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Potassium in PDB 7oxa: Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna Guide

Protein crystallography data

The structure of Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna Guide, PDB code: 7oxa 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) 47.66 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.926, 67.574, 189.232, 90, 112.52, 90
R / Rfree (%) 19.8 / 22.6

Other elements in 7oxa:

The structure of Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna Guide also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Potassium atom in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna Guide (pdb code 7oxa). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 14 binding sites of Potassium where determined in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna Guide, PDB code: 7oxa:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in 7oxa

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Potassium binding site 1 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:65.4
occ:1.00
 OP2 A:A65 2.7 40.7 1.0
O4 A:U66 2.8 48.8 1.0
OG1 B:THR1102 2.9 38.0 1.0
O A:HOH259 2.9 38.4 1.0
O A:HOH247 2.9 52.2 1.0
O B:HOH1646 2.9 41.1 1.0
O A:HOH284 3.0 36.4 1.0
CG2 B:THR1102 3.6 44.8 1.0
C4 A:U66 3.7 47.8 1.0
CB B:THR1102 3.8 43.3 1.0
C5 A:U66 4.0 47.7 1.0
P A:A65 4.1 40.3 1.0
OP1 A:U64 4.2 41.4 1.0
O B:HOH1589 4.2 41.5 1.0
O A:HOH266 4.3 41.8 1.0
N4 A:C67 4.5 41.4 1.0
N7 A:A65 4.6 47.1 1.0
O5' A:A65 4.7 43.3 1.0
OP1 A:A65 4.8 38.9 1.0
O A:HOH263 4.8 35.3 1.0
O B:HOH1761 4.8 42.8 1.0
OP2 A:U64 4.9 34.4 1.0
P A:U64 4.9 40.0 1.0
O B:VAL1100 4.9 35.1 1.0
C8 A:A65 5.0 45.4 1.0
N3 A:U66 5.0 49.3 1.0

Potassium binding site 2 out of 14 in 7oxa

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Potassium binding site 2 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:67.7
occ:1.00
 O A:HOH362 2.7 56.0 1.0
OP2 A:G21 2.8 42.9 1.0
O A:HOH357 2.8 62.6 1.0
O A:HOH277 2.8 42.6 1.0
O A:HOH240 3.0 35.4 1.0
O A:HOH230 3.0 49.5 1.0
O A:HOH314 3.5 74.3 1.0
P A:G21 3.7 48.2 1.0
OP1 A:G21 3.7 46.5 1.0
O A:HOH218 3.7 65.5 1.0
O A:HOH349 3.8 67.0 1.0
O A:HOH203 3.8 70.8 1.0
O A:HOH278 4.1 60.3 1.0
O A:HOH303 4.2 62.3 1.0
OP2 A:U45 4.2 51.4 1.0
MG A:MG101 4.3 74.7 1.0
CB B:ARG403 4.4 42.0 1.0
O B:HOH1725 4.6 80.7 1.0
O5' A:G21 4.7 51.5 1.0
O A:HOH273 4.7 43.0 1.0
O B:ARG403 4.8 50.3 1.0
O3' A:U20 5.0 53.4 1.0

Potassium binding site 3 out of 14 in 7oxa

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Potassium binding site 3 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:46.5
occ:1.00
 O B:GLN1350 2.7 41.1 1.0
O B:HOH1637 2.8 39.5 1.0
O A:HOH220 2.8 56.7 1.0
O B:HOH1759 2.8 45.6 1.0
O A:HOH360 2.8 61.5 1.0
O4' A:A68 3.1 52.4 1.0
C1' A:A68 3.5 53.6 1.0
O B:HOH1803 3.6 42.8 1.0
C B:GLN1350 3.8 44.2 1.0
O B:SER1351 4.0 44.3 1.0
N9 A:A68 4.2 57.6 1.0
C B:SER1351 4.2 41.0 1.0
OG1 B:THR1098 4.2 39.0 1.0
C4' A:A68 4.3 47.8 1.0
O A:HOH233 4.4 46.7 1.0
C8 A:A68 4.4 59.7 1.0
O5' A:A68 4.5 43.2 1.0
OP1 A:A68 4.6 47.7 1.0
CA B:SER1351 4.6 44.8 1.0
OP2 A:A68 4.6 42.0 1.0
O B:HOH1701 4.7 47.6 1.0
N B:ILE1352 4.7 37.5 1.0
N B:SER1351 4.7 43.5 1.0
CA B:GLN1350 4.7 44.2 1.0
CB B:GLN1350 4.7 41.6 1.0
CG1 B:VAL1095 4.7 34.5 1.0
N B:THR1098 4.7 40.8 1.0
P A:A68 4.8 41.6 1.0
N B:GLN1350 4.8 46.4 1.0
CA B:ILE1352 4.8 40.9 1.0
C2' A:A68 4.8 53.3 1.0
O2' A:A68 4.9 49.5 1.0
C5' A:A68 4.9 44.3 1.0

