Potassium in PDB 7zo1: SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Protein crystallography data
The structure of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate, PDB code: 7zo1
was solved by
M.Pacesa,
M.Jinek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.51 /
2.40
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.41,
69.2,
188.46,
90,
111.77,
90
|
R / Rfree (%)
|
21.2 /
25
|
Other elements in 7zo1:
The structure of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
(pdb code 7zo1). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the
SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate, PDB code: 7zo1:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 1 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K103
b:75.2
occ:1.00
|
OP2
|
A:A65
|
2.7
|
62.7
|
1.0
|
O4
|
A:U66
|
2.7
|
55.1
|
1.0
|
OG1
|
B:THR1102
|
2.8
|
54.8
|
1.0
|
O
|
A:HOH238
|
2.9
|
48.3
|
1.0
|
O
|
B:HOH1592
|
3.0
|
51.8
|
1.0
|
O
|
A:HOH252
|
3.1
|
50.1
|
1.0
|
O
|
A:HOH259
|
3.1
|
68.2
|
1.0
|
C4
|
A:U66
|
3.6
|
62.5
|
1.0
|
CG2
|
B:THR1102
|
3.8
|
45.8
|
1.0
|
CB
|
B:THR1102
|
3.9
|
58.2
|
1.0
|
C5
|
A:U66
|
4.0
|
68.0
|
1.0
|
P
|
A:A65
|
4.0
|
58.8
|
1.0
|
O
|
B:HOH1537
|
4.1
|
56.8
|
1.0
|
OP1
|
A:U64
|
4.3
|
50.5
|
1.0
|
O
|
A:HOH226
|
4.3
|
61.0
|
1.0
|
N4
|
A:C67
|
4.5
|
45.6
|
1.0
|
OP1
|
A:A65
|
4.5
|
46.6
|
1.0
|
O
|
A:HOH203
|
4.6
|
50.1
|
1.0
|
O5'
|
A:A65
|
4.7
|
52.0
|
1.0
|
N7
|
A:A65
|
4.7
|
61.9
|
1.0
|
O
|
B:HOH1634
|
4.7
|
55.3
|
1.0
|
O
|
A:HOH224
|
4.8
|
62.0
|
1.0
|
OP2
|
A:U64
|
4.9
|
38.7
|
1.0
|
N3
|
A:U66
|
4.9
|
61.9
|
1.0
|
O
|
B:VAL1100
|
4.9
|
46.1
|
1.0
|
P
|
A:U64
|
5.0
|
68.8
|
1.0
|
|
Potassium binding site 2 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 2 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K104
b:86.5
occ:1.00
|
O
|
B:HOH1618
|
2.7
|
59.7
|
1.0
|
O
|
B:GLN1350
|
2.7
|
55.5
|
1.0
|
O
|
B:HOH1579
|
2.8
|
40.4
|
1.0
|
O4'
|
A:A68
|
2.9
|
56.7
|
1.0
|
O
|
A:HOH217
|
3.1
|
50.5
|
1.0
|
O
|
A:HOH295
|
3.3
|
58.4
|
1.0
|
C1'
|
A:A68
|
3.4
|
56.7
|
1.0
|
C
|
B:GLN1350
|
3.9
|
51.8
|
1.0
|
N9
|
A:A68
|
4.0
|
65.8
|
1.0
|
O
|
B:SER1351
|
4.0
|
59.5
|
1.0
|
C4'
|
A:A68
|
