Potassium in PDB 7zo1: SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate

Protein crystallography data

The structure of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate, PDB code: 7zo1 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) 46.51 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.41, 69.2, 188.46, 90, 111.77, 90
R / Rfree (%) 21.2 / 25

Other elements in 7zo1:

The structure of SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate (pdb code 7zo1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate, PDB code: 7zo1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 7zo1

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Potassium binding site 1 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:75.2
occ:1.00
 OP2 A:A65 2.7 62.7 1.0
O4 A:U66 2.7 55.1 1.0
OG1 B:THR1102 2.8 54.8 1.0
O A:HOH238 2.9 48.3 1.0
O B:HOH1592 3.0 51.8 1.0
O A:HOH252 3.1 50.1 1.0
O A:HOH259 3.1 68.2 1.0
C4 A:U66 3.6 62.5 1.0
CG2 B:THR1102 3.8 45.8 1.0
CB B:THR1102 3.9 58.2 1.0
C5 A:U66 4.0 68.0 1.0
P A:A65 4.0 58.8 1.0
O B:HOH1537 4.1 56.8 1.0
OP1 A:U64 4.3 50.5 1.0
O A:HOH226 4.3 61.0 1.0
N4 A:C67 4.5 45.6 1.0
OP1 A:A65 4.5 46.6 1.0
O A:HOH203 4.6 50.1 1.0
O5' A:A65 4.7 52.0 1.0
N7 A:A65 4.7 61.9 1.0
O B:HOH1634 4.7 55.3 1.0
O A:HOH224 4.8 62.0 1.0
OP2 A:U64 4.9 38.7 1.0
N3 A:U66 4.9 61.9 1.0
O B:VAL1100 4.9 46.1 1.0
P A:U64 5.0 68.8 1.0

Potassium binding site 2 out of 8 in 7zo1

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Potassium binding site 2 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:86.5
occ:1.00
 O B:HOH1618 2.7 59.7 1.0
O B:GLN1350 2.7 55.5 1.0
O B:HOH1579 2.8 40.4 1.0
O4' A:A68 2.9 56.7 1.0
O A:HOH217 3.1 50.5 1.0
O A:HOH295 3.3 58.4 1.0
C1' A:A68 3.4 56.7 1.0
C B:GLN1350 3.9 51.8 1.0
N9 A:A68 4.0 65.8 1.0
O B:SER1351 4.0 59.5 1.0
C4' A:A68 4.1 58.4 1.0
OG1 B:THR1098 4.1 65.5 1.0
C8 A:A68 4.2 58.4 1.0
O5' A:A68 4.2 56.8 1.0
C B:SER1351 4.3 53.5 1.0
O B:HOH1600 4.4 53.1 1.0
OP1 A:A68 4.6 70.9 1.0
CA B:SER1351 4.7 59.0 1.0
OP2 A:A68 4.7 69.0 1.0
C5' A:A68 4.7 55.2 1.0
P A:A68 4.7 62.2 1.0
CA B:GLN1350 4.7 54.7 1.0
N B:SER1351 4.7 59.8 1.0
CB B:GLN1350 4.7 52.5 1.0
N B:ILE1352 4.8 54.3 1.0
C2' A:A68 4.8 66.0 1.0
N B:THR1098 4.8 45.0 1.0
CG1 B:VAL1095 4.8 60.9 1.0
N B:GLN1350 4.8 54.0 1.0
O2' A:A68 4.9 55.2 1.0
CA B:ILE1352 4.9 52.2 1.0

Potassium binding site 3 out of 8 in 7zo1

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Potassium binding site 3 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:73.2
occ:1.00
 O A:HOH230 2.9 61.4 1.0
O A:HOH228 2.9 53.8 1.0
OP2 A:G21 3.1 69.3 1.0
O A:HOH242 3.2 65.7 1.0
O B:HOH1658 3.3 73.2 1.0
O A:HOH280 3.7 54.2 1.0
O A:HOH201 3.7 71.2 1.0
O A:HOH231 4.0 75.4 1.0
P A:G21 4.0 58.3 1.0
O B:HOH1593 4.1 68.9 1.0
OP1 A:G21 4.1 60.8 1.0
OP2 A:U45 4.2 59.3 1.0
MG A:MG102 4.5 68.5 1.0
CB B:ARG403 4.5 65.3 1.0
O A:HOH288 4.5 53.2 1.0
O5' A:G21 4.9 56.0 1.0
CG B:ARG403 5.0 61.0 1.0

Potassium binding site 4 out of 8 in 7zo1

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Potassium binding site 4 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1401

b:96.9
occ:1.00
 O B:TYR656 2.8 77.4 1.0
O B:PHE626 2.8 90.0 1.0
O B:LEU623 2.8 82.3 1.0
O B:THR624 3.5 63.9 1.0
C B:PHE626 3.5 86.1 1.0
C B:TYR656 3.9 76.6 1.0
C B:THR624 3.9 67.6 1.0
C B:LEU623 3.9 74.0 1.0
N B:GLU627 4.0 78.8 1.0
OP1 C:DC8 4.0 91.4 1.0
CA B:GLU627 4.0 91.8 1.0
CA B:THR624 4.1 70.8 1.0
N B:TYR656 4.1 83.1 1.0
CB B:ARG655 4.1 114.2 1.0
CG2 B:THR657 4.1 69.6 1.0
CB B:GLU627 4.3 72.5 1.0
N B:PHE626 4.3 81.9 1.0
N B:THR624 4.5 72.5 1.0
CA B:PHE626 4.5 73.0 1.0
CD B:ARG655 4.6 122.3 1.0
CG B:ARG655 4.6 117.0 1.0
CA B:TYR656 4.7 82.8 1.0
N B:THR657 4.8 73.3 1.0
N B:LEU625 4.8 70.2 1.0
C B:LEU625 4.8 75.3 1.0
CA B:ARG655 4.9 114.0 1.0
C B:ARG655 4.9 103.7 1.0
CG B:GLU627 5.0 90.5 1.0