Potassium binding site 4 out of 14 in 7oxa

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Potassium binding site 4 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K106

b:106.7
occ:1.00
 O A:HOH308 2.9 80.0 1.0
O6 A:G13 3.0 44.1 1.0
O A:HOH356 3.0 81.0 1.0
O6 A:G12 3.5 48.7 1.0
O A:HOH205 3.6 67.3 1.0
O C:HOH218 4.0 57.9 1.0
N4 C:DC8 4.0 46.0 1.0
C6 A:G13 4.1 39.5 1.0
C6 A:G12 4.5 45.7 1.0
O A:HOH248 4.6 36.5 1.0
N7 A:G13 4.6 41.2 1.0
C5 A:G13 4.7 39.3 1.0
O C:HOH205 4.7 62.3 1.0
N7 A:G12 4.7 47.8 1.0
N4 C:DC9 4.9 42.4 1.0
C5 A:G12 5.0 46.1 1.0

Potassium binding site 5 out of 14 in 7oxa

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Potassium binding site 5 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K107

b:117.3
occ:1.00
 O A:HOH363 2.9 84.9 1.0
O C:HOH213 3.3 75.3 1.0
O6 A:DG4 3.4 55.5 1.0
O A:HOH339 3.6 70.1 1.0
O A:HOH330 3.6 57.3 1.0
O6 C:DG16 3.8 78.5 1.0
N4 A:DC5 4.1 54.3 1.0
O6 A:DG3 4.1 52.6 1.0
N4 C:DC17 4.3 91.0 1.0
C6 A:DG4 4.5 52.0 1.0
N7 A:DG4 4.7 55.6 1.0
C6 A:DG3 4.8 54.0 1.0
N7 A:DG3 4.9 57.7 1.0
C6 C:DG16 4.9 83.4 1.0

Potassium binding site 6 out of 14 in 7oxa

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Potassium binding site 6 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1401

b:85.7
occ:1.00
 O B:HOH1850 2.8 64.5 1.0
O B:THR38 2.9 49.1 1.0
O B:HOH1558 3.2 46.8 1.0
O B:GLY36 3.3 53.0 1.0
O B:HOH1866 3.3 67.3 1.0
N B:THR38 3.7 51.8 1.0
C B:ASN37 3.8 54.5 1.0
CA B:ASN37 3.9 58.9 1.0
C B:THR38 4.0 53.0 1.0
C B:GLY36 4.0 52.6 1.0
O B:HOH1602 4.2 42.0 1.0
N B:ASN37 4.2 58.0 1.0
CA B:THR38 4.5 52.9 1.0
O B:ASN37 4.5 50.6 1.0
O B:ARG40 4.9 53.4 1.0

Potassium binding site 7 out of 14 in 7oxa

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Potassium binding site 7 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1402

b:102.5
occ:1.00
 O B:HOH1838 2.8 44.8 1.0
O A:HOH247 2.8 52.2 1.0
O B:HOH1842 2.9 96.0 1.0
O B:HOH1761 2.9 42.8 1.0
OE2 B:GLU57 3.0 76.4 1.0
O B:HOH1531 3.3 51.5 1.0
CD B:GLU57 3.5 67.3 1.0
OE1 B:GLU57 3.8 75.0 1.0
O B:HOH1712 3.8 64.4 1.0
O A:HOH264 3.9 47.2 1.0
O B:HOH1589 4.3 41.5 1.0
O B:HOH1646 4.4 41.1 1.0
CG B:GLU57 4.4 51.7 1.0
O B:HOH1586 4.6 53.7 1.0
O B:HOH1762 4.8 59.0 1.0
O B:THR1102 4.9 42.5 1.0
OP1 A:U64 4.9 41.4 1.0
O B:HOH1679 5.0 59.3 1.0

