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Potassium in PDB 5b2t: Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)

Protein crystallography data

The structure of Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam), PDB code: 5b2t was solved by S.Hirano, H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.01 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.967, 69.448, 188.199, 90.00, 109.67, 90.00
R / Rfree (%) 20.4 / 22.3

Other elements in 5b2t:

The structure of Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) (pdb code 5b2t). 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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam), PDB code: 5b2t:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 5b2t

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Potassium binding site 1 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:29.7
occ:1.00
 O4 A:U66 2.7 33.8 1.0
OP2 A:A65 2.8 30.2 1.0
OG1 B:THR1102 2.8 28.4 1.0
O B:HOH1740 2.8 28.4 1.0
O A:HOH310 2.9 27.5 1.0
O A:HOH206 2.9 36.0 1.0
O A:HOH337 3.0 26.8 1.0
C4 A:U66 3.6 33.3 1.0
CG2 B:THR1102 3.8 28.6 1.0
C5 A:U66 3.9 33.2 1.0
CB B:THR1102 3.9 29.1 1.0
P A:A65 4.2 29.5 1.0
N4 A:C67 4.2 30.0 1.0
O B:HOH1610 4.3 32.1 1.0
OP1 A:U64 4.4 27.1 1.0
O A:HOH311 4.4 31.1 1.0
O B:HOH1773 4.5 34.3 1.0
N7 A:A65 4.6 33.3 1.0
O5' A:A65 4.7 32.1 1.0
O B:VAL1100 4.7 28.5 1.0
OP2 A:U64 4.9 30.2 1.0
N3 A:U66 4.9 31.8 1.0
OP1 A:A65 4.9 31.7 1.0
C8 A:A65 4.9 33.6 1.0
P A:U64 5.0 31.0 1.0
N B:THR1102 5.0 28.4 1.0
O A:HOH246 5.0 29.4 1.0

Potassium binding site 2 out of 10 in 5b2t

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Potassium binding site 2 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:36.8
occ:1.00
 O B:GLN1350 2.7 28.7 1.0
O B:HOH1794 2.8 37.8 1.0
O A:HOH286 2.8 42.4 1.0
O A:HOH287 2.8 35.1 1.0
O4' A:A68 3.1 36.8 1.0
C1' A:A68 3.6 35.3 1.0
O B:HOH1741 3.7 44.7 1.0
C B:GLN1350 3.9 31.4 1.0
O B:SER1351 4.0 32.0 1.0
O A:HOH317 4.2 36.0 1.0
C4' A:A68 4.2 34.1 1.0
C B:SER1351 4.2 31.2 1.0
N9 A:A68 4.3 36.1 1.0
OG1 B:THR1098 4.3 31.2 1.0
O5' A:A68 4.4 41.5 1.0
OP1 A:A68 4.6 35.0 1.0
C8 A:A68 4.6 41.5 1.0
OP2 A:A68 4.6 38.3 1.0
CA B:SER1351 4.7 30.3 1.0
O B:HOH1710 4.7 37.1 1.0
CA B:GLN1350 4.7 34.7 1.0
N B:SER1351 4.7 31.3 1.0
P A:A68 4.7 34.1 1.0
N B:ILE1352 4.7 31.8 1.0
CB B:GLN1350 4.8 37.4 1.0
CG1 B:VAL1095 4.8 28.6 1.0
N B:GLN1350 4.8 35.6 1.0
C5' A:A68 4.9 40.6 1.0
N B:THR1098 4.9 28.9 1.0
C2' A:A68 4.9 39.9 1.0
CA B:ILE1352 4.9 31.7 1.0
O2' A:A68 5.0 40.6 1.0

Potassium binding site 3 out of 10 in 5b2t

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Potassium binding site 3 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:39.6
occ:1.00
 O A:HOH379 2.8 41.9 1.0
O A:HOH263 2.8 32.4 1.0
O A:HOH370 2.8 36.2 1.0
OP2 A:G21 2.8 28.0 1.0
O A:HOH312 2.9 31.0 1.0
O A:HOH285 3.0 33.9 1.0
OP1 A:G21 3.1 31.8 1.0
P A:G21 3.4 30.8 1.0
O A:HOH375 3.5 57.5 1.0
O A:HOH299 4.1 33.8 1.0
O A:HOH245 4.1 48.9 1.0
CB B:ARG403 4.3 29.9 1.0
MG A:MG105 4.3 57.8 1.0
OP2 A:U45 4.4 33.8 1.0
O5' A:G21 4.4 33.5 1.0
O A:HOH243 4.6 32.9 1.0
O B:ARG403 4.7 31.1 1.0
O3' A:C20 4.7 29.3 1.0
O B:HOH1543 4.9 42.3 1.0
CG B:ARG403 4.9 30.0 1.0

