9 40.4 1.0

Potassium binding site 3 out of 9 in 7qqx

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Potassium binding site 3 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1401

b:115.4
occ:1.00
 O B:HOH1769 2.7 70.1 1.0
O B:HOH1714 2.8 58.0 1.0
O A:HOH306 2.8 61.4 1.0
OE2 B:GLU57 2.9 89.8 1.0
O B:HOH1752 3.0 76.0 1.0
O B:HOH1594 3.3 60.0 1.0
CD B:GLU57 3.6 83.0 1.0
OE1 B:GLU57 3.9 89.4 1.0
O B:HOH1768 4.0 66.6 1.0
O B:HOH1720 4.0 56.0 1.0
O B:HOH1677 4.2 49.2 1.0
O A:HOH213 4.3 53.7 1.0
CG B:GLU57 4.6 67.2 1.0
O B:HOH1621 4.8 72.0 1.0
NE2 B:GLN1101 4.8 48.8 1.0
O B:THR1102 4.9 41.0 1.0
O B:HOH1551 4.9 51.4 1.0

Potassium binding site 4 out of 9 in 7qqx

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Potassium binding site 4 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1402

b:56.0
occ:1.00
 O C:HOH124 2.7 85.5 1.0
O B:TYR656 2.7 48.0 1.0
O B:THR624 2.8 42.0 1.0
O B:LEU623 2.9 45.1 1.0
O C:HOH128 2.9 94.0 1.0
O B:PHE626 2.9 62.9 1.0
C B:THR624 3.4 45.8 1.0
C B:PHE626 3.6 55.7 1.0
CA B:THR624 3.7 47.4 1.0
C B:LEU623 3.9 44.0 1.0
C B:TYR656 3.9 47.3 1.0
N B:PHE626 4.2 55.0 1.0
N B:GLU627 4.2 61.0 1.0
N B:THR624 4.2 46.3 1.0
CA B:GLU627 4.3 64.0 1.0
N B:TYR656 4.3 55.1 1.0
N B:LEU625 4.4 47.0 1.0
CB B:ARG655 4.5 74.0 1.0
CA B:PHE626 4.5 52.0 1.0
C B:LEU625 4.5 53.1 1.0
CG2 B:THR657 4.6 59.9 1.0
CB B:GLU627 4.6 70.6 1.0
CG B:ARG655 4.6 80.8 1.0
CA B:TYR656 4.8 48.0 1.0
N B:THR657 4.8 49.4 1.0
CD B:ARG655 4.9 87.8 1.0
CA B:THR657 4.9 51.9 1.0
CG B:GLU627 5.0 77.2 1.0
O B:LEU625 5.0 56.4 1.0

Potassium binding site 5 out of 9 in 7qqx

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Potassium binding site 5 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1403

b:77.5
occ:1.00
 O B:GLY365 2.8 62.3 1.0
O B:TYR362 2.8 60.1 1.0
O B:ALA367 2.8 56.9 1.0
O B:HOH1649 2.8 96.7 1.0
O A:HOH294 3.0 100.2 1.0
O B:GLY361 3.2 67.3 1.0
C B:TYR362 3.5 62.6 1.0
N B:ALA367 3.5 57.1 1.0
O B:HOH1670 3.5 71.8 1.0
C B:GLY365 3.6 62.1 1.0
C B:ALA367 3.8 54.8 1.0
C B:GLY366 3.9 60.9 1.0
CA B:TYR362 4.0 66.0 1.0
NZ B:LYS401 4.0 51.4 1.0
CA B:GLY366 4.0 61.5 1.0
N B:GLY366 4.1 61.8 1.0
CA B:ALA367 4.2 54.0 1.0
C B:GLY361 4.2 67.9 1.0
N B:GLY365 4.4 69.0 1.0
N B:ILE363 4.4 63.4 1.0
O B:HOH1658 4.5 54.1 1.0
C B:ILE363 4.5 60.8 1.0
O B:ILE363 4.5 63.3 1.0
CA B:GLY365 4.6 64.0 1.0
OP1 A:U22 4.6 53.9 1.0
N B:TYR362 4.6 68.4 1.0
O B:GLY366 4.6 60.3 1.0
CA B:ILE363 4.8 62.5 1.0
N B:ASP364 4.8 60.9 1.0
C B:ASP364 4.8 69.4 1.0
CB B:ALA367 4.9 54.6 1.0
N B:SER368 4.9 55.2 1.0

