Atomistry » Potassium » PDB 7yze-7zrh » 7zo1
Atomistry »
  Potassium »
    PDB 7yze-7zrh »
      7zo1 »

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

Go back to Potassium Binding Sites List in 7zo1
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

Go back to Potassium Binding Sites List in 7zo1
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

Go back to Potassium Binding Sites List in 7zo1
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

Go back to Potassium Binding Sites List in 7zo1
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

Go back to Potassium Binding Sites List in 7zo1
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

Go back to Potassium Binding Sites List in 7zo1
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

Go back to Potassium Binding Sites List in 7zo1
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy