Potassium in PDB 5fw1: Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna

The structure of Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna, PDB code: 5fw1 was solved by C.Anders, K.Bargsten, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.62 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.637, 66.984, 187.228, 90.00, 111.12, 90.00
R / Rfree (%)	21.8 / 25.4

The structure of Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna (pdb code 5fw1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 13 binding sites of Potassium where determined in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna, PDB code: 5fw1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:K2081 b:83.7 occ:1.00 O A:HOH3017 3.2 36.9 1.0 O6 A:G13 3.2 29.1 1.0 O A:HOH3016 3.3 35.1 1.0 O4 A:U12 3.4 45.2 1.0 H41 C:DC16 3.6 44.9 1.0 H42 C:DC16 3.9 44.9 1.0 N4 C:DC16 4.1 37.5 1.0 H5 A:U12 4.3 31.1 1.0 C4 A:U12 4.3 28.7 1.0 H61 C:DA17 4.3 45.0 1.0 C6 A:G13 4.4 28.7 1.0 C5 A:U12 4.6 25.9 1.0 N6 C:DA17 4.9 37.5 1.0 N7 A:G13 5.0 33.9 1.0 H62 C:DA17 5.0 45.0 1.0

Potassium binding site 2 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:K2082 b:88.5 occ:1.00 O B:GLY365 2.9 59.0 1.0 OP1 A:U22 2.9 35.2 1.0 C B:GLY365 3.7 49.7 1.0 P A:U22 3.8 34.4 1.0 HA2 B:GLY366 3.9 64.2 1.0 OP2 A:U23 4.0 38.9 1.0 H5'' A:U22 4.0 37.3 1.0 O B:ASP364 4.1 47.7 1.0 OP2 A:U22 4.1 40.2 1.0 O5' A:U22 4.2 33.2 1.0 HA2 B:GLY365 4.4 54.4 1.0 CA B:GLY365 4.5 45.4 1.0 C B:ASP364 4.5 48.1 1.0 N B:GLY366 4.5 49.8 1.0 N B:GLY365 4.6 50.6 1.0 C5' A:U22 4.6 31.1 1.0 CA B:GLY366 4.6 53.5 1.0 K B:K3369 4.9 72.7 1.0 P A:U23 4.9 33.1 1.0 HA3 B:GLY366 5.0 64.2 1.0

Potassium binding site 3 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3365 b:45.4 occ:1.00 O A:HOH3091 2.8 54.9 1.0 O B:GLN1350 2.9 44.7 1.0 O4' A:A68 3.1 42.3 1.0 O A:HOH3093 3.2 28.4 1.0 H1' A:A68 3.3 54.4 1.0 HG1 B:THR1098 3.5 39.6 1.0 C1' A:A68 3.7 45.4 1.0 HB2 B:GLN1350 3.7 42.3 1.0 H B:THR1098 3.9 45.1 1.0 C B:GLN1350 3.9 39.8 1.0 HG21 B:THR1098 3.9 34.3 1.0 O B:SER1351 4.0 36.7 1.0 H B:GLN1350 4.1 43.1 1.0 N9 A:A68 4.2 48.9 1.0 OG1 B:THR1098 4.2 33.0 1.0 H8 A:A68 4.3 59.9 1.0 O5' A:A68 4.3 31.5 1.0 C B:SER1351 4.3 32.4 1.0 HA B:ILE1352 4.3 34.8 1.0 HG12 B:VAL1095 4.3 48.6 1.0 C4' A:A68 4.4 41.1 1.0 HA B:LYS1097 4.4 39.5 1.0 C8 A:A68 4.4 50.0 1.0 O A:HOH3094 4.5 47.0 1.0 H4' A:A68 4.5 49.4 1.0 CB B:GLN1350 4.5 35.3 1.0 CA B:GLN1350 4.6 36.5 1.0 HA B:SER1351 4.7 36.8 1.0 CG2 B:THR1098 4.7 28.6 1.0 HG22 B:THR1098 4.7 34.3 1.0 OP1 A:A68 4.7 42.9 1.0 N B:GLN1350 4.7 36.0 1.0 N B:THR1098 4.7 37.6 1.0 N B:SER1351 4.7 34.7 1.0 HG13 B:VAL1095 4.8 48.6 1.0 HB3 B:GLN1350 4.8 42.3 1.0 HG11 B:VAL1095 4.8 48.6 1.0 CG1 B:VAL1095 4.8 40.5 1.0 CA B:SER1351 4.8 30.7 1.0 N B:ILE1352 4.9 27.4 1.0 P A:A68 4.9 34.0 1.0 C5' A:A68 4.9 29.9 1.0 OP2 A:A68 4.9 33.7 1.0

