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Potassium in PDB 7ox7: Target-Bound SPCAS9 Complex with Trac Chimeric Rna-Dna Guide

Protein crystallography data

The structure of Target-Bound SPCAS9 Complex with Trac Chimeric Rna-Dna Guide, PDB code: 7ox7 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) 42.46 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.542, 67.406, 188.136, 90, 112.54, 90
R / Rfree (%) 20.9 / 22.9

Other elements in 7ox7:

The structure of Target-Bound SPCAS9 Complex with Trac 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 Trac Chimeric Rna-Dna Guide (pdb code 7ox7). 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 Trac Chimeric Rna-Dna Guide, PDB code: 7ox7:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in 7ox7

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

b:80.3
occ:1.00
 O A:HOH206 2.8 65.8 1.0
O A:HOH244 2.8 78.1 1.0
O B:HOH1597 2.8 59.1 1.0
O4 A:U66 2.9 53.2 1.0
OP2 A:A65 2.9 46.9 1.0
O A:HOH262 3.0 30.3 1.0
OG1 B:THR1102 3.0 50.9 1.0
C4 A:U66 3.7 54.4 1.0
CG2 B:THR1102 3.7 52.7 1.0
C5 A:U66 3.8 54.0 1.0
CB B:THR1102 3.9 50.9 1.0
O B:HOH1615 4.1 59.5 1.0
P A:A65 4.2 43.5 1.0
N4 A:C67 4.3 41.8 1.0
OP1 A:U64 4.5 40.1 1.0
N7 A:A65 4.7 56.8 1.0
OP1 A:A65 4.7 45.0 1.0
O B:VAL1100 4.7 35.4 1.0
O5' A:A65 4.8 47.8 1.0
O A:HOH220 4.8 88.4 1.0
O B:HOH1641 4.9 60.7 1.0
O A:HOH216 4.9 49.8 1.0
OP2 A:U64 5.0 38.5 1.0
N3 A:U66 5.0 56.3 1.0

Potassium binding site 2 out of 14 in 7ox7

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

b:82.6
occ:1.00
 O A:HOH316 2.8 70.7 1.0
O A:HOH228 2.8 55.4 1.0
O A:HOH315 2.8 70.1 1.0
O A:HOH236 2.9 66.8 1.0
OP2 A:G21 3.0 54.5 1.0
O A:HOH226 3.2 58.7 1.0
O A:HOH274 3.5 75.8 1.0
P A:G21 4.0 53.9 1.0
O A:HOH242 4.0 36.8 1.0
OP2 A:U45 4.0 51.3 1.0
O A:HOH202 4.0 62.0 1.0
OP1 A:G21 4.1 55.8 1.0
CB B:ARG403 4.4 45.7 1.0
MG A:MG101 4.4 70.9 1.0
O A:HOH278 4.7 57.2 1.0
O B:ARG403 4.8 56.9 1.0
O5' A:G21 4.9 50.7 1.0
O B:HOH1593 4.9 73.8 1.0

Potassium binding site 3 out of 14 in 7ox7

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

b:79.6
occ:1.00
 O B:GLN1350 2.7 48.4 1.0
O B:HOH1596 2.8 41.7 1.0
O B:HOH1576 2.8 61.1 1.0
O A:HOH233 3.0 75.0 1.0
O B:HOH1730 3.1 62.2 1.0
O4' A:A68 3.1 55.1 1.0
O B:HOH1656 3.3 40.8 1.0
C1' A:A68 3.6 57.2 1.0
O B:SER1351 3.8 42.6 1.0
C B:GLN1350 3.8 47.1 1.0
OG1 B:THR1098 4.2 42.4 1.0
C B:SER1351 4.2 43.0 1.0
C4' A:A68 4.2 54.3 1.0
N9 A:A68 4.2 61.2 1.0
O5' A:A68 4.4 50.0 1.0
CB B:GLN1350 4.5 43.4 1.0
CA B:GLN1350 4.6 45.6 1.0
C8 A:A68 4.6 60.8 1.0
N B:SER1351 4.7 47.5 1.0
CA B:SER1351 4.7 46.7 1.0
N B:GLN1350 4.7 45.4 1.0
OP1 A:A68 4.7 54.3 1.0
N B:THR1098 4.7 43.0 1.0
CG1 B:VAL1095 4.7 42.4 1.0
O B:HOH1559 4.7 38.5 1.0
O A:HOH248 4.8 61.0 1.0
C2' A:A68 4.8 56.4 1.0
N B:ILE1352 4.8 42.4 1.0
O2' A:A68 4.9 55.1 1.0
C5' A:A68 4.9 52.9 1.0
P A:A68 4.9 50.8 1.0
CG2 B:THR1098 5.0 42.6 1.0
CA B:ILE1352 5.0 42.1 1.0
OP2 A:A68 5.0 53.0 1.0