4.1
|
58.4
|
1.0
|
OG1
|
B:THR1098
|
4.1
|
65.5
|
1.0
|
C8
|
A:A68
|
4.2
|
58.4
|
1.0
|
O5'
|
A:A68
|
4.2
|
56.8
|
1.0
|
C
|
B:SER1351
|
4.3
|
53.5
|
1.0
|
O
|
B:HOH1600
|
4.4
|
53.1
|
1.0
|
OP1
|
A:A68
|
4.6
|
70.9
|
1.0
|
CA
|
B:SER1351
|
4.7
|
59.0
|
1.0
|
OP2
|
A:A68
|
4.7
|
69.0
|
1.0
|
C5'
|
A:A68
|
4.7
|
55.2
|
1.0
|
P
|
A:A68
|
4.7
|
62.2
|
1.0
|
CA
|
B:GLN1350
|
4.7
|
54.7
|
1.0
|
N
|
B:SER1351
|
4.7
|
59.8
|
1.0
|
CB
|
B:GLN1350
|
4.7
|
52.5
|
1.0
|
N
|
B:ILE1352
|
4.8
|
54.3
|
1.0
|
C2'
|
A:A68
|
4.8
|
66.0
|
1.0
|
N
|
B:THR1098
|
4.8
|
45.0
|
1.0
|
CG1
|
B:VAL1095
|
4.8
|
60.9
|
1.0
|
N
|
B:GLN1350
|
4.8
|
54.0
|
1.0
|
O2'
|
A:A68
|
4.9
|
55.2
|
1.0
|
CA
|
B:ILE1352
|
4.9
|
52.2
|
1.0
|
|
Potassium binding site 3 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 3 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K105
b:73.2
occ:1.00
|
O
|
A:HOH230
|
2.9
|
61.4
|
1.0
|
O
|
A:HOH228
|
2.9
|
53.8
|
1.0
|
OP2
|
A:G21
|
3.1
|
69.3
|
1.0
|
O
|
A:HOH242
|
3.2
|
65.7
|
1.0
|
O
|
B:HOH1658
|
3.3
|
73.2
|
1.0
|
O
|
A:HOH280
|
3.7
|
54.2
|
1.0
|
O
|
A:HOH201
|
3.7
|
71.2
|
1.0
|
O
|
A:HOH231
|
4.0
|
75.4
|
1.0
|
P
|
A:G21
|
4.0
|
58.3
|
1.0
|
O
|
B:HOH1593
|
4.1
|
68.9
|
1.0
|
OP1
|
A:G21
|
4.1
|
60.8
|
1.0
|
OP2
|
A:U45
|
4.2
|
59.3
|
1.0
|
MG
|
A:MG102
|
4.5
|
68.5
|
1.0
|
CB
|
B:ARG403
|
4.5
|
65.3
|
1.0
|
O
|
A:HOH288
|
4.5
|
53.2
|
1.0
|
O5'
|
A:G21
|
4.9
|
56.0
|
1.0
|
CG
|
B:ARG403
|
5.0
|
61.0
|
1.0
|
|
Potassium binding site 4 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 4 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1401
b:96.9
occ:1.00
|
O
|
B:TYR656
|
2.8
|
77.4
|
1.0
|
O
|
B:PHE626
|
2.8
|
90.0
|
1.0
|
O
|
B:LEU623
|
2.8
|
82.3
|
1.0
|
O
|
B:THR624
|
3.5
|
63.9
|
1.0
|
C
|
B:PHE626
|
3.5
|
86.1
|
1.0
|
C
|
B:TYR656
|
3.9
|
76.6
|
1.0
|
C
|
B:THR624
|
3.9
|
67.6
|
1.0
|
C
|
B:LEU623
|
3.9
|
74.0
|
1.0
|
N
|
B:GLU627
|
4.0
|
78.8
|
1.0
|
OP1
|
C:DC8
|
4.0
|
91.4
|
1.0
|
CA
|
B:GLU627
|
4.0
|
91.8
|
1.0
|
CA
|
B:THR624
|
4.1
|
70.8
|
1.0
|
N
|
B:TYR656
|
4.1
|
83.1
|
1.0
|
CB
|
B:ARG655
|
4.1
|
114.2
|
1.0
|
CG2
|
B:THR657
|
4.1
|
69.6
|
1.0
|
CB
|
B:GLU627
|
4.3
|
72.5
|
1.0
|
N
|
B:PHE626
|
4.3
