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Potassium in PDB 5fw2: Crystal Structure of SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna

Protein crystallography data

The structure of Crystal Structure of SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna, PDB code: 5fw2 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) 48.25 / 2.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.740, 68.240, 188.220, 90.00, 110.95, 90.00
R / Rfree (%) 20.5 / 23.1

Other elements in 5fw2:

The structure of Crystal Structure of SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna (pdb code 5fw2). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Crystal Structure of SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna, PDB code: 5fw2:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 5fw2

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Potassium binding site 1 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1182

b:79.9
occ:1.00
 O A:HOH2001 2.2 30.0 1.0
O A:HOH2023 2.5 30.0 1.0
OP2 A:G21 2.8 29.5 1.0
O A:HOH2038 2.9 30.0 1.0
O A:HOH2037 2.9 30.0 1.0
O A:HOH2022 3.0 30.0 1.0
HB2 B:ARG403 3.7 45.0 1.0
P A:G21 3.8 29.8 1.0
OP1 A:G21 3.9 28.8 1.0
O A:HOH2026 4.0 43.3 1.0
O A:HOH2041 4.0 39.2 1.0
O A:HOH2021 4.2 35.0 1.0
OP2 A:U45 4.2 32.4 1.0
MG A:MG1083 4.3 63.5 1.0
HB3 B:ARG403 4.4 45.0 1.0
CB B:ARG403 4.5 37.5 1.0
O A:HOH2039 4.5 44.0 1.0
HG3 B:ARG403 4.5 43.8 1.0
O5' A:G21 4.7 29.8 1.0
O B:ARG403 5.0 36.6 1.0
H5'' A:A20 5.0 32.3 1.0

Potassium binding site 2 out of 10 in 5fw2

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Potassium binding site 2 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1183

b:50.0
occ:1.00
 O A:HOH2012 2.8 30.0 1.0
O6 A:G13 3.3 25.1 1.0
O4 A:U12 3.5 32.5 1.0
H41 C:DC16 3.7 36.5 1.0
H5 A:U12 4.1 33.8 1.0
H42 C:DC16 4.2 36.5 1.0
H61 C:DA17 4.3 40.2 1.0
C4 A:U12 4.3 31.0 1.0
N4 C:DC16 4.3 30.4 1.0
C6 A:G13 4.4 25.3 1.0
C5 A:U12 4.5 28.2 1.0
N7 A:G13 4.8 26.0 1.0
N6 C:DA17 4.9 33.5 1.0

Potassium binding site 3 out of 10 in 5fw2

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Potassium binding site 3 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2366

b:39.2
occ:1.00
 O B:GLN1350 2.7 33.4 1.0
O B:HOH2075 2.7 30.0 1.0
O A:HOH2081 2.8 35.0 1.0
O B:HOH2105 3.0 44.6 1.0
O4' A:A68 3.1 29.8 1.0
H1' A:A68 3.4 41.2 1.0
HG1 B:THR1098 3.7 37.8 1.0
C B:GLN1350 3.7 30.1 1.0
C1' A:A68 3.7 34.4 1.0
HB2 B:GLN1350 3.8 35.3 1.0
H B:THR1098 4.0 34.1 1.0
O A:HOH2079 4.1 44.2 1.0
O B:SER1351 4.1 30.1 1.0
HA B:SER1351 4.1 36.0 1.0
HG21 B:THR1098 4.2 34.2 1.0
N9 A:A68 4.2 37.0 1.0
H B:GLN1350 4.2 35.3 1.0
HA B:ILE1352 4.2 39.8 1.0
C B:SER1351 4.2 32.8 1.0
O5' A:A68 4.3 27.3 1.0
HA B:LYS1097 4.3 33.5 1.0
HG12 B:VAL1095 4.3 38.9 1.0
H8 A:A68 4.4 43.1 1.0
C4' A:A68 4.4 29.4 1.0
OG1 B:THR1098 4.4 31.5 1.0
CB B:GLN1350 4.5 29.4 1.0
HB3 B:GLN1350 4.5 35.3 1.0
C8 A:A68 4.5 35.9 1.0
CA B:GLN1350 4.5 30.3 1.0
CA B:SER1351 4.5 30.0 1.0
H4' A:A68 4.6 35.3 1.0
N B:SER1351 4.6 29.8 1.0
OP1 A:A68 4.6 28.6 1.0
N B:ILE1352 4.7 34.5 1.0
N B:GLN1350 4.7 29.4 1.0
HG11 B:VAL1095 4.8 38.9 1.0
HG13 B:VAL1095 4.8 38.9 1.0
P A:A68 4.8 27.4 1.0
N B:THR1098 4.8 28.4 1.0
CG1 B:VAL1095 4.8 32.4 1.0
C5' A:A68 4.9 27.8 1.0
OP2 A:A68 4.9 26.8 1.0
O B:HOH2106 4.9 30.0 1.0
CG2 B:THR1098 4.9 28.5 1.0
CA B:ILE1352 4.9 33.2 1.0
HG22 B:THR1098 5.0 34.2 1.0

