Potassium in PDB 7z4d: Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
Protein crystallography data
The structure of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate, PDB code: 7z4d
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)
|
66.49 /
3.10
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.636,
95.509,
169.797,
80.83,
78.04,
62.34
|
R / Rfree (%)
|
24.7 /
27.6
|
Potassium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Potassium atom in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
(pdb code 7z4d). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 16 binding sites of Potassium where determined in the
Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate, PDB code: 7z4d:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 16 in 7z4d
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Potassium Binding Sites List in 7z4d
Potassium binding site 1 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K101
b:98.5
occ:1.00
|
N3
|
A:A32
|
4.3
|
67.5
|
1.0
|
N3
|
A:A38
|
4.4
|
60.0
|
1.0
|
O2'
|
A:A38
|
4.5
|
67.3
|
1.0
|
C1'
|
A:A32
|
5.0
|
67.4
|
1.0
|
C2
|
A:A32
|
5.0
|
61.1
|
1.0
|
|
Potassium binding site 2 out
of 16 in 7z4d
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Potassium Binding Sites List in 7z4d
Potassium binding site 2 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K102
b:69.7
occ:1.00
|
O
|
C:HOH201
|
2.9
|
34.0
|
1.0
|
O4
|
A:U63
|
3.0
|
23.9
|
1.0
|
O
|
B:HOH1522
|
3.1
|
24.3
|
1.0
|
CD
|
B:GLU1108
|
3.5
|
44.2
|
1.0
|
CG
|
B:GLU1108
|
3.6
|
41.8
|
1.0
|
OE2
|
B:GLU1108
|
3.8
|
65.1
|
1.0
|
OE1
|
B:GLU1108
|
3.9
|
47.8
|
1.0
|
C4
|
A:U63
|
4.0
|
24.5
|
1.0
|
N3
|
A:U63
|
4.2
|
29.1
|
1.0
|
CE
|
B:LYS65
|
4.3
|
58.2
|
1.0
|
CB
|
B:GLU1108
|
4.5
|
34.6
|
1.0
|
CG
|
B:LYS65
|
4.5
|
28.7
|
1.0
|
O4'
|
A:A51
|
4.6
|
25.7
|
1.0
|
CD
|
B:LYS65
|
4.8
|
22.7
|
1.0
|
O2'
|
A:U50
|
4.8
|
49.3
|
1.0
|
C1'
|
A:A51
|
4.9
|
28.6
|
1.0
|
|
Potassium binding site 3 out
of 16 in 7z4d
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Potassium Binding Sites List in 7z4d
Potassium binding site 3 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K103
b:52.7
occ:1.00
|
O4'
|
A:A68
|
3.5
|
39.2
|
1.0
|
OG1
|
B:THR1098
|
3.7
|
31.9
|
1.0
|
O
|
B:GLN1350
|
3.8
|
37.2
|
1.0
|
N
|
B:THR1098
|
3.9
|
23.8
|
1.0
|
O5'
|
A:A68