|
81.9
|
1.0
|
N
|
B:THR624
|
4.5
|
72.5
|
1.0
|
CA
|
B:PHE626
|
4.5
|
73.0
|
1.0
|
CD
|
B:ARG655
|
4.6
|
122.3
|
1.0
|
CG
|
B:ARG655
|
4.6
|
117.0
|
1.0
|
CA
|
B:TYR656
|
4.7
|
82.8
|
1.0
|
N
|
B:THR657
|
4.8
|
73.3
|
1.0
|
N
|
B:LEU625
|
4.8
|
70.2
|
1.0
|
C
|
B:LEU625
|
4.8
|
75.3
|
1.0
|
CA
|
B:ARG655
|
4.9
|
114.0
|
1.0
|
C
|
B:ARG655
|
4.9
|
103.7
|
1.0
|
CG
|
B:GLU627
|
5.0
|
90.5
|
1.0
|
|
Potassium binding site 5 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 5 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1402
b:83.3
occ:1.00
|
O
|
B:HOH1582
|
2.7
|
69.7
|
1.0
|
O
|
B:ALA367
|
2.7
|
73.9
|
1.0
|
O
|
B:GLY365
|
2.8
|
79.1
|
1.0
|
O
|
B:GLY361
|
2.9
|
78.0
|
1.0
|
O
|
B:TYR362
|
3.0
|
73.9
|
1.0
|
N
|
B:ALA367
|
3.2
|
84.4
|
1.0
|
C
|
B:ALA367
|
3.6
|
82.1
|
1.0
|
C
|
B:TYR362
|
3.6
|
72.8
|
1.0
|
C
|
B:GLY365
|
3.6
|
67.9
|
1.0
|
C
|
B:GLY366
|
3.7
|
88.7
|
1.0
|
CA
|
B:GLY366
|
3.8
|
82.2
|
1.0
|
CA
|
B:TYR362
|
3.9
|
73.8
|
1.0
|
CA
|
B:ALA367
|
4.0
|
74.6
|
1.0
|
C
|
B:GLY361
|
4.0
|
77.8
|
1.0
|
N
|
B:GLY366
|
4.0
|
69.1
|
1.0
|
NZ
|
B:LYS401
|
4.1
|
78.2
|
1.0
|
O
|
B:HOH1522
|
4.4
|
48.5
|
1.0
|
N
|
B:TYR362
|
4.5
|
81.8
|
1.0
|
N
|
B:ILE363
|
4.5
|
73.1
|
1.0
|
OP1
|
A:U22
|
4.5
|
58.0
|
1.0
|
N
|
B:SER368
|
4.6
|
82.9
|
1.0
|
O
|
B:GLY366
|
4.6
|
92.2
|
1.0
|
CB
|
B:ALA367
|
4.7
|
77.4
|
1.0
|
N
|
B:GLY365
|
4.7
|
75.1
|
1.0
|
O
|
B:ILE363
|
4.7
|
78.6
|
1.0
|
CA
|
B:GLY365
|
4.7
|
70.9
|
1.0
|
C
|
B:ILE363
|
4.7
|
72.8
|
1.0
|
O
|
B:HOH1593
|
4.8
|
68.9
|
1.0
|
CA
|
B:ILE363
|
5.0
|
70.4
|
1.0
|
|
Potassium binding site 6 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 6 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1403
b:133.5
occ:1.00
|
O
|
B:ILE226
|
2.7
|
126.7
|
1.0
|
O
|
B:LEU229
|
2.7
|
130.6
|
1.0
|
O
|
B:GLU232
|
3.0
|
134.6
|
1.0
|
C
|
B:ILE226
|
3.6
|
123.2
|
1.0
|
C
|
B:LEU229
|
3.7
|
127.0
|
1.0
|
CG2
|
B:ILE226
|
3.7
|
98.1
|
1.0
|
CA
|
B:ALA227
|
3.9
|
133.1
|
1.0
|
N
|
B:ALA227
|
4.1
|
123.1
|
1.0
|
C
|
B:GLU232
|
4.3
|
137.7
|
1.0
|
O
|
B:ALA227
|
4.3
|
122.3
|
1.0
|
CA
|
B:PRO230
|
4.3
|
128.6
|
1.0
|
C
|
B:ALA227
|
4.3
|
129.9
|
1.0
|
N
|
B:PRO230
|
4.3
|
123.9
|
1.0