Potassium binding site 4 out of 10 in 5fw2

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Potassium binding site 4 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2367

b:57.7
occ:1.00
 O B:HOH2052 2.6 30.0 1.0
OD1 B:ASN588 2.8 33.6 1.0
O B:ARG586 2.9 52.1 1.0
O B:HOH2053 2.9 37.4 1.0
O B:GLU584 3.0 65.3 1.0
H B:ARG586 3.6 70.4 1.0
CG B:ASN588 3.8 33.8 1.0
H B:GLU584 3.8 74.1 1.0
HD22 B:ASN588 3.9 40.9 1.0
HB3 B:GLU584 3.9 86.2 1.0
HG3 B:ARG586 4.1 72.5 1.0
C B:ARG586 4.1 52.1 1.0
C B:GLU584 4.1 64.8 1.0
ND2 B:ASN588 4.2 34.0 1.0
HB3 B:ASP585 4.3 96.2 1.0
N B:ARG586 4.4 58.6 1.0
HG21 B:VAL583 4.5 49.9 1.0
OE1 B:GLU584 4.5 73.9 1.0
N B:GLU584 4.5 61.7 1.0
H B:ASN588 4.6 41.9 1.0
N B:ASN588 4.7 34.9 1.0
HA B:ASN588 4.7 41.0 1.0
CA B:GLU584 4.7 65.8 1.0
CB B:GLU584 4.7 71.8 1.0
CA B:ARG586 4.8 56.5 1.0
HG2 B:ARG586 4.9 72.5 1.0
HA B:PHE587 4.9 55.2 1.0
CG B:ARG586 4.9 60.4 1.0
C B:PHE587 4.9 42.1 1.0
HG23 B:VAL583 5.0 49.9 1.0

Potassium binding site 5 out of 10 in 5fw2

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Potassium binding site 5 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2368

b:32.7
occ:1.00
 O A:HOH2077 2.4 30.0 1.0
OP2 A:A65 2.7 23.9 1.0
O4 A:U66 2.7 28.3 1.0
O A:HOH2073 2.7 30.0 1.0
O A:HOH2072 2.8 30.0 1.0
OG1 B:THR1102 2.9 31.5 1.0
O A:HOH2078 3.0 30.0 1.0
H5 A:U66 3.3 32.4 1.0
HG1 B:THR1102 3.4 37.8 1.0
HG22 B:THR1102 3.5 31.9 1.0
C4 A:U66 3.6 27.1 1.0
HG21 B:THR1102 3.8 31.9 1.0
C5 A:U66 3.8 27.0 1.0
CG2 B:THR1102 3.9 26.5 1.0
CB B:THR1102 4.0 28.6 1.0
P A:A65 4.1 22.6 1.0
H42 A:C67 4.1 26.6 1.0
N7 A:A65 4.3 21.7 1.0
OP1 A:U64 4.3 24.5 1.0
HB B:THR1102 4.4 34.3 1.0
H8 A:A65 4.5 26.7 1.0
H3' A:U64 4.6 33.5 1.0
O5' A:A65 4.6 22.8 1.0
C8 A:A65 4.7 22.2 1.0
N4 A:C67 4.7 22.2 1.0
OP1 A:A65 4.8 20.9 1.0
H B:THR1102 4.8 33.9 1.0
OP2 A:U64 4.8 23.4 1.0
HG23 B:THR1102 4.8 31.9 1.0
N3 A:U66 4.9 25.6 1.0
P A:U64 4.9 22.1 1.0
O5' A:U64 4.9 22.1 1.0
H41 A:C67 5.0 26.6 1.0
O B:VAL1100 5.0 22.8 1.0