Potassium binding site 4 out of 14 in 7ox7

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

b:88.9
occ:1.00
 O A:HOH251 2.8 49.8 1.0
O6 A:G16 3.0 46.4 1.0
O A:HOH291 3.0 55.5 1.0
O B:HOH1720 3.4 53.4 1.0
O6 A:G15 3.4 48.9 1.0
O A:HOH201 3.5 71.7 1.0
C6 A:G16 4.0 42.1 1.0
C6 A:G15 4.1 44.3 1.0
N7 A:G16 4.2 44.2 1.0
CD2 B:LEU64 4.2 42.9 1.0
OG1 B:THR67 4.2 49.3 1.0
O4 A:U17 4.2 62.2 1.0
N4 C:DC5 4.3 50.8 1.0
NH2 B:ARG63 4.4 39.6 1.0
N7 A:G15 4.4 43.2 1.0
C5 A:G16 4.5 40.0 1.0
C5 A:G15 4.5 41.5 1.0
CG2 B:THR67 4.6 48.9 1.0
CB B:THR67 4.8 46.9 1.0
N4 C:DC6 4.8 51.5 1.0
C4 A:U17 4.9 49.2 1.0

Potassium binding site 5 out of 14 in 7ox7

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

b:89.2
occ:1.00
 O A:HOH220 3.3 88.4 1.0
N3 A:U66 3.3 56.3 1.0
O A:HOH299 3.3 67.9 1.0
NH2 B:ARG1171 3.7 57.3 1.0
O4 A:U66 3.7 53.2 1.0
NH1 B:ARG1171 3.8 56.7 1.0
C4 A:U66 4.0 54.4 1.0
C2 A:U66 4.2 55.6 1.0
O2 A:U66 4.2 60.8 1.0
CZ B:ARG1171 4.3 55.7 1.0
C2 A:C67 4.7 44.0 1.0
N3 A:C67 4.7 43.5 1.0
N6 A:A65 4.9 64.1 1.0
CB B:VAL1100 4.9 38.7 1.0
C4 A:C67 4.9 44.3 1.0
N1 A:C67 4.9 45.3 1.0
CG2 B:THR1102 4.9 52.7 1.0
CG1 B:VAL1100 5.0 38.1 1.0
O2 A:C67 5.0 42.8 1.0

Potassium binding site 6 out of 14 in 7ox7

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

b:119.2
occ:1.00
 O B:GLY36 3.0 57.1 1.0
O B:HOH1506 3.1 55.5 1.0
O B:THR38 3.2 63.9 1.0
O B:HOH1727 3.2 78.8 1.0
O B:HOH1699 3.5 70.7 1.0
N B:THR38 3.7 60.2 1.0
C B:GLY36 3.7 57.5 1.0
CA B:ASN37 3.8 63.0 1.0
C B:ASN37 3.9 63.0 1.0
O B:HOH1529 4.0 64.2 1.0
N B:ASN37 4.0 60.4 1.0
C B:THR38 4.2 64.1 1.0
CA B:THR38 4.6 59.9 1.0
O B:ASN37 4.7 67.7 1.0
O B:ARG40 4.7 55.6 1.0
CE1 B:HIS41 4.7 82.1 1.0
ND1 B:HIS41 4.8 80.5 1.0
N B:GLY36 4.8 55.5 1.0
CA B:GLY36 4.9 56.5 1.0

Potassium binding site 7 out of 14 in 7ox7

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

b:138.1
occ:1.00
 O B:HOH1701 2.8 81.8 1.0
O B:HOH1641 2.8 60.7 1.0
O B:HOH1684 2.8 82.9 1.0
OE2 B:GLU57 2.9 92.8 1.0
O B:HOH1539 3.3 65.1 1.0
O A:HOH206 3.3 65.8 1.0
CD B:GLU57 3.4 87.6 1.0
OE1 B:GLU57 3.7 94.8 1.0
O B:HOH1689 3.8 65.1 1.0
O B:HOH1739 4.0 70.8 1.0
O A:HOH221 4.0 81.0 1.0
O B:HOH1615 4.1 59.5 1.0
O B:HOH1597 4.3 59.1 1.0
CG B:GLU57 4.4 73.6 1.0
O B:HOH1611 4.6 69.0 1.0
O B:HOH1617 4.8 66.7 1.0
NE2 B:GLN1101 4.9 49.9 1.0
O B:THR1102 4.9 51.6 1.0
O B:HOH1504 5.0 52.6 1.0

