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:
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
Go back to
Potassium Binding Sites List in 6ai6
Potassium binding site 1 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 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
Go back to
Potassium Binding Sites List in 6ai6
Potassium binding site 2 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 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
Go back to
Potassium Binding Sites List in 6ai6
Potassium binding site 3 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 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
Go back to
Potassium Binding Sites List in 6ai6
Potassium binding site 4 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 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
Go back to
Potassium Binding Sites List in 6ai6
Potassium binding site 5 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 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
Go back to
Potassium Binding Sites List in 6ai6
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
Go back to
Potassium Binding Sites List in 6ai6
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
Go back to
Potassium Binding Sites List in 6ai6
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
Go back to
Potassium Binding Sites List in 6ai6
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
Go back to
Potassium Binding Sites List in 6ai6
Potassium binding site 10 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 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
|