Potassium binding site 8 out of 14 in 7oxa

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Potassium binding site 8 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1403

b:65.1
occ:1.00
 O B:GLU584 2.8 73.0 1.0
O B:ARG586 2.8 44.9 1.0
O B:HOH1874 2.8 75.8 1.0
OD1 B:ASN588 2.9 46.4 1.0
O B:HOH1617 3.0 62.6 1.0
CG B:ASN588 3.8 46.1 1.0
C B:GLU584 4.0 70.3 1.0
C B:ARG586 4.0 43.7 1.0
ND2 B:ASN588 4.2 44.4 1.0
N B:ARG586 4.2 55.6 1.0
N B:GLU584 4.4 69.2 1.0
CG B:ARG586 4.5 66.9 1.0
N B:ASN588 4.6 51.0 1.0
CA B:GLU584 4.6 75.4 1.0
CB B:GLU584 4.7 89.2 1.0
CA B:ARG586 4.7 49.1 1.0
C B:PHE587 4.8 48.3 1.0
CA B:ASN588 5.0 47.2 1.0
CB B:ASP585 5.0 77.2 1.0
CB B:ASN588 5.0 44.5 1.0
N B:PHE587 5.0 42.5 1.0

Potassium binding site 9 out of 14 in 7oxa

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Potassium binding site 9 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1404

b:68.3
occ:1.00
 O C:HOH221 2.7 48.0 1.0
O B:TYR656 2.8 43.8 1.0
O B:THR624 2.9 44.6 1.0
O B:LEU623 2.9 39.6 1.0
O B:PHE626 3.0 56.5 1.0
O B:HOH1769 3.0 51.8 1.0
C B:THR624 3.4 38.0 1.0
C B:PHE626 3.7 52.1 1.0
CA B:THR624 3.7 36.0 1.0
C B:LEU623 3.9 43.5 1.0
C B:TYR656 4.0 42.2 1.0
N B:PHE626 4.2 51.7 1.0
N B:THR624 4.2 38.9 1.0
N B:GLU627 4.3 50.0 1.0
CA B:GLU627 4.3 46.9 1.0
N B:TYR656 4.4 53.3 1.0
CG2 B:THR657 4.4 50.3 1.0
OP1 C:DC8 4.4 53.4 1.0
N B:LEU625 4.4 37.5 1.0
C B:LEU625 4.5 49.5 1.0
CG B:ARG655 4.5 88.4 1.0
CA B:PHE626 4.5 50.3 1.0
CB B:GLU627 4.6 48.4 1.0
CB B:ARG655 4.6 78.9 1.0
O B:LEU625 4.8 48.7 1.0
CD B:ARG655 4.8 95.5 1.0
CA B:TYR656 4.9 46.6 1.0
N B:THR657 4.9 37.8 1.0
CA B:THR657 5.0 43.1 1.0

Potassium binding site 10 out of 14 in 7oxa

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Potassium binding site 10 out of 14 in the Target-Bound SPCAS9 Complex with AAVS1 Chimeric Rna-Dna 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 AAVS1 Chimeric Rna-Dna Guide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1405

b:68.0
occ:1.00
 O B:ALA367 2.7 59.6 1.0
O B:TYR362 2.8 57.0 1.0
O B:HOH1819 2.8 52.2 1.0
O B:HOH1776 2.9 71.2 1.0
O B:GLY365 3.0 69.6 1.0
O B:GLY361 3.1 59.2 1.0
O B:HOH1536 3.2 56.4 1.0
C B:TYR362 3.5 59.5 1.0
N B:ALA367 3.5 74.5 1.0
C B:ALA367 3.7 64.5 1.0
C B:GLY365 3.7 69.5 1.0
NZ B:LYS401 3.9 48.7 1.0
CA B:TYR362 3.9 62.8 1.0
C B:GLY366 3.9 76.4 1.0
C B:GLY361 4.2 61.6 1.0
CA B:ALA367 4.2 68.1 1.0
CA B:GLY366 4.2 74.4 1.0
N B:GLY366 4.3 72.9 1.0
O B:HOH1522 4.3 45.6 1.0
N B:ILE363 4.5 56.8 1.0
OP1 A:U22 4.5 48.7 1.0
N B:GLY365 4.5 60.5 1.0
N B:TYR362 4.5 63.8 1.0
O B:GLY366 4.7 83.1 1.0
C B:ILE363 4.7 55.6 1.0
CA B:GLY365 4.7 65.3 1.0
N B:SER368 4.7 60.7 1.0
CB B:ALA367 4.8 68.3 1.0
O B:ILE363 4.8 58.0 1.0
CA B:ILE363 4.9 55.8 1.0
N B:ASP364 4.9 55.0 1.0
O A:HOH218 5.0 65.5 1.0

Reference:

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
Page generated: Mon Aug 12 19:46:38 2024

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