Potassium binding site 4 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3366 b:51.0 occ:1.00 O B:HOH3093 2.5 31.8 1.0 OD1 B:ASN588 2.8 40.8 1.0 O B:GLU584 2.8 46.0 1.0 O B:ARG586 2.9 44.1 1.0 O B:HOH3092 3.2 41.7 1.0 H B:ARG586 3.5 46.1 1.0 HD22 B:ASN588 3.5 41.8 1.0 CG B:ASN588 3.6 38.8 1.0 HB3 B:GLU584 3.7 68.2 1.0 H B:GLU584 3.8 47.5 1.0 ND2 B:ASN588 3.9 34.8 1.0 C B:GLU584 4.0 44.1 1.0 C B:ARG586 4.1 40.1 1.0 HG2 B:ARG586 4.1 64.5 1.0 N B:ARG586 4.3 38.4 1.0 HG3 B:ARG586 4.4 64.5 1.0 HB3 B:ASP585 4.5 60.1 1.0 CB B:GLU584 4.5 56.8 1.0 H B:ASN588 4.5 39.0 1.0 N B:GLU584 4.5 39.5 1.0 CA B:GLU584 4.6 44.8 1.0 OE1 B:GLU584 4.6 80.0 1.0 N B:ASN588 4.6 32.5 1.0 HA B:ASN588 4.6 42.3 1.0 HD21 B:ASN588 4.7 41.8 1.0 HG21 B:VAL583 4.7 40.4 1.0 CG B:ARG586 4.7 53.8 1.0 HG2 B:GLU584 4.7 83.3 1.0 CA B:ARG586 4.7 39.0 1.0 CB B:ASN588 4.9 38.8 1.0 HG23 B:VAL583 4.9 40.4 1.0 HA B:PHE587 4.9 45.4 1.0 C B:PHE587 4.9 36.7 1.0 CA B:ASN588 5.0 35.3 1.0

Potassium binding site 5 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3367 b:31.1 occ:1.00 OP2 A:A65 2.6 26.3 1.0 O4 A:U66 2.7 33.1 1.0 OG1 B:THR1102 2.9 41.9 1.0 O A:HOH3083 3.0 34.1 1.0 HG1 B:THR1102 3.4 50.3 1.0 H5 A:U66 3.4 38.9 1.0 HG22 B:THR1102 3.4 27.5 1.0 C4 A:U66 3.6 29.4 1.0 HG21 B:THR1102 3.8 27.5 1.0 C5 A:U66 3.9 32.4 1.0 CG2 B:THR1102 3.9 22.9 1.0 CB B:THR1102 3.9 33.6 1.0 P A:A65 4.0 30.1 1.0 H42 A:C67 4.1 36.1 1.0 OP1 A:U64 4.3 29.3 1.0 HB B:THR1102 4.4 40.4 1.0 O A:HOH3087 4.5 47.0 1.0 H3' A:U64 4.6 41.4 1.0 N7 A:A65 4.6 31.9 1.0 O5' A:A65 4.6 30.9 1.0 N4 A:C67 4.7 30.1 1.0 OP1 A:A65 4.7 29.5 1.0 H8 A:A65 4.7 34.1 1.0 H B:THR1102 4.7 38.0 1.0 OP2 A:U64 4.8 34.5 1.0 HG23 B:THR1102 4.8 27.5 1.0 N3 A:U66 4.8 27.1 1.0 P A:U64 4.9 31.6 1.0 H41 A:C67 4.9 36.1 1.0 O5' A:U64 4.9 32.6 1.0 C8 A:A65 4.9 28.4 1.0 O B:VAL1100 4.9 31.8 1.0