Potassium binding site 5 out of 8 in 7zo1

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Potassium binding site 5 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1402

b:83.3
occ:1.00
 O B:HOH1582 2.7 69.7 1.0
O B:ALA367 2.7 73.9 1.0
O B:GLY365 2.8 79.1 1.0
O B:GLY361 2.9 78.0 1.0
O B:TYR362 3.0 73.9 1.0
N B:ALA367 3.2 84.4 1.0
C B:ALA367 3.6 82.1 1.0
C B:TYR362 3.6 72.8 1.0
C B:GLY365 3.6 67.9 1.0
C B:GLY366 3.7 88.7 1.0
CA B:GLY366 3.8 82.2 1.0
CA B:TYR362 3.9 73.8 1.0
CA B:ALA367 4.0 74.6 1.0
C B:GLY361 4.0 77.8 1.0
N B:GLY366 4.0 69.1 1.0
NZ B:LYS401 4.1 78.2 1.0
O B:HOH1522 4.4 48.5 1.0
N B:TYR362 4.5 81.8 1.0
N B:ILE363 4.5 73.1 1.0
OP1 A:U22 4.5 58.0 1.0
N B:SER368 4.6 82.9 1.0
O B:GLY366 4.6 92.2 1.0
CB B:ALA367 4.7 77.4 1.0
N B:GLY365 4.7 75.1 1.0
O B:ILE363 4.7 78.6 1.0
CA B:GLY365 4.7 70.9 1.0
C B:ILE363 4.7 72.8 1.0
O B:HOH1593 4.8 68.9 1.0
CA B:ILE363 5.0 70.4 1.0

Potassium binding site 6 out of 8 in 7zo1

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Potassium binding site 6 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1403

b:133.5
occ:1.00
 O B:ILE226 2.7 126.7 1.0
O B:LEU229 2.7 130.6 1.0
O B:GLU232 3.0 134.6 1.0
C B:ILE226 3.6 123.2 1.0
C B:LEU229 3.7 127.0 1.0
CG2 B:ILE226 3.7 98.1 1.0
CA B:ALA227 3.9 133.1 1.0
N B:ALA227 4.1 123.1 1.0
C B:GLU232 4.3 137.7 1.0
O B:ALA227 4.3 122.3 1.0
CA B:PRO230 4.3 128.6 1.0
C B:ALA227 4.3 129.9 1.0
N B:PRO230 4.3 123.9 1.0
N B:LEU229 4.5 118.0 1.0
CA B:LEU229 4.6 121.2 1.0
CA B:ILE226 4.7 118.4 1.0
N B:GLU232 4.7 145.1 1.0
CB B:ILE226 4.8 106.7 1.0
N B:GLY231 4.9 153.4 1.0
C B:PRO230 4.9 125.3 1.0

Potassium binding site 7 out of 8 in 7zo1

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Potassium binding site 7 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1404

b:102.0
occ:1.00
 O B:LYS111 2.7 78.6 1.0
O B:HOH1653 3.0 87.7 1.0
O B:GLU108 3.0 66.7 1.0
O B:HOH1666 3.2 84.6 1.0
C B:LYS111 3.8 56.9 1.0
O B:GLU109 4.1 72.3 1.0
C B:GLU108 4.2 64.0 1.0
C B:GLU109 4.5 68.4 1.0
CA B:LYS111 4.6 67.7 1.0
N B:LYS111 4.6 70.1 1.0
CB B:LYS111 4.6 49.8 1.0
CA B:GLU109 4.7 67.9 1.0
N B:LYS112 4.8 61.2 1.0
CG B:GLU108 4.9 81.5 1.0
O B:HIS113 4.9 62.2 1.0
N B:GLU109 4.9 62.2 1.0
CA B:LYS112 5.0 68.8 1.0

Potassium binding site 8 out of 8 in 7zo1

Go back to Potassium Binding Sites List in 7zo1
Potassium binding site 8 out of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 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 CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1405

b:119.4
occ:1.00
 OD1 B:ASN588 2.9 125.5 1.0
O B:GLU584 2.9 142.6 1.0
O B:ARG586 3.2 118.2 1.0
CG B:ASN588 3.8 103.4 1.0
C B:GLU584 4.0 133.1 1.0
ND2 B:ASN588 4.1 96.7 1.0
N B:GLU584 4.2 128.8 1.0
CB B:GLU584 4.3 125.7 1.0
CA B:GLU584 4.4 125.5 1.0
C B:ARG586 4.4 113.7 1.0
N B:ARG586 4.5 131.3 1.0
CG B:ARG586 4.7 134.2 1.0
O4' C:DT17 4.9 112.3 1.0
N B:ASN588 5.0 100.5 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 21:50:32 2024

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