Potassium binding site 4 out of 10 in 5b2t

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Potassium binding site 4 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1401

b:49.3
occ:1.00
 O B:TYR656 2.8 47.9 1.0
O C:HOH127 2.8 59.5 1.0
O B:PHE626 2.8 56.7 1.0
O B:LEU623 2.9 43.7 1.0
O B:THR624 2.9 38.7 1.0
C B:THR624 3.4 40.7 1.0
C B:PHE626 3.6 57.4 1.0
CA B:THR624 3.7 43.0 1.0
O B:HOH1715 3.7 50.3 1.0
C B:LEU623 3.8 43.5 1.0
C B:TYR656 3.9 48.1 1.0
N B:PHE626 4.1 53.8 1.0
N B:TYR656 4.2 52.0 1.0
N B:THR624 4.2 43.5 1.0
N B:GLU627 4.2 59.5 1.0
N B:LEU625 4.3 42.1 1.0
CA B:GLU627 4.3 61.2 1.0
CA B:PHE626 4.5 55.8 1.0
C B:LEU625 4.5 42.8 1.0
CB B:ARG655 4.5 59.6 1.0
CG2 B:THR657 4.7 46.8 1.0
CA B:TYR656 4.7 49.6 1.0
CB B:GLU627 4.8 65.1 1.0
N B:THR657 4.9 47.1 1.0
C B:ARG655 4.9 54.5 1.0
CA B:LEU625 4.9 43.9 1.0
O B:LEU625 4.9 41.5 1.0
CG B:ARG655 4.9 62.2 1.0
CA B:ARG655 5.0 57.6 1.0

Potassium binding site 5 out of 10 in 5b2t

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Potassium binding site 5 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1402

b:48.2
occ:1.00
 O B:ALA367 2.8 47.1 1.0
O B:GLY365 2.8 46.9 1.0
O B:TYR362 2.8 39.9 1.0
O B:GLY361 3.1 43.8 1.0
N B:ALA367 3.5 48.0 1.0
C B:TYR362 3.5 41.0 1.0
C B:GLY365 3.6 47.5 1.0
C B:ALA367 3.7 47.5 1.0
C B:GLY366 3.9 50.6 1.0
CA B:TYR362 4.0 41.8 1.0
CA B:GLY366 4.1 48.0 1.0
NZ B:LYS401 4.1 38.7 1.0
CA B:ALA367 4.2 48.5 1.0
N B:GLY366 4.2 47.3 1.0
C B:GLY361 4.2 44.1 1.0
N B:ILE363 4.5 40.4 1.0
K B:K1403 4.5 70.1 1.0
OP1 A:U22 4.5 37.5 1.0
N B:GLY365 4.5 47.8 1.0
N B:TYR362 4.6 43.5 1.0
CA B:GLY365 4.7 47.0 1.0
C B:ILE363 4.7 42.9 1.0
O B:GLY366 4.7 54.3 1.0
O B:ILE363 4.7 41.9 1.0
N B:SER368 4.8 46.2 1.0
CB B:ALA367 4.8 50.3 1.0
CA B:ILE363 4.9 40.7 1.0
N B:ASP364 5.0 45.5 1.0
C B:ASP364 5.0 46.1 1.0

Potassium binding site 6 out of 10 in 5b2t

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Potassium binding site 6 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1403

b:70.1
occ:1.00
 OP1 A:U22 2.8 37.5 1.0
O B:GLY365 2.8 46.9 1.0
O B:ASP364 3.4 45.7 1.0
C B:GLY365 3.8 47.5 1.0
P A:U22 3.8 35.2 1.0
O B:HOH1842 4.0 58.8 1.0
C B:ASP364 4.1 46.1 1.0
O5' A:U22 4.1 35.9 1.0
OP2 A:U22 4.2 33.8 1.0
OP2 A:U23 4.3 40.8 1.0
CA B:GLY365 4.5 47.0 1.0
K B:K1402 4.5 48.2 1.0
N B:GLY365 4.5 47.8 1.0
N B:GLY366 4.6 47.3 1.0
C5' A:U22 4.7 37.4 1.0
CA B:GLY366 4.7 48.0 1.0
CA B:ASP364 4.9 46.2 1.0