|
3.9
|
45.7
|
1.0
|
C1'
|
A:A68
|
4.3
|
39.0
|
1.0
|
C4'
|
A:A68
|
4.3
|
41.4
|
1.0
|
CA
|
B:LYS1097
|
4.4
|
32.2
|
1.0
|
CG2
|
B:THR1098
|
4.4
|
25.4
|
1.0
|
CB
|
B:THR1098
|
4.5
|
23.5
|
1.0
|
OP2
|
A:A68
|
4.6
|
58.8
|
1.0
|
C
|
B:LYS1097
|
4.6
|
36.8
|
1.0
|
CG1
|
B:VAL1095
|
4.7
|
35.8
|
1.0
|
C5'
|
A:A68
|
4.7
|
36.4
|
1.0
|
O
|
B:LYS1096
|
4.8
|
44.0
|
1.0
|
CA
|
B:THR1098
|
4.8
|
22.6
|
1.0
|
P
|
A:A68
|
4.8
|
55.1
|
1.0
|
O
|
B:SER1351
|
4.9
|
31.2
|
1.0
|
O
|
B:THR1098
|
4.9
|
34.1
|
1.0
|
C
|
B:GLN1350
|
4.9
|
28.4
|
1.0
|
CG
|
B:LYS1097
|
4.9
|
25.8
|
1.0
|
|
Potassium binding site 4 out
of 16 in 7z4d
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Potassium Binding Sites List in 7z4d
Potassium binding site 4 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K104
b:68.1
occ:1.00
|
N4
|
A:C67
|
3.2
|
27.3
|
1.0
|
O
|
B:HOH1508
|
3.2
|
40.3
|
1.0
|
OE1
|
B:GLU1099
|
3.4
|
36.1
|
1.0
|
CD
|
B:GLU1099
|
3.5
|
26.5
|
1.0
|
O
|
B:HOH1516
|
3.5
|
19.8
|
1.0
|
OE2
|
B:GLU1099
|
3.6
|
21.0
|
1.0
|
CB
|
B:GLU1099
|
4.3
|
20.3
|
1.0
|
C4
|
A:C67
|
4.3
|
33.7
|
1.0
|
CG
|
B:GLU1099
|
4.3
|
20.2
|
1.0
|
O
|
B:VAL1100
|
4.4
|
20.2
|
1.0
|
NZ
|
B:LYS735
|
4.4
|
33.8
|
1.0
|
O4
|
A:U66
|
4.5
|
53.1
|
1.0
|
C5
|
A:C67
|
4.6
|
29.2
|
1.0
|
OP2
|
A:A65
|
4.7
|
33.8
|
1.0
|
O
|
B:HOH1513
|
4.8
|
30.5
|
1.0
|
C5
|
A:U66
|
4.9
|
29.6
|
1.0
|
OP1
|
A:A65
|
4.9
|
35.7
|
1.0
|
C4
|
A:U66
|
4.9
|
32.2
|
1.0
|
OG1
|
B:THR1102
|
5.0
|
24.4
|
1.0
|
|
Potassium binding site 5 out
of 16 in 7z4d
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Potassium Binding Sites List in 7z4d
Potassium binding site 5 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_05.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K105
b:73.2
occ:1.00
|
O
|
A:HOH215
|
3.1
|
46.4
|
1.0
|
OP1
|
A:U50
|
3.1
|
28.2
|
1.0
|
O6
|
A:G62
|
3.1
|
30.4
|
1.0
|
O6
|
A:G53
|
3.4
|
41.8
|
1.0
|
C6
|
A:G62
|
4.0
|
26.1
|
1.0
|
N1
|
A:G62
|
4.0
|
28.9
|
1.0
|
C6
|
A:G53
|
4.1
|
39.2
|
1.0
|
N7
|
A:G53
|
4.1
|
27.2
|
1.0
|
OP2
|
A:A52
|
4.3
|
29.2
|
1.0
|
P
|
A:U50
|
4.4
|
60.0
|
1.0
|
OP1
|
A:A51
|
4.4
|
26.4
|
1.0
|
C5
|
A:G53
|
4.5
|
29.7
|
1.0
|
OP1
|
A:A52
|
4.5
|
25.8
|
1.0
|
O5'
|
A:U50
|
4.9
|
30.4
|
1.0
|
C5'
|
A:U50
|
4.9
|
24.2
|
1.0
|
P
|
A:A52
|
4.9
|
28.5
|
1.0
|
|
Potassium binding site 6 out