Potassium binding site 6 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3368 b:46.2 occ:0.97 O B:TYR656 2.7 43.1 1.0 O B:THR624 2.8 30.1 1.0 O B:LEU623 2.8 36.2 1.0 O B:PHE626 3.1 44.3 1.0 HA B:THR624 3.1 43.8 1.0 C B:THR624 3.4 35.9 1.0 HB3 B:GLU627 3.5 62.8 1.0 HG23 B:THR657 3.6 50.4 1.0 HA B:GLU627 3.6 61.7 1.0 C B:PHE626 3.7 39.2 1.0 CA B:THR624 3.7 36.5 1.0 H B:TYR656 3.8 50.6 1.0 C B:LEU623 3.9 35.2 1.0 C B:TYR656 3.9 40.0 1.0 HB3 B:ARG655 3.9 58.0 1.0 N B:GLU627 4.0 41.5 1.0 CA B:GLU627 4.1 51.4 1.0 H B:PHE626 4.2 52.3 1.0 CB B:GLU627 4.2 52.3 1.0 HA B:THR657 4.2 47.4 1.0 N B:THR624 4.3 40.7 1.0 N B:PHE626 4.3 43.6 1.0 HB2 B:GLU627 4.3 62.8 1.0 N B:TYR656 4.3 42.1 1.0 HG2 B:ARG655 4.3 76.7 1.0 HD2 B:ARG655 4.3 85.9 1.0 HG21 B:THR657 4.4 50.4 1.0 N B:LEU625 4.4 36.8 1.0 CG2 B:THR657 4.4 42.0 1.0 H B:GLU627 4.5 49.9 1.0 OP1 C:DC16 4.5 44.8 1.0 CA B:PHE626 4.6 39.8 1.0 C B:LEU625 4.7 44.8 1.0 CB B:ARG655 4.7 48.4 1.0 CA B:TYR656 4.8 43.2 1.0 N B:THR657 4.8 40.4 1.0 HG21 B:THR624 4.8 33.5 1.0 HD12 B:ILE632 4.8 58.2 1.0 CA B:THR657 4.9 39.5 1.0 HA B:ARG655 4.9 59.7 1.0 CG B:ARG655 4.9 63.9 1.0 H B:LEU625 4.9 44.1 1.0 HA B:PHE626 4.9 47.8 1.0

Potassium binding site 7 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3369 b:72.7 occ:1.00 O B:ALA367 2.5 44.1 1.0 O B:GLY365 2.9 59.0 1.0 O B:TYR362 2.9 31.2 1.0 H B:ALA367 3.1 57.5 1.0 N B:ALA367 3.3 47.9 1.0 HZ2 B:LYS401 3.3 58.2 1.0 C B:ALA367 3.4 41.6 1.0 HA2 B:GLY366 3.5 64.2 1.0 HA B:TYR362 3.5 58.9 1.0 O B:GLY361 3.5 50.8 1.0 C B:GLY365 3.6 49.7 1.0 C B:GLY366 3.7 50.7 1.0 C B:TYR362 3.8 42.9 1.0 HZ3 B:LYS401 3.8 58.2 1.0 CA B:GLY366 3.9 53.5 1.0 CA B:ALA367 3.9 46.6 1.0 NZ B:LYS401 3.9 48.5 1.0 N B:GLY366 4.0 49.8 1.0 CA B:TYR362 4.1 49.1 1.0 H B:GLY365 4.2 60.8 1.0 HZ1 B:LYS401 4.2 58.2 1.0 HB1 B:ALA367 4.3 63.0 1.0 HA B:SER368 4.3 49.7 1.0 O B:GLY366 4.4 41.9 1.0 N B:SER368 4.5 37.2 1.0 HD1 B:TYR362 4.6 48.7 1.0 N B:GLY365 4.6 50.6 1.0 C B:GLY361 4.6 52.1 1.0 CA B:GLY365 4.6 45.4 1.0 OP1 A:U22 4.7 35.2 1.0 CB B:ALA367 4.7 52.5 1.0 HA B:ALA367 4.7 55.9 1.0 H B:GLY366 4.7 59.8 1.0 HA3 B:GLY366 4.8 64.2 1.0 N B:ILE363 4.9 44.0 1.0 O B:ILE363 4.9 52.1 1.0 N B:TYR362 4.9 54.1 1.0 CA B:SER368 4.9 41.4 1.0 K A:K2082 4.9 88.5 1.0 HA3 B:GLY365 4.9 54.4 1.0