Potassium binding site 6 out of 10 in 5fw2

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Potassium binding site 6 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2369

b:43.4
occ:1.00
 O B:HOH2057 2.4 30.0 1.0
O B:TYR656 2.7 34.1 1.0
O C:HOH2007 2.7 30.0 1.0
O B:THR624 2.8 25.7 1.0
O B:LEU623 2.8 24.8 1.0
O B:PHE626 3.0 38.7 1.0
HA B:THR624 3.0 33.8 1.0
C B:THR624 3.4 27.2 1.0
HB3 B:GLU627 3.5 60.8 1.0
H B:TYR656 3.5 42.2 1.0
HA B:GLU627 3.6 60.8 1.0
C B:PHE626 3.6 37.1 1.0
CA B:THR624 3.6 28.2 1.0
HG23 B:THR657 3.6 50.8 1.0
HB3 B:ARG655 3.6 65.1 1.0
C B:LEU623 3.8 24.3 1.0
C B:TYR656 3.9 33.2 1.0
N B:GLU627 4.0 46.0 1.0
HB2 B:GLU627 4.0 60.8 1.0
CB B:GLU627 4.1 50.7 1.0
CA B:GLU627 4.1 50.6 1.0
N B:TYR656 4.1 35.2 1.0
N B:THR624 4.1 25.6 1.0
HD2 B:ARG655 4.2 77.3 1.0
HG2 B:ARG655 4.3 73.0 1.0
N B:PHE626 4.3 33.9 1.0
H B:PHE626 4.3 40.6 1.0
HG21 B:THR657 4.4 50.8 1.0
HA B:THR657 4.4 46.2 1.0
CG2 B:THR657 4.4 42.3 1.0
CB B:ARG655 4.5 54.2 1.0
N B:LEU625 4.5 27.8 1.0
CA B:PHE626 4.6 37.0 1.0
C B:LEU625 4.6 30.9 1.0
H B:GLU627 4.6 55.2 1.0
HA B:ARG655 4.6 61.1 1.0
CA B:TYR656 4.6 33.5 1.0
OP1 C:DC16 4.7 36.1 1.0
CG B:ARG655 4.7 60.8 1.0
HG21 B:THR624 4.8 38.0 1.0
HD12 B:ILE632 4.8 35.9 1.0
N B:THR657 4.8 36.0 1.0
C B:ARG655 4.9 47.9 1.0
O B:LEU625 4.9 28.9 1.0
CD B:ARG655 4.9 64.5 1.0
CA B:ARG655 4.9 51.0 1.0
H B:THR624 4.9 30.8 1.0
HA B:LEU623 5.0 31.0 1.0
CB B:THR624 5.0 29.1 1.0
HA B:PHE626 5.0 44.5 1.0

Potassium binding site 7 out of 10 in 5fw2

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Potassium binding site 7 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2370

b:50.0
occ:1.00
 H B:ALA367 1.9 50.3 1.0
N B:ALA367 2.4 42.0 1.0
O B:ALA367 2.5 43.5 1.0
O B:GLY361 2.8 43.1 1.0
O B:GLY365 2.8 57.0 1.0
O B:TYR362 2.8 31.9 1.0
C B:ALA367 3.1 41.8 1.0
HA2 B:GLY366 3.2 65.0 1.0
C B:GLY366 3.2 52.6 1.0
HA B:TYR362 3.2 43.3 1.0
C B:GLY365 3.2 53.3 1.0
CA B:ALA367 3.2 40.9 1.0
HB1 B:ALA367 3.3 50.0 1.0
CA B:GLY366 3.5 54.2 1.0
C B:TYR362 3.5 33.6 1.0
N B:GLY366 3.6 55.0 1.0
CA B:TYR362 3.8 36.1 1.0
HZ2 B:LYS401 3.8 38.0 1.0
CB B:ALA367 3.8 41.7 1.0
C B:GLY361 3.8 43.4 1.0
H B:GLY365 3.9 62.4 1.0
HA B:ALA367 4.1 49.1 1.0
O B:GLY366 4.2 50.1 1.0
CA B:GLY365 4.2 51.2 1.0
H B:GLY366 4.2 66.0 1.0
N B:GLY365 4.2 52.0 1.0
N B:TYR362 4.3 39.5 1.0
HB3 B:ALA367 4.3 50.0 1.0
N B:SER368 4.4 44.6 1.0
HZ3 B:LYS401 4.4 38.0 1.0
HA3 B:GLY365 4.4 61.5 1.0
HA3 B:GLY366 4.4 65.0 1.0
NZ B:LYS401 4.5 31.7 1.0
HD1 B:TYR362 4.5 50.0 1.0
N B:ILE363 4.6 33.6 1.0
HB2 B:ALA367 4.6 50.0 1.0
HA B:SER368 4.6 51.7 1.0
HZ1 B:LYS401 4.8 38.0 1.0
C B:ILE363 4.9 37.2 1.0
H B:SER368 5.0 53.5 1.0
OP1 A:U22 5.0 28.8 1.0

