Potassium in PDB 7z4d: Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate

The structure of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate, PDB code: 7z4d 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)	66.49 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	88.636, 95.509, 169.797, 80.83, 78.04, 62.34
R / Rfree (%)	24.7 / 27.6

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate (pdb code 7z4d). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 16 binding sites of Potassium where determined in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate, PDB code: 7z4d:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:98.5 occ:1.00 N3 A:A32 4.3 67.5 1.0 N3 A:A38 4.4 60.0 1.0 O2' A:A38 4.5 67.3 1.0 C1' A:A32 5.0 67.4 1.0 C2 A:A32 5.0 61.1 1.0

Potassium binding site 2 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:69.7 occ:1.00 O C:HOH201 2.9 34.0 1.0 O4 A:U63 3.0 23.9 1.0 O B:HOH1522 3.1 24.3 1.0 CD B:GLU1108 3.5 44.2 1.0 CG B:GLU1108 3.6 41.8 1.0 OE2 B:GLU1108 3.8 65.1 1.0 OE1 B:GLU1108 3.9 47.8 1.0 C4 A:U63 4.0 24.5 1.0 N3 A:U63 4.2 29.1 1.0 CE B:LYS65 4.3 58.2 1.0 CB B:GLU1108 4.5 34.6 1.0 CG B:LYS65 4.5 28.7 1.0 O4' A:A51 4.6 25.7 1.0 CD B:LYS65 4.8 22.7 1.0 O2' A:U50 4.8 49.3 1.0 C1' A:A51 4.9 28.6 1.0

Potassium binding site 3 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:52.7 occ:1.00 O4' A:A68 3.5 39.2 1.0 OG1 B:THR1098 3.7 31.9 1.0 O B:GLN1350 3.8 37.2 1.0 N B:THR1098 3.9 23.8 1.0 O5' A:A68 3.9 45.7 1.0 C1' A:A68 4.3 39.0 1.0 C4' A:A68 4.3 41.4 1.0 CA B:LYS1097 4.4 32.2 1.0 CG2 B:THR1098 4.4 25.4 1.0 CB B:THR1098 4.5 23.5 1.0 OP2 A:A68 4.6 58.8 1.0 C B:LYS1097 4.6 36.8 1.0 CG1 B:VAL1095 4.7 35.8 1.0 C5' A:A68 4.7 36.4 1.0 O B:LYS1096 4.8 44.0 1.0 CA B:THR1098 4.8 22.6 1.0 P A:A68 4.8 55.1 1.0 O B:SER1351 4.9 31.2 1.0 O B:THR1098 4.9 34.1 1.0 C B:GLN1350 4.9 28.4 1.0 CG B:LYS1097 4.9 25.8 1.0

Potassium binding site 4 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:68.1 occ:1.00 N4 A:C67 3.2 27.3 1.0 O B:HOH1508 3.2 40.3 1.0 OE1 B:GLU1099 3.4 36.1 1.0 CD B:GLU1099 3.5 26.5 1.0 O B:HOH1516 3.5 19.8 1.0 OE2 B:GLU1099 3.6 21.0 1.0 CB B:GLU1099 4.3 20.3 1.0 C4 A:C67 4.3 33.7 1.0 CG B:GLU1099 4.3 20.2 1.0 O B:VAL1100 4.4 20.2 1.0 NZ B:LYS735 4.4 33.8 1.0 O4 A:U66 4.5 53.1 1.0 C5 A:C67 4.6 29.2 1.0 OP2 A:A65 4.7 33.8 1.0 O B:HOH1513 4.8 30.5 1.0 C5 A:U66 4.9 29.6 1.0 OP1 A:A65 4.9 35.7 1.0 C4 A:U66 4.9 32.2 1.0 OG1 B:THR1102 5.0 24.4 1.0

Potassium binding site 5 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:73.2 occ:1.00 O A:HOH215 3.1 46.4 1.0 OP1 A:U50 3.1 28.2 1.0 O6 A:G62 3.1 30.4 1.0 O6 A:G53 3.4 41.8 1.0 C6 A:G62 4.0 26.1 1.0 N1 A:G62 4.0 28.9 1.0 C6 A:G53 4.1 39.2 1.0 N7 A:G53 4.1 27.2 1.0 OP2 A:A52 4.3 29.2 1.0 P A:U50 4.4 60.0 1.0 OP1 A:A51 4.4 26.4 1.0 C5 A:G53 4.5 29.7 1.0 OP1 A:A52 4.5 25.8 1.0 O5' A:U50 4.9 30.4 1.0 C5' A:U50 4.9 24.2 1.0 P A:A52 4.9 28.5 1.0