Potassium binding site 8 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3370 b:79.7 occ:1.00 O B:LEU229 1.5 84.4 1.0 H B:GLU232 2.5 95.7 1.0 O B:HOH3043 2.6 59.6 1.0 C B:LEU229 2.7 73.4 1.0 O B:ILE226 2.7 59.0 1.0 HA B:PRO230 2.9 83.1 1.0 O B:GLU232 3.0 74.5 1.0 H B:GLY231 3.0 87.2 1.0 N B:GLY231 3.2 72.7 1.0 N B:GLU232 3.3 79.7 1.0 CA B:PRO230 3.3 69.3 1.0 C B:PRO230 3.3 73.4 1.0 N B:PRO230 3.4 72.0 1.0 HB2 B:LEU229 3.6 72.0 1.0 HB3 B:GLU232 3.7 79.5 1.0 HD13 B:ILE226 3.7 84.4 1.0 CA B:LEU229 3.8 68.4 1.0 C B:GLU232 3.8 66.6 1.0 H B:LEU229 3.9 81.6 1.0 CA B:GLU232 4.0 70.4 1.0 C B:ILE226 4.0 61.0 1.0 O B:PRO230 4.1 75.9 1.0 C B:GLY231 4.1 81.4 1.0 N B:LEU229 4.1 68.0 1.0 CB B:LEU229 4.1 60.0 1.0 CA B:GLY231 4.1 75.7 1.0 CB B:GLU232 4.2 66.2 1.0 HA B:ALA227 4.2 74.7 1.0 O B:ALA227 4.2 70.9 1.0 HB2 B:GLU232 4.2 79.5 1.0 HB3 B:LEU229 4.3 72.0 1.0 HB B:ILE226 4.4 71.2 1.0 HA2 B:GLY231 4.4 90.8 1.0 HA B:LEU229 4.6 82.1 1.0 C B:ALA227 4.6 59.9 1.0 CD1 B:ILE226 4.6 70.4 1.0 CA B:ALA227 4.7 62.2 1.0 HD11 B:ILE226 4.8 84.4 1.0 HA B:ILE226 4.8 71.7 1.0 CB B:PRO230 4.8 69.5 1.0 N B:ALA227 4.8 66.9 1.0 CD B:PRO230 4.9 72.7 1.0 HA B:GLU232 4.9 84.5 1.0 CA B:ILE226 4.9 59.8 1.0 HA3 B:GLY231 5.0 90.8 1.0

Potassium binding site 9 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3371 b:77.2 occ:1.00 O B:HOH3028 2.5 43.1 1.0 O B:HOH3027 2.7 53.5 1.0 O B:LYS111 2.7 52.3 1.0 O B:GLU108 3.2 44.3 1.0 C B:LYS111 3.9 42.1 1.0 HB2 B:LYS111 3.9 49.8 1.0 H B:LYS111 4.0 41.1 1.0 O B:GLU109 4.1 58.5 1.0 N B:LYS111 4.3 34.2 1.0 HG2 B:GLU108 4.4 57.1 1.0 HA B:GLU109 4.4 60.6 1.0 CA B:LYS111 4.5 40.1 1.0 C B:GLU108 4.5 44.5 1.0 CB B:LYS111 4.5 41.5 1.0 C B:GLU109 4.5 50.8 1.0 HB3 B:LYS111 4.7 49.8 1.0 HA B:LYS112 4.8 54.3 1.0 CA B:GLU109 4.9 50.5 1.0 N B:LYS112 4.9 42.6 1.0

Potassium binding site 10 out of 13 in the Crystal Structure of SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna


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 SPYCAS9 Variant Vqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K3372 b:70.9 occ:1.00 O B:PHE643 2.9 66.7 1.0 O B:ALA640 3.1 57.6 1.0 HA B:ASP644 3.2 77.4 1.0 HA B:HIS641 3.5 61.3 1.0 C B:PHE643 3.7 59.3 1.0 O B:HIS641 3.9 59.6 1.0 CA B:ASP644 4.0 64.5 1.0 H B:ASP645 4.1 79.6 1.0 C B:ALA640 4.2 54.9 1.0 C B:HIS641 4.2 56.4 1.0 CA B:HIS641 4.2 51.1 1.0 N B:ASP644 4.2 59.6 1.0 H B:PHE643 4.3 70.1 1.0 N B:ASP645 4.3 66.3 1.0 C B:ASP644 4.5 62.1 1.0 OD1 B:ASP644 4.5 82.3 1.0 N B:PHE643 4.6 58.4 1.0 N B:HIS641 4.7 50.5 1.0 CA B:PHE643 4.8 58.7 1.0 HB2 B:ASP645 4.9 87.0 1.0 HA B:ASP645 5.0 79.3 1.0 H B:ASP644 5.0 71.5 1.0

C.Anders, K.Bargsten, M.Jinek. Structural Plasticity of Pam Recognition By Engineered Variants of the Rna-Guided Endonuclease CAS9. Mol.Cell V. 61 895 2016.
ISSN: ISSN 1097-2765
PubMed: 26990992
DOI: 10.1016/J.MOLCEL.2016.02.020