Potassium binding site 6 out of 9 in 7qqx

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Potassium binding site 6 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1404

b:83.3
occ:1.00
 O B:PHE643 2.6 82.8 1.0
O B:ALA640 3.0 64.0 1.0
O B:HOH1738 3.4 56.4 1.0
C B:PHE643 3.8 77.4 1.0
C B:ALA640 4.1 61.7 1.0
CA B:HIS641 4.1 60.4 1.0
O B:HIS641 4.2 64.2 1.0
C B:HIS641 4.2 61.9 1.0
OD1 B:ASP645 4.2 107.5 1.0
CA B:ASP644 4.5 86.1 1.0
N B:HIS641 4.5 62.2 1.0
N B:PHE643 4.6 62.7 1.0
N B:ASP644 4.6 82.1 1.0
CA B:PHE643 4.9 68.7 1.0
C B:ASP644 4.9 86.7 1.0
N B:LEU642 5.0 59.7 1.0
N B:ASP645 5.0 94.3 1.0

Potassium binding site 7 out of 9 in 7qqx

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Potassium binding site 7 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1405

b:87.3
occ:1.00
 O B:HOH1802 2.7 74.2 1.0
O B:LEU229 2.8 75.6 1.0
O B:GLU232 2.8 71.2 1.0
O B:ILE226 2.9 61.4 1.0
O B:HOH1790 3.0 92.0 1.0
C B:LEU229 3.7 70.2 1.0
CA B:PRO230 3.9 71.2 1.0
C B:ILE226 3.9 66.0 1.0
C B:GLU232 4.0 69.3 1.0
N B:GLU232 4.0 78.8 1.0
CG2 B:ILE226 4.1 61.2 1.0
N B:GLY231 4.2 73.7 1.0
N B:PRO230 4.2 71.4 1.0
CA B:ALA227 4.3 71.5 1.0
C B:PRO230 4.4 72.0 1.0
O B:ALA227 4.5 76.7 1.0
N B:ALA227 4.5 70.5 1.0
CA B:GLU232 4.5 72.5 1.0
C B:ALA227 4.6 73.0 1.0
N B:LEU229 4.7 70.9 1.0
CA B:LEU229 4.8 65.4 1.0
CB B:GLU232 4.9 70.8 1.0
CA B:ILE226 5.0 65.4 1.0

Potassium binding site 8 out of 9 in 7qqx

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Potassium binding site 8 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1406

b:102.0
occ:1.00
 O B:HOH1536 2.7 68.2 1.0
O B:HOH1778 2.9 73.8 1.0
O B:HOH1795 2.9 90.2 1.0
O B:GLU108 2.9 63.4 1.0
O B:LYS111 3.0 64.9 1.0
O B:HOH1686 3.4 86.3 1.0
O B:HOH1782 3.4 71.2 1.0
C B:LYS111 3.9 59.9 1.0
C B:GLU108 4.1 61.5 1.0
CB B:LYS111 4.3 55.3 1.0
O B:HIS113 4.3 62.8 1.0
CG B:GLU108 4.4 72.0 1.0
CA B:LYS111 4.5 55.8 1.0
O B:GLU109 4.5 67.7 1.0
N B:LYS111 4.5 55.6 1.0
N B:LYS112 4.8 58.6 1.0
C B:GLU109 4.9 66.2 1.0
CA B:GLU108 4.9 59.7 1.0

Potassium binding site 9 out of 9 in 7qqx

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Potassium binding site 9 out of 9 in the SPCAS9 Bound to Fancf Off-TARGET5 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 Fancf Off-TARGET5 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1407

b:56.5
occ:1.00
 O C:HOH129 2.7 50.3 1.0
O B:ARG586 2.8 52.1 1.0
O B:GLU584 2.8 51.5 1.0
OD1 B:ASN588 2.9 49.8 1.0
O B:HOH1713 3.1 49.1 1.0
O B:HOH1805 3.3 72.2 1.0
CG B:ASN588 3.6 48.9 1.0
ND2 B:ASN588 3.9 49.9 1.0
C B:GLU584 4.0 57.3 1.0
C B:ARG586 4.0 51.1 1.0
O C:HOH111 4.1 57.8 1.0
O B:HOH1710 4.1 62.5 1.0
N B:ARG586 4.2 52.3 1.0
N B:GLU584 4.4 52.0 1.0
CA B:GLU584 4.6 61.1 1.0
N B:ASN588 4.6 39.4 1.0
CA B:ARG586 4.7 53.4 1.0
CB B:GLU584 4.8 74.5 1.0
CG B:ARG586 4.8 71.7 1.0
C B:PHE587 4.8 42.6 1.0
O A:HOH328 4.9 73.6 1.0
CB B:ASN588 4.9 44.9 1.0
CA B:ASN588 5.0 43.6 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 20:41:41 2024

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