Potassium binding site 6 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:80.6 occ:1.00 N7 A:G19 3.7 31.2 1.0 C5 A:C18 4.2 46.7 1.0 C8 A:G19 4.4 36.0 1.0 OP2 A:C18 4.5 47.6 1.0 OP2 A:G19 4.6 28.4 1.0 C4 A:C18 4.6 36.2 1.0 N4 A:C18 4.7 37.2 1.0 C6 A:C18 4.7 38.7 1.0 C5 A:G19 4.9 30.0 1.0 NH1 B:ARG71 4.9 58.5 1.0 O6 A:G19 4.9 28.8 1.0 NE B:ARG71 4.9 25.1 1.0 NH2 B:ARG75 5.0 42.0 1.0

Potassium binding site 7 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:K1401 b:53.9 occ:1.00 O B:ALA59 2.7 34.5 1.0 NH1 B:ARG66 2.7 41.1 1.0 N B:ARG63 3.0 25.8 1.0 CB B:THR62 3.2 42.9 1.0 CB B:ALA59 3.2 38.2 1.0 OP1 A:G14 3.3 38.4 1.0 C B:THR62 3.5 37.3 1.0 CA B:ARG63 3.5 17.6 1.0 CB B:ARG63 3.5 35.9 1.0 CG2 B:THR62 3.5 43.6 1.0 C B:ALA59 3.6 41.6 1.0 CA B:ALA59 3.8 39.8 1.0 CA B:THR62 3.8 43.8 1.0 CZ B:ARG66 3.9 32.1 1.0 OP2 A:G14 3.9 30.6 1.0 P A:G14 4.1 48.5 1.0 O B:THR62 4.2 34.1 1.0 OG1 B:THR62 4.3 40.5 1.0 N B:THR62 4.4 29.2 1.0 NH2 B:ARG66 4.4 29.0 1.0 CG B:ARG63 4.8 41.4 1.0 NE B:ARG66 4.8 28.7 1.0 N B:GLU60 4.8 44.8 1.0 O4' A:U64 5.0 36.9 1.0 C B:ARG63 5.0 30.4 1.0

Potassium binding site 8 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:K1402 b:60.9 occ:1.00 NH1 B:ARG1171 3.0 22.3 1.0 NH2 B:ARG1171 3.5 36.4 1.0 CZ B:ARG1171 3.7 26.9 1.0 N3 A:U66 3.7 33.5 1.0 O4 A:U66 4.1 53.1 1.0 C4 A:U66 4.4 32.2 1.0 O2 A:U66 4.4 58.0 1.0 CG2 B:THR1102 4.5 20.3 1.0 C2 A:U66 4.6 36.3 1.0 CB B:VAL1100 4.7 23.1 1.0 CG1 B:VAL1100 4.7 24.5 1.0 N6 A:A65 4.8 41.5 1.0 N3 A:C67 5.0 33.6 1.0 C2 A:C67 5.0 29.9 1.0 O2 A:C67 5.0 41.3 1.0

Potassium binding site 9 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:K1403 b:56.7 occ:1.00 O B:GLY408 3.3 31.6 1.0 O2 A:C18 3.5 39.2 1.0 O2' A:C18 3.6 53.0 1.0 O2 C:DT4 3.7 40.6 1.0 C1' A:C18 3.8 34.2 1.0 C2' A:C18 4.2 38.3 1.0 C B:GLY408 4.2 40.4 1.0 CB B:HIS167 4.2 30.3 1.0 CA B:GLY408 4.3 32.0 1.0 C2 A:C18 4.4 44.1 1.0 N1 A:C18 4.6 33.3 1.0 CD1 B:LEU169 4.7 38.8 1.0 C1' C:DT4 4.8 33.8 1.0 C2 C:DT4 4.8 36.6 1.0 O4' A:C18 4.8 34.2 1.0 CG B:HIS167 4.8 32.0 1.0 O4' C:DC5 4.8 49.9 1.0 C2' C:DT4 4.9 34.2 1.0 CD2 B:HIS167 4.9 32.6 1.0 N2 C:DG3 4.9 37.7 1.0

Potassium binding site 10 out of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:43.5 occ:1.00 O6 C:DG3 3.4 48.2 1.0 N7 C:DG3 4.2 40.6 1.0 O4 C:DT4 4.3 39.8 1.0 C6 C:DG3 4.3 43.0 1.0 N4 C:DC2 4.5 33.7 1.0 NH1 B:ARG71 4.6 58.5 1.0 C5 C:DG3 4.6 42.3 1.0 C4 C:DC2 4.6 39.1 1.0 C5 C:DC2 4.7 37.0 1.0 CB B:LEU64 4.7 27.8 1.0 CD1 B:LEU64 5.0 48.1 1.0 N4 A:C18 5.0 37.2 1.0

M.Pacesa, L.Loeff, I.Querques, L.M.Muckenfuss, M.Sawicka, M.Jinek. R-Loop Formation and Conformational Activation Mechanisms of CAS9. Nature V. 609 191 2022.
ISSN: ESSN 1476-4687
PubMed: 36002571
DOI: 10.1038/S41586-022-05114-0