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Potassium in PDB 6ai6: Crystal Structure of SPCAS9-Ng

Protein crystallography data

The structure of Crystal Structure of SPCAS9-Ng, PDB code: 6ai6 was solved by H.Nishimasu, S.Hirano, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.377, 68.568, 187.968, 90.00, 111.51, 90.00
R / Rfree (%) 21.8 / 24.4

Other elements in 6ai6:

The structure of Crystal Structure of SPCAS9-Ng also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of SPCAS9-Ng (pdb code 6ai6). 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-Ng, PDB code: 6ai6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 6ai6

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Potassium binding site 1 out of 10 in the Crystal Structure of SPCAS9-Ng


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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-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1401

b:67.8
occ:1.00
 O A:TYR656 2.7 68.1 1.0
O A:PHE626 2.8 74.3 1.0
O A:THR624 3.0 61.2 1.0
O A:LEU623 3.0 62.6 1.0
C A:THR624 3.6 60.8 1.0
C A:PHE626 3.6 75.7 1.0
CA A:THR624 3.8 58.8 1.0
C A:TYR656 3.9 68.1 1.0
CG2 A:THR657 4.0 68.2 1.0
C A:LEU623 4.0 61.0 1.0
N A:PHE626 4.2 71.8 1.0
N A:GLU627 4.3 79.7 1.0
N A:TYR656 4.3 78.4 1.0
N A:THR624 4.4 57.8 1.0
CA A:GLU627 4.4 83.2 1.0
CB A:ARG655 4.4 97.2 1.0
CA A:PHE626 4.5 73.1 1.0
CB A:GLU627 4.6 84.4 1.0
N A:LEU625 4.6 62.1 1.0
OP1 C:DG16 4.6 84.6 1.0
C A:LEU625 4.7 67.9 1.0
CA A:TYR656 4.8 72.5 1.0
N A:THR657 4.8 65.5 1.0
CA A:THR657 4.9 65.5 1.0

Potassium binding site 2 out of 10 in 6ai6

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Potassium binding site 2 out of 10 in the Crystal Structure of SPCAS9-Ng


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1402

b:82.9
occ:1.00
 O A:ALA367 2.8 77.4 1.0
O A:GLY365 3.0 85.6 1.0
O A:TYR362 3.0 61.2 1.0
O A:GLY361 3.3 70.9 1.0
N A:ALA367 3.5 85.7 1.0
C A:TYR362 3.7 64.5 1.0
C A:ALA367 3.7 78.1 1.0
C A:GLY365 3.7 86.9 1.0
C A:GLY366 3.9 88.4 1.0
CA A:GLY366 4.0 88.7 1.0
NZ A:LYS401 4.0 61.6 1.0
CA A:TYR362 4.1 68.0 1.0
N A:GLY366 4.2 90.0 1.0
CA A:ALA367 4.2 81.7 1.0
C A:GLY361 4.4 72.2 1.0
OP1 B:U22 4.5 54.9 1.0
N A:ILE363 4.6 64.7 1.0
O A:GLY366 4.6 89.0 1.0
K A:K1408 4.6 0.4 1.0
O A:ILE363 4.7 69.5 1.0
N A:SER368 4.7 74.4 1.0
N A:GLY365 4.7 82.5 1.0
C A:ILE363 4.7 69.1 1.0
N A:TYR362 4.8 72.2 1.0
CA A:GLY365 4.8 85.4 1.0
CB A:ALA367 4.9 82.2 1.0
CA A:ILE363 5.0 64.3 1.0

Potassium binding site 3 out of 10 in 6ai6

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Potassium binding site 3 out of 10 in the Crystal Structure of SPCAS9-Ng


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1403

b:0.0
occ:1.00
 OE2 A:GLU57 3.3 75.9 1.0
CD A:GLU57 4.1 73.2 1.0
OE1 A:GLN1101 4.4 53.2 1.0
OE1 A:GLU57 4.8 74.5 1.0
O A:THR1102 4.8 48.0 1.0
CG A:GLU57 4.9 68.7 1.0

