Potassium in PDB 7ox8: Target-Bound SPCAS9 Complex with Trac Full Rna Guide

The structure of Target-Bound SPCAS9 Complex with Trac Full Rna Guide, PDB code: 7ox8 was solved by P.Donohoue, M.Pacesa, E.Lau, B.Vidal, M.J.Irby, D.B.Nyer, T.Rotstein, L.Banh, M.T.Toh, J.Gibson, B.Kohrs, K.Baek, A.L.G.Owen, E.M.Slorach, M.Vanoverbeek, C.K.Fuller, A.P.May, M.Jinek, P.Cameron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.177, 67.549, 187.854, 90, 111.23, 90
R / Rfree (%)	20.9 / 24.8

The structure of Target-Bound SPCAS9 Complex with Trac Full Rna Guide also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Potassium atom in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide (pdb code 7ox8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide, PDB code: 7ox8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:73.2 occ:1.00 OG1 B:THR1102 2.9 67.7 1.0 OP2 A:A65 2.9 61.5 1.0 O B:HOH1557 3.0 65.9 1.0 O4 A:U66 3.1 66.1 1.0 O A:HOH221 3.2 45.8 1.0 CG2 B:THR1102 3.7 40.5 1.0 CB B:THR1102 3.9 55.1 1.0 C4 A:U66 3.9 65.9 1.0 C5 A:U66 4.1 63.9 1.0 P A:A65 4.3 54.8 1.0 OP1 A:U64 4.4 52.8 1.0 N4 A:C67 4.5 57.0 1.0 O B:VAL1100 4.6 62.7 1.0 OP1 A:A65 4.8 49.1 1.0 O B:HOH1539 4.9 57.9 1.0 N B:THR1102 4.9 46.3 1.0 O5' A:A65 5.0 56.8 1.0 CA B:THR1102 5.0 50.1 1.0

Potassium binding site 2 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:116.0 occ:1.00 O A:HOH249 2.7 72.0 1.0 O A:HOH233 2.8 72.8 1.0 O A:HOH227 3.0 72.4 1.0 O A:HOH234 3.2 89.1 1.0 OP2 A:G21 3.2 62.6 1.0 OP1 A:G21 3.8 63.2 1.0 P A:G21 3.9 61.9 1.0 CB B:ARG403 4.1 50.7 1.0 OP2 A:U45 4.2 69.6 1.0 O A:HOH204 4.6 88.6 1.0 MG A:MG101 4.7 77.8 1.0 CG B:ARG403 4.7 48.9 1.0 O B:ARG403 4.7 58.2 1.0 OP2 A:A46 4.9 56.9 1.0 O A:HOH219 4.9 72.7 1.0 O5' A:G21 4.9 68.5 1.0

Potassium binding site 3 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:121.8 occ:1.00 O B:HOH1510 2.9 88.1 1.0 O A:HOH214 2.9 55.8 1.0 O B:GLN1350 3.0 61.3 1.0 O4' A:A68 3.2 74.2 1.0 O A:HOH237 3.2 85.7 1.0 C1' A:A68 3.7 71.2 1.0 O B:HOH1561 3.7 55.5 1.0 C B:GLN1350 4.1 54.1 1.0 C4' A:A68 4.2 65.2 1.0 OG1 B:THR1098 4.3 51.4 1.0 O B:SER1351 4.4 53.7 1.0 O5' A:A68 4.4 53.9 1.0 N9 A:A68 4.4 71.3 1.0 N B:THR1098 4.5 47.3 1.0 CG2 B:THR1098 4.5 32.8 1.0 C B:SER1351 4.6 51.2 1.0 CG1 B:VAL1095 4.7 40.9 1.0 CB B:GLN1350 4.7 57.9 1.0 C8 A:A68 4.7 73.7 1.0 CA B:GLN1350 4.8 54.5 1.0 OP2 A:A68 4.8 57.8 1.0 N B:GLN1350 4.8 57.1 1.0 O2' A:A68 4.9 68.1 1.0 C2' A:A68 4.9 66.7 1.0 C5' A:A68 4.9 54.8 1.0 OP1 A:A68 4.9 58.2 1.0 P A:A68 4.9 60.8 1.0 CB B:THR1098 4.9 53.8 1.0 CA B:LYS1097 5.0 45.5 1.0 N B:ILE1352 5.0 49.1 1.0