of 16 in 7z4d
Go back to
Potassium Binding Sites List in 7z4d
Potassium binding site 6 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_06.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K106
b:80.6
occ:1.00
|
N7
|
A:G19
|
3.7
|
31.2
|
1.0
|
C5
|
A:C18
|
4.2
|
46.7
|
1.0
|
C8
|
A:G19
|
4.4
|
36.0
|
1.0
|
OP2
|
A:C18
|
4.5
|
47.6
|
1.0
|
OP2
|
A:G19
|
4.6
|
28.4
|
1.0
|
C4
|
A:C18
|
4.6
|
36.2
|
1.0
|
N4
|
A:C18
|
4.7
|
37.2
|
1.0
|
C6
|
A:C18
|
4.7
|
38.7
|
1.0
|
C5
|
A:G19
|
4.9
|
30.0
|
1.0
|
NH1
|
B:ARG71
|
4.9
|
58.5
|
1.0
|
O6
|
A:G19
|
4.9
|
28.8
|
1.0
|
NE
|
B:ARG71
|
4.9
|
25.1
|
1.0
|
NH2
|
B:ARG75
|
5.0
|
42.0
|
1.0
|
|
Potassium binding site 7 out
of 16 in 7z4d
Go back to
Potassium Binding Sites List in 7z4d
Potassium binding site 7 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_07.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1401
b:53.9
occ:1.00
|
O
|
B:ALA59
|
2.7
|
34.5
|
1.0
|
NH1
|
B:ARG66
|
2.7
|
41.1
|
1.0
|
N
|
B:ARG63
|
3.0
|
25.8
|
1.0
|
CB
|
B:THR62
|
3.2
|
42.9
|
1.0
|
CB
|
B:ALA59
|
3.2
|
38.2
|
1.0
|
OP1
|
A:G14
|
3.3
|
38.4
|
1.0
|
C
|
B:THR62
|
3.5
|
37.3
|
1.0
|
CA
|
B:ARG63
|
3.5
|
17.6
|
1.0
|
CB
|
B:ARG63
|
3.5
|
35.9
|
1.0
|
CG2
|
B:THR62
|
3.5
|
43.6
|
1.0
|
C
|
B:ALA59
|
3.6
|
41.6
|
1.0
|
CA
|
B:ALA59
|
3.8
|
39.8
|
1.0
|
CA
|
B:THR62
|
3.8
|
43.8
|
1.0
|
CZ
|
B:ARG66
|
3.9
|
32.1
|
1.0
|
OP2
|
A:G14
|
3.9
|
30.6
|
1.0
|
P
|
A:G14
|
4.1
|
48.5
|
1.0
|
O
|
B:THR62
|
4.2
|
34.1
|
1.0
|
OG1
|
B:THR62
|
4.3
|
40.5
|
1.0
|
N
|
B:THR62
|
4.4
|
29.2
|
1.0
|
NH2
|
B:ARG66
|
4.4
|
29.0
|
1.0
|
CG
|
B:ARG63
|
4.8
|
41.4
|
1.0
|
NE
|
B:ARG66
|
4.8
|
28.7
|
1.0
|
N
|
B:GLU60
|
4.8
|
44.8
|
1.0
|
O4'
|
A:U64
|
5.0
|
36.9
|
1.0
|
C
|
B:ARG63
|
5.0
|
30.4
|
1.0
|
|
Potassium binding site 8 out
of 16 in 7z4d
Go back to
Potassium Binding Sites List in 7z4d
Potassium binding site 8 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_08.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1402
b:60.9
occ:1.00
|
NH1
|
B:ARG1171
|
3.0
|
22.3
|
1.0
|
NH2
|
B:ARG1171
|
3.5
|
36.4
|
1.0
|
CZ
|
B:ARG1171
|
3.7
|
26.9
|
1.0
|
N3
|
A:U66
|
3.7
|
33.5
|
1.0
|
O4
|
A:U66
|
4.1
|
53.1
|
1.0
|
C4
|
A:U66
|
4.4
|
32.2
|
1.0
|
O2
|
A:U66
|
4.4
|
58.0
|
1.0
|
CG2
|
B:THR1102
|
4.5
|
20.3
|
1.0
|
C2
|
A:U66
|
4.6
|
36.3
|
1.0
|
CB
|
B:VAL1100
|
4.7