Potassium binding site 4 out of 10 in 6ai6

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Potassium binding site 4 out of 10 in the Crystal Structure of SPCAS9-Ng


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1404

b:0.0
occ:1.00
 O A:LYS111 3.1 73.2 1.0
C A:LYS111 4.1 68.3 1.0
O A:HIS113 4.2 63.7 1.0
C A:LYS112 4.3 71.1 1.0
O A:GLU108 4.3 66.7 1.0
O A:LYS112 4.4 74.9 1.0
CA A:LYS112 4.5 71.1 1.0
N A:HIS113 4.6 65.1 1.0
N A:LYS112 4.7 69.2 1.0
C A:HIS113 4.8 63.1 1.0
CB A:LYS111 5.0 61.8 1.0

Potassium binding site 5 out of 10 in 6ai6

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Potassium binding site 5 out of 10 in the Crystal Structure of SPCAS9-Ng


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1405

b:0.5
occ:1.00
 O A:LEU229 2.9 0.3 1.0
O A:ILE226 3.0 0.2 1.0
O A:GLU232 3.2 0.5 1.0
CG2 A:ILE226 3.8 0.8 1.0
N A:GLU232 3.9 0.3 1.0
C A:ILE226 3.9 0.1 1.0
C A:GLU232 3.9 0.7 1.0
C A:LEU229 4.0 0.2 1.0
CA A:PRO230 4.3 0.8 1.0
N A:GLY231 4.3 0.1 1.0
CA A:GLU232 4.4 0.4 1.0
CA A:ALA227 4.5 0.9 1.0
N A:ALA227 4.6 0.5 1.0
C A:PRO230 4.6 0.6 1.0
N A:PRO230 4.7 0.7 1.0
CB A:GLU232 4.7 0.2 1.0
O A:ALA227 4.8 0.7 1.0
C A:ALA227 4.9 0.6 1.0
CA A:ILE226 4.9 0.2 1.0
N A:LYS233 4.9 0.8 1.0
CB A:ILE226 5.0 0.2 1.0
C A:GLY231 5.0 0.5 1.0

Potassium binding site 6 out of 10 in 6ai6

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Potassium binding site 6 out of 10 in the Crystal Structure of SPCAS9-Ng


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-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1406

b:0.7
occ:1.00
 O A:GLU584 2.9 0.1 1.0
O A:ARG586 2.9 88.5 1.0
OD1 A:ASN588 3.1 67.0 1.0
CG A:ASN588 4.0 64.6 1.0
C A:GLU584 4.0 0.9 1.0
C A:ARG586 4.1 89.1 1.0
N A:ARG586 4.3 0.2 1.0
ND2 A:ASN588 4.3 63.2 1.0
N A:GLU584 4.4 93.6 1.0
CG A:ARG586 4.5 94.9 1.0
CA A:GLU584 4.7 0.7 1.0
CA A:ARG586 4.7 94.7 1.0
CB A:GLU584 4.8 0.2 1.0
N A:ASN588 4.9 67.9 1.0
CB A:ASP585 5.0 0.1 1.0
CG2 A:VAL583 5.0 76.3 1.0

Potassium binding site 7 out of 10 in 6ai6

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Potassium binding site 7 out of 10 in the Crystal Structure of SPCAS9-Ng


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-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1407

b:64.8
occ:1.00
 O A:GLN1350 2.8 51.6 1.0
O A:HOH1506 2.8 30.3 1.0
O4' B:A68 3.2 55.5 1.0
C1' B:A68 3.8 58.7 1.0
C A:GLN1350 3.9 51.0 1.0
O A:SER1351 4.2 45.5 1.0
C4' B:A68 4.3 54.0 1.0
C A:SER1351 4.3 47.4 1.0
OG1 A:THR1098 4.4 46.8 1.0
O5' B:A68 4.4 49.3 1.0
N9 B:A68 4.4 58.1 1.0
OP1 B:A68 4.6 58.3 1.0
CG1 A:VAL1095 4.7 44.3 1.0
N A:THR1098 4.7 51.3 1.0
CB A:GLN1350 4.7 54.1 1.0
CA A:GLN1350 4.7 53.0 1.0
CA A:SER1351 4.7 50.5 1.0
N A:SER1351 4.8 51.0 1.0
OP2 B:A68 4.8 49.3 1.0
P B:A68 4.8 52.9 1.0
N A:ILE1352 4.8 48.9 1.0
C8 B:A68 4.8 56.8 1.0
N A:GLN1350 4.8 52.3 1.0
CG2 A:THR1098 4.9 42.7 1.0
C5' B:A68 5.0 50.6 1.0