Potassium binding site 8 out of 14 in 7ox7

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

b:87.2
occ:1.00
 OD1 B:ASN588 2.9 60.4 1.0
O C:HOH114 3.0 78.2 1.0
O B:GLU584 3.0 86.6 1.0
O B:ARG586 3.1 65.9 1.0
O B:HOH1726 3.3 72.5 1.0
CG B:ASN588 3.6 58.9 1.0
ND2 B:ASN588 3.9 56.4 1.0
C B:GLU584 4.1 86.3 1.0
C B:ARG586 4.3 67.1 1.0
N B:GLU584 4.4 76.5 1.0
N B:ARG586 4.6 79.7 1.0
N B:ASN588 4.6 57.2 1.0
CA B:GLU584 4.7 86.1 1.0
CB B:GLU584 4.8 97.0 1.0
CB B:ASN588 4.9 58.1 1.0
CG B:ARG586 4.9 82.1 1.0
CG2 B:VAL583 5.0 59.6 1.0
CA B:ASN588 5.0 56.1 1.0

Potassium binding site 9 out of 14 in 7ox7

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

b:83.2
occ:1.00
 O B:TYR656 2.8 56.3 1.0
O C:HOH106 3.0 72.4 1.0
O B:LEU623 3.1 50.4 1.0
O B:THR624 3.1 46.9 1.0
O B:HOH1691 3.1 60.5 1.0
O B:PHE626 3.2 66.2 1.0
C B:THR624 3.7 46.4 1.0
C B:TYR656 3.9 57.0 1.0
C B:PHE626 3.9 62.7 1.0
CA B:THR624 4.0 47.9 1.0
OP1 C:DG8 4.1 59.8 1.0
C B:LEU623 4.1 50.8 1.0
CG2 B:THR657 4.2 56.4 1.0
N B:TYR656 4.3 72.2 1.0
CA B:GLU627 4.4 70.0 1.0
N B:GLU627 4.4 65.9 1.0
CB B:GLU627 4.4 74.7 1.0
CB B:ARG655 4.4 98.5 1.0
CG B:ARG655 4.4 106.0 1.0
N B:THR624 4.5 51.0 1.0
N B:PHE626 4.6 56.6 1.0
CD B:ARG655 4.6 108.5 1.0
C B:LEU625 4.7 53.7 1.0
CA B:TYR656 4.7 63.5 1.0
N B:LEU625 4.8 45.4 1.0
N B:THR657 4.8 54.0 1.0
CA B:PHE626 4.8 57.9 1.0
CG B:GLU627 4.9 78.5 1.0
O B:LEU625 4.9 55.3 1.0
CA B:THR657 4.9 53.9 1.0

Potassium binding site 10 out of 14 in 7ox7

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

b:82.7
occ:1.00
 O A:HOH289 2.8 65.4 1.0
O B:TYR362 2.9 60.6 1.0
O B:ALA367 2.9 60.0 1.0
O B:GLY365 3.1 64.4 1.0
O B:HOH1685 3.1 56.3 1.0
O B:GLY361 3.2 67.4 1.0
C B:TYR362 3.5 58.8 1.0
O B:HOH1612 3.7 69.7 1.0
N B:ALA367 3.7 65.0 1.0
C B:GLY365 3.8 66.8 1.0
NZ B:LYS401 3.8 60.1 1.0
C B:ALA367 3.9 61.3 1.0
CA B:TYR362 4.0 58.2 1.0
C B:GLY366 4.1 66.5 1.0
CA B:GLY366 4.2 67.4 1.0
C B:GLY361 4.2 65.3 1.0
N B:GLY366 4.2 66.3 1.0
N B:ILE363 4.3 58.5 1.0
CA B:ALA367 4.3 62.2 1.0
C B:ILE363 4.4 63.6 1.0
N B:GLY365 4.4 71.1 1.0
O B:ILE363 4.5 65.2 1.0
OP1 A:U22 4.5 43.9 1.0
O B:HOH1562 4.5 49.8 1.0
N B:TYR362 4.6 61.5 1.0
CA B:ILE363 4.6 58.8 1.0
CA B:GLY365 4.7 70.1 1.0
N B:ASP364 4.8 65.1 1.0
O B:GLY366 4.9 68.1 1.0
C B:ASP364 4.9 69.7 1.0
N B:SER368 5.0 61.0 1.0
CB B:ALA367 5.0 60.8 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 19:46:11 2024

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