|
23.1
|
1.0
|
CG1
|
B:VAL1100
|
4.7
|
24.5
|
1.0
|
N6
|
A:A65
|
4.8
|
41.5
|
1.0
|
N3
|
A:C67
|
5.0
|
33.6
|
1.0
|
C2
|
A:C67
|
5.0
|
29.9
|
1.0
|
O2
|
A:C67
|
5.0
|
41.3
|
1.0
|
|
Potassium binding site 9 out
of 16 in 7z4d
Go back to
Potassium Binding Sites List in 7z4d
Potassium binding site 9 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_09.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K1403
b:56.7
occ:1.00
|
O
|
B:GLY408
|
3.3
|
31.6
|
1.0
|
O2
|
A:C18
|
3.5
|
39.2
|
1.0
|
O2'
|
A:C18
|
3.6
|
53.0
|
1.0
|
O2
|
C:DT4
|
3.7
|
40.6
|
1.0
|
C1'
|
A:C18
|
3.8
|
34.2
|
1.0
|
C2'
|
A:C18
|
4.2
|
38.3
|
1.0
|
C
|
B:GLY408
|
4.2
|
40.4
|
1.0
|
CB
|
B:HIS167
|
4.2
|
30.3
|
1.0
|
CA
|
B:GLY408
|
4.3
|
32.0
|
1.0
|
C2
|
A:C18
|
4.4
|
44.1
|
1.0
|
N1
|
A:C18
|
4.6
|
33.3
|
1.0
|
CD1
|
B:LEU169
|
4.7
|
38.8
|
1.0
|
C1'
|
C:DT4
|
4.8
|
33.8
|
1.0
|
C2
|
C:DT4
|
4.8
|
36.6
|
1.0
|
O4'
|
A:C18
|
4.8
|
34.2
|
1.0
|
CG
|
B:HIS167
|
4.8
|
32.0
|
1.0
|
O4'
|
C:DC5
|
4.8
|
49.9
|
1.0
|
C2'
|
C:DT4
|
4.9
|
34.2
|
1.0
|
CD2
|
B:HIS167
|
4.9
|
32.6
|
1.0
|
N2
|
C:DG3
|
4.9
|
37.7
|
1.0
|
|
Potassium binding site 10 out
of 16 in 7z4d
Go back to
Potassium Binding Sites List in 7z4d
Potassium binding site 10 out
of 16 in the Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate
![](/pictures/K/pdb/z4/7z4d-K-sphere_10.jpg) Mono view
![](/pictures/K/pdb/z4/7z4d-K-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 10 of Crystal Structure of SPCAS9 Bound to A 10 Nucleotide Complementary Dna Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K101
b:43.5
occ:1.00
|
O6
|
C:DG3
|
3.4
|
48.2
|
1.0
|
N7
|
C:DG3
|
4.2
|
40.6
|
1.0
|
O4
|
C:DT4
|
4.3
|
39.8
|
1.0
|
C6
|
C:DG3
|
4.3
|
43.0
|
1.0
|
N4
|
C:DC2
|
4.5
|
33.7
|
1.0
|
NH1
|
B:ARG71
|
4.6
|
58.5
|
1.0
|
C5
|
C:DG3
|
4.6
|
42.3
|
1.0
|
C4
|
C:DC2
|
4.6
|
39.1
|
1.0
|
C5
|
C:DC2
|
4.7
|
37.0
|
1.0
|
CB
|
B:LEU64
|
4.7
|
27.8
|
1.0
|
CD1
|
B:LEU64
|
5.0
|
48.1
|
1.0
|
N4
|
A:C18
|
5.0
|
37.2
|
1.0
|
|
Reference:
M.Pacesa,
L.Loeff,
I.Querques,
L.M.Muckenfuss,
M.Sawicka,
M.Jinek.
R-Loop Formation and Conformational Activation Mechanisms of CAS9. Nature V. 609 191 2022.
ISSN: ESSN 1476-4687
PubMed: 36002571
DOI: 10.1038/S41586-022-05114-0
Page generated: Mon Aug 12 21:45:08 2024
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