Potassium binding site 8 out of 10 in 6ai6

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Potassium binding site 8 out of 10 in the Crystal Structure of SPCAS9-Ng


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-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1408

b:0.4
occ:1.00
 O A:GLY365 2.9 85.6 1.0
OP1 B:U22 3.0 54.9 1.0
O A:ASP364 3.5 74.3 1.0
C A:GLY365 3.9 86.9 1.0
P B:U22 3.9 54.2 1.0
OP2 B:U23 4.1 62.3 1.0
C A:ASP364 4.1 77.3 1.0
OP2 B:U22 4.2 53.5 1.0
O5' B:U22 4.3 52.4 1.0
K A:K1402 4.6 82.9 1.0
CA A:GLY365 4.7 85.4 1.0
N A:GLY365 4.7 82.5 1.0
N A:GLY366 4.7 90.0 1.0
CA A:GLY366 4.8 88.7 1.0
CA A:ASP364 4.9 76.5 1.0
C5' B:U22 5.0 55.8 1.0
O A:ILE363 5.0 69.5 1.0

Potassium binding site 9 out of 10 in 6ai6

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Potassium binding site 9 out of 10 in the Crystal Structure of SPCAS9-Ng


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-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1413

b:62.0
occ:1.00
 OP2 B:A65 2.8 54.0 1.0
O4 B:U66 2.8 49.0 1.0
OG1 A:THR1102 2.9 50.2 1.0
C4 B:U66 3.6 50.6 1.0
CG2 A:THR1102 3.8 44.6 1.0
C5 B:U66 3.8 54.0 1.0
CB A:THR1102 3.9 47.2 1.0
P B:A65 4.1 47.9 1.0
OP1 B:U64 4.3 48.9 1.0
N7 B:A65 4.4 54.2 1.0
O5' B:A65 4.7 50.1 1.0
N4 B:C67 4.7 55.4 1.0
OP2 B:U64 4.7 45.1 1.0
C8 B:A65 4.8 53.4 1.0
P B:U64 4.8 48.4 1.0
O A:VAL1100 4.8 52.0 1.0
OP1 B:A65 4.9 45.5 1.0
N3 B:U66 4.9 51.0 1.0
O5' B:U64 5.0 48.9 1.0

Potassium binding site 10 out of 10 in 6ai6

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Potassium binding site 10 out of 10 in the Crystal Structure of SPCAS9-Ng


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of SPCAS9-Ng within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:77.7
occ:1.00
 OP2 B:G21 2.9 53.6 1.0
OP1 B:G21 3.1 62.6 1.0
P B:G21 3.4 55.6 1.0
OP2 B:U45 4.2 61.6 1.0
MG B:MG103 4.4 59.7 1.0
CB A:ARG403 4.4 54.9 1.0
O5' B:G21 4.4 57.2 1.0
O3' B:C20 4.8 62.3 1.0
O A:ARG403 4.8 62.7 1.0
CG A:ARG403 5.0 54.4 1.0

Reference:

H.Nishimasu, X.Shi, S.Ishiguro, L.Gao, S.Hirano, S.Okazaki, T.Noda, O.O.Abudayyeh, J.S.Gootenberg, H.Mori, S.Oura, B.Holmes, M.Tanaka, M.Seki, H.Hirano, H.Aburatani, R.Ishitani, M.Ikawa, N.Yachie, F.Zhang, O.Nureki. Engineered Crispr-CAS9 Nuclease with Expanded Targeting Space Science V. 361 1259 2018.
ISSN: ESSN 1095-9203
PubMed: 30166441
DOI: 10.1126/SCIENCE.AAS9129
Page generated: Mon Aug 12 15:22:26 2024

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