|
N
|
B:LEU229
|
4.5
|
118.0
|
1.0
|
CA
|
B:LEU229
|
4.6
|
121.2
|
1.0
|
CA
|
B:ILE226
|
4.7
|
118.4
|
1.0
|
N
|
B:GLU232
|
4.7
|
145.1
|
1.0
|
CB
|
B:ILE226
|
4.8
|
106.7
|
1.0
|
N
|
B:GLY231
|
4.9
|
153.4
|
1.0
|
C
|
B:PRO230
|
4.9
|
125.3
|
1.0
|
|
Potassium binding site 7 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 7 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1404
b:102.0
occ:1.00
|
O
|
B:LYS111
|
2.7
|
78.6
|
1.0
|
O
|
B:HOH1653
|
3.0
|
87.7
|
1.0
|
O
|
B:GLU108
|
3.0
|
66.7
|
1.0
|
O
|
B:HOH1666
|
3.2
|
84.6
|
1.0
|
C
|
B:LYS111
|
3.8
|
56.9
|
1.0
|
O
|
B:GLU109
|
4.1
|
72.3
|
1.0
|
C
|
B:GLU108
|
4.2
|
64.0
|
1.0
|
C
|
B:GLU109
|
4.5
|
68.4
|
1.0
|
CA
|
B:LYS111
|
4.6
|
67.7
|
1.0
|
N
|
B:LYS111
|
4.6
|
70.1
|
1.0
|
CB
|
B:LYS111
|
4.6
|
49.8
|
1.0
|
CA
|
B:GLU109
|
4.7
|
67.9
|
1.0
|
N
|
B:LYS112
|
4.8
|
61.2
|
1.0
|
CG
|
B:GLU108
|
4.9
|
81.5
|
1.0
|
O
|
B:HIS113
|
4.9
|
62.2
|
1.0
|
N
|
B:GLU109
|
4.9
|
62.2
|
1.0
|
CA
|
B:LYS112
|
5.0
|
68.8
|
1.0
|
|
Potassium binding site 8 out
of 8 in 7zo1
Go back to
Potassium Binding Sites List in 7zo1
Potassium binding site 8 out
of 8 in the SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of SPCAS9 Bound to CD34 Off-TARGET9 Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1405
b:119.4
occ:1.00
|
OD1
|
B:ASN588
|
2.9
|
125.5
|
1.0
|
O
|
B:GLU584
|
2.9
|
142.6
|
1.0
|
O
|
B:ARG586
|
3.2
|
118.2
|
1.0
|
CG
|
B:ASN588
|
3.8
|
103.4
|
1.0
|
C
|
B:GLU584
|
4.0
|
133.1
|
1.0
|
ND2
|
B:ASN588
|
4.1
|
96.7
|
1.0
|
N
|
B:GLU584
|
4.2
|
128.8
|
1.0
|
CB
|
B:GLU584
|
4.3
|
125.7
|
1.0
|
CA
|
B:GLU584
|
4.4
|
125.5
|
1.0
|
C
|
B:ARG586
|
4.4
|
113.7
|
1.0
|
N
|
B:ARG586
|
4.5
|
131.3
|
1.0
|
CG
|
B:ARG586
|
4.7
|
134.2
|
1.0
|
O4'
|
C:DT17
|
4.9
|
112.3
|
1.0
|
N
|
B:ASN588
|
5.0
|
100.5
|
1.0
|
|
Reference:
M.Pacesa,
C.H.Lin,
A.Clery,
A.Saha,
P.R.Arantes,
K.Bargsten,
M.J.Irby,
F.H.Allain,
G.Palermo,
P.Cameron,
P.D.Donohoue,
M.Jinek.
Structural Basis For CAS9 Off-Target Activity. Cell V. 185 4067 2022.
ISSN: ISSN 1097-4172
PubMed: 36306733
DOI: 10.1016/J.CELL.2022.09.026
Page generated: Mon Aug 12 21:50:32 2024
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