Potassium binding site 4 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:127.4 occ:1.00 O A:HOH257 3.1 89.9 1.0 N3 A:U66 3.6 67.6 1.0 O4 A:U66 4.1 66.1 1.0 NH2 B:ARG1171 4.1 62.7 1.0 NH1 B:ARG1171 4.2 67.9 1.0 C4 A:U66 4.2 65.9 1.0 C2 A:C67 4.3 59.0 1.0 N3 A:C67 4.3 61.0 1.0 C2 A:U66 4.3 66.7 1.0 O2 A:U66 4.4 73.5 1.0 CZ B:ARG1171 4.5 65.7 1.0 O2 A:C67 4.6 64.0 1.0 C4 A:C67 4.6 58.7 1.0 N1 A:C67 4.6 53.3 1.0 CB B:VAL1100 4.7 49.2 1.0 CG1 B:VAL1100 4.9 57.9 1.0 C6 A:C67 4.9 50.7 1.0 C5 A:C67 4.9 55.0 1.0

Potassium binding site 5 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ A:K107 b:135.2 occ:1.00 O A:HOH244 3.0 66.6 1.0 O C:HOH107 3.0 75.5 1.0 O A:HOH255 3.2 82.4 1.0 O A:HOH226 3.3 82.6 1.0 O4 A:U5 3.6 60.3 1.0 O6 A:G4 4.0 61.7 1.0 N7 A:G4 4.1 61.0 1.0 N7 A:A3 4.6 63.8 1.0 N6 C:DA16 4.6 60.6 1.0 C4 A:U5 4.7 58.9 1.0 C6 A:G4 4.8 60.3 1.0 N6 A:A3 4.8 71.3 1.0 C5 A:G4 4.8 59.2 1.0 C5 A:A3 4.8 62.9 1.0 C6 A:A3 5.0 72.1 1.0

Potassium binding site 6 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ A:K108 b:137.6 occ:1.00 O A:HOH222 2.9 92.8 1.0 O A:HOH242 3.0 91.4 1.0 O A:HOH212 3.1 108.0 1.0 N7 A:G27 3.2 60.2 1.0 O A:HOH250 3.5 69.0 1.0 O A:HOH208 3.6 54.8 1.0 C8 A:G27 3.8 59.1 1.0 OP2 A:G27 4.1 55.4 1.0 C5 A:G27 4.5 59.2 1.0 N7 A:A26 4.5 50.0 1.0 C8 A:A26 4.8 51.1 1.0 O6 A:G27 5.0 70.0 1.0

Potassium binding site 7 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ B:K1401 b:77.6 occ:1.00 O B:TYR656 2.8 71.0 1.0 O C:HOH101 2.8 97.5 1.0 O B:PHE626 2.9 70.3 1.0 O B:THR624 3.0 56.9 1.0 O B:LEU623 3.2 59.0 1.0 O C:HOH102 3.5 74.9 1.0 C B:THR624 3.6 58.3 1.0 C B:PHE626 3.8 69.4 1.0 CA B:THR624 3.9 56.8 1.0 C B:TYR656 3.9 66.9 1.0 C B:LEU623 4.2 51.7 1.0 OP1 C:DG8 4.2 76.1 1.0 CG2 B:THR657 4.3 76.3 1.0 N B:PHE626 4.4 69.2 1.0 N B:TYR656 4.5 73.2 1.0 N B:GLU627 4.5 69.8 1.0 CA B:GLU627 4.5 69.7 1.0 N B:THR624 4.5 54.2 1.0 N B:LEU625 4.6 58.5 1.0 CB B:GLU627 4.6 71.8 1.0 CA B:PHE626 4.7 65.9 1.0 N B:THR657 4.7 68.0 1.0 CA B:THR657 4.7 69.7 1.0 C B:LEU625 4.7 66.5 1.0 CG B:GLU627 4.8 79.0 1.0 CA B:TYR656 4.8 63.1 1.0 CB B:ARG655 4.9 76.8 1.0