Potassium binding site 7 out of 10 in 5b2t

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Potassium binding site 7 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1404

b:70.4
occ:1.00
 O B:HOH1862 2.8 39.9 1.0
O B:HOH1848 2.8 34.0 1.0
OE2 B:GLU57 2.8 38.0 1.0
O B:HOH1773 2.9 34.3 1.0
O B:HOH1656 2.9 34.1 1.0
O A:HOH206 3.0 36.0 1.0
CD B:GLU57 3.4 34.9 1.0
OE1 B:GLU57 3.9 33.1 1.0
O B:HOH1610 4.1 32.1 1.0
O B:HOH1740 4.1 28.4 1.0
O A:HOH321 4.2 41.5 1.0
CG B:GLU57 4.3 33.0 1.0
O B:HOH1665 4.8 48.7 1.0
O B:SER55 4.9 30.8 1.0
OP2 A:A65 4.9 30.2 1.0
OP1 A:U64 4.9 27.1 1.0
OP1 A:A65 5.0 31.7 1.0

Potassium binding site 8 out of 10 in 5b2t

Go back to Potassium Binding Sites List in 5b2t
Potassium binding site 8 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1405

b:70.6
occ:1.00
 O B:LYS111 2.8 46.4 1.0
O B:HOH1850 2.8 64.2 1.0
O B:GLU108 2.8 38.5 1.0
O B:GLU109 3.5 45.4 1.0
C B:LYS111 3.8 44.5 1.0
C B:GLU109 3.9 45.7 1.0
C B:GLU108 4.0 39.2 1.0
N B:LYS111 4.2 39.5 1.0
CA B:GLU109 4.2 46.9 1.0
CA B:LYS111 4.4 41.2 1.0
O B:HOH1732 4.5 43.7 1.0
N B:GLU109 4.6 40.8 1.0
CB B:LYS111 4.6 40.7 1.0
N B:ASP110 4.7 41.5 1.0
C B:ASP110 4.8 41.2 1.0
O B:HOH1567 4.8 57.7 1.0
N B:LYS112 4.9 44.9 1.0

Potassium binding site 9 out of 10 in 5b2t

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Potassium binding site 9 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1406

b:0.9
occ:1.00
 O B:ILE226 2.9 75.8 1.0
O B:LEU229 3.0 84.9 1.0
O B:GLU232 3.1 76.0 1.0
CG2 B:ILE226 3.8 74.7 1.0
C B:ILE226 3.8 75.7 1.0
C B:LEU229 4.0 84.9 1.0
CA B:ALA227 4.1 78.4 1.0
N B:ALA227 4.3 76.5 1.0
C B:GLU232 4.3 76.6 1.0
O B:ALA227 4.4 81.5 1.0
CA B:PRO230 4.5 84.6 1.0
C B:ALA227 4.5 80.7 1.0
N B:GLU232 4.5 80.1 1.0
N B:GLY231 4.5 82.8 1.0
N B:PRO230 4.7 84.4 1.0
CA B:ILE226 4.8 74.6 1.0
C B:PRO230 4.8 83.3 1.0
CB B:ILE226 4.9 73.9 1.0
N B:LEU229 4.9 83.6 1.0
CA B:GLU232 4.9 78.3 1.0

Potassium binding site 10 out of 10 in 5b2t

Go back to Potassium Binding Sites List in 5b2t
Potassium binding site 10 out of 10 in the Crystal Structure of the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam)


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 the Streptococcus Pyogenes CAS9 Vrer Variant in Complex with Sgrna and Target Dna (Tgcg Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1407

b:0.1
occ:1.00
 O B:HOH1852 2.9 59.1 1.0
OD1 B:ASN588 2.9 60.0 1.0
O B:GLU584 3.0 85.7 1.0
O B:ARG586 3.0 78.9 1.0
O B:HOH1661 3.5 63.7 1.0
CG B:ASN588 3.7 59.6 1.0
ND2 B:ASN588 4.0 59.6 1.0
C B:GLU584 4.0 85.2 1.0
C B:ARG586 4.2 77.1 1.0
N B:ARG586 4.4 81.3 1.0
N B:GLU584 4.4 78.2 1.0
CB B:GLU584 4.5 86.6 1.0
CA B:GLU584 4.6 84.2 1.0
N B:ASN588 4.8 62.4 1.0
CA B:ARG586 4.9 80.6 1.0
CG B:ARG586 4.9 82.6 1.0

Reference:

S.Hirano, H.Nishimasu, R.Ishitani, O.Nureki. Structural Basis For the Altered Pam Specificities of Engineered Crispr-CAS9 Mol.Cell V. 61 886 2016.
ISSN: ISSN 1097-2765
PubMed: 26990991
DOI: 10.1016/J.MOLCEL.2016.02.018
Page generated: Mon Aug 12 12:59:29 2024

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