Potassium binding site 8 out of 10 in 5fw2

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Potassium binding site 8 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2371

b:50.0
occ:1.00
 O B:ALA640 2.9 80.5 1.0
O B:PHE643 3.0 73.0 1.0
HA B:HIS641 3.2 79.7 1.0
HA B:ASP644 3.5 93.5 1.0
C B:PHE643 4.0 73.6 1.0
C B:ALA640 4.0 76.3 1.0
CA B:HIS641 4.0 66.4 1.0
CA B:ASP644 4.3 78.0 1.0
O B:HIS641 4.3 70.1 1.0
C B:HIS641 4.4 66.0 1.0
H B:PHE643 4.4 81.3 1.0
N B:HIS641 4.5 64.2 1.0
N B:ASP644 4.6 75.8 1.0
C B:ASP644 4.7 79.6 1.0
OD1 B:ASP644 4.7 78.4 1.0
N B:PHE643 4.8 67.8 1.0
HB2 B:ALA640 4.9 91.1 1.0
H B:ASP645 4.9 0.9 1.0
N B:ASP645 4.9 94.9 1.0

Potassium binding site 9 out of 10 in 5fw2

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Potassium binding site 9 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2372

b:50.0
occ:1.00
 O B:HOH2007 2.5 30.0 1.0
O B:HOH2001 2.8 30.0 1.0
O A:HOH2073 3.0 30.0 1.0
H B:THR1102 3.2 33.9 1.0
O B:HOH2008 3.3 30.0 1.0
O B:THR1102 3.5 24.7 1.0
HG1 B:THR1102 3.9 37.8 1.0
HE22 B:GLN1101 4.0 41.0 1.0
N B:THR1102 4.0 28.2 1.0
O A:HOH2077 4.0 30.0 1.0
HA B:GLN1101 4.1 33.4 1.0
OG1 B:THR1102 4.1 31.5 1.0
NE2 B:GLN1101 4.2 34.1 1.0
C B:THR1102 4.3 24.2 1.0
OE2 B:GLU57 4.3 34.7 1.0
HE21 B:GLN1101 4.4 41.0 1.0
OP1 A:U64 4.5 24.5 1.0
HB3 B:GLN1101 4.6 36.6 1.0
CA B:THR1102 4.7 27.4 1.0
CD B:GLN1101 4.8 30.7 1.0
CA B:GLN1101 4.9 27.8 1.0
CD B:GLU57 4.9 35.4 1.0
OE1 B:GLU57 4.9 36.7 1.0
C B:GLN1101 5.0 25.1 1.0
HA3 B:GLY1103 5.0 23.2 1.0

Potassium binding site 10 out of 10 in 5fw2

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Potassium binding site 10 out of 10 in the Crystal Structure of SPCAS9 Variant Eqr 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 SPCAS9 Variant Eqr Bound to Sgrna and Tgag Pam Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2373

b:50.0
occ:1.00
 O B:HOH2013 2.4 30.0 1.0
O B:HOH2011 2.4 30.0 1.0
O B:HOH2012 2.5 58.5 1.0
O B:LYS111 3.4 34.3 1.0
O B:LYS112 4.2 48.1 1.0
C B:LYS111 4.4 34.2 1.0
HA B:LYS112 4.6 54.5 1.0
C B:LYS112 4.6 44.4 1.0
O B:GLU108 4.8 37.6 1.0
O B:HIS113 4.9 28.6 1.0
HB2 B:LYS111 4.9 39.1 1.0
CA B:LYS112 5.0 45.4 1.0

Reference:

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
Page generated: Mon Aug 12 13:35:58 2024

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