Potassium binding site 8 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ B:K1402 b:96.2 occ:1.00 O B:ALA367 2.7 71.5 1.0 O B:TYR362 2.9 80.3 1.0 O B:GLY365 2.9 81.1 1.0 O B:GLY361 3.0 78.2 1.0 N B:ALA367 3.0 82.1 1.0 C B:GLY365 3.4 86.4 1.0 C B:GLY366 3.4 89.0 1.0 CA B:GLY366 3.5 91.0 1.0 C B:ALA367 3.5 71.3 1.0 N B:GLY366 3.6 91.2 1.0 C B:TYR362 3.6 78.2 1.0 CA B:ALA367 3.8 74.2 1.0 CA B:TYR362 4.0 76.0 1.0 C B:GLY361 4.1 77.6 1.0 O B:GLY366 4.2 90.6 1.0 N B:GLY365 4.4 87.2 1.0 CA B:GLY365 4.4 88.5 1.0 NZ B:LYS401 4.4 45.6 1.0 N B:TYR362 4.6 76.1 1.0 CB B:ALA367 4.6 70.9 1.0 N B:SER368 4.6 66.7 1.0 N B:ILE363 4.6 76.1 1.0 OP1 A:U22 4.6 54.0 1.0 C B:ILE363 4.8 79.0 1.0 O B:ILE363 4.9 84.3 1.0 C B:ASP364 4.9 82.5 1.0

Potassium binding site 9 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ B:K1403 b:108.0 occ:1.00 O B:PHE643 2.7 97.7 1.0 O B:ALA640 2.8 82.2 1.0 O B:HOH1527 3.5 58.7 1.0 C B:PHE643 3.8 95.2 1.0 C B:ALA640 4.0 76.4 1.0 CA B:HIS641 4.1 73.2 1.0 O B:HIS641 4.2 78.6 1.0 OD1 B:ASP645 4.2 131.1 1.0 C B:HIS641 4.3 79.3 1.0 CA B:ASP644 4.5 108.5 1.0 N B:HIS641 4.5 71.5 1.0 N B:ASP644 4.6 101.4 1.0 N B:PHE643 4.6 82.0 1.0 C B:ASP644 4.8 109.8 1.0 CA B:PHE643 4.9 87.9 1.0

Potassium binding site 10 out of 12 in the Target-Bound SPCAS9 Complex with Trac Full Rna Guide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Target-Bound SPCAS9 Complex with Trac Full Rna Guide within 5.0Å range: probe atom residue distance (Å) B Occ B:K1404 b:108.9 occ:1.00 O B:LEU229 2.8 92.8 1.0 O B:HOH1563 2.9 94.9 1.0 O B:GLU232 3.2 78.7 1.0 O B:ILE226 3.2 94.9 1.0 CA B:PRO230 3.4 84.7 1.0 C B:LEU229 3.5 90.3 1.0 N B:GLY231 3.8 89.8 1.0 N B:PRO230 3.8 87.4 1.0 C B:PRO230 4.0 87.2 1.0 N B:GLU232 4.0 90.7 1.0 C B:GLU232 4.2 84.8 1.0 C B:ILE226 4.3 94.9 1.0 O B:ALA227 4.3 85.1 1.0 CA B:ALA227 4.4 90.2 1.0 C B:ALA227 4.6 84.2 1.0 CB B:PRO230 4.6 80.9 1.0 N B:LEU229 4.7 88.3 1.0 CA B:LEU229 4.7 88.6 1.0 CG2 B:ILE226 4.7 102.6 1.0 CA B:GLU232 4.7 85.9 1.0 N B:ALA227 4.8 95.9 1.0 CA B:GLY231 4.8 90.6 1.0 C B:GLY231 4.9 90.9 1.0 O B:PRO230 5.0 86.2 1.0

P.D.Donohoue, M.Pacesa, E.Lau, B.Vidal, M.J.Irby, D.B.Nyer, T.Rotstein, L.Banh, M.S.Toh, J.Gibson, B.Kohrs, K.Baek, A.L.G.Owen, E.M.Slorach, M.Van Overbeek, C.K.Fuller, A.P.May, M.Jinek, P.Cameron. Conformational Control of CAS9 By Crispr Hybrid Rna-Dna Guides Mitigates Off-Target Activity in T Cells. Mol.Cell V. 81 3637 2021.
ISSN: ISSN 1097-2765
PubMed: 34478654
DOI: 10.1016/J.MOLCEL.2021.07.035