Potassium in PDB 7xxk: Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk
was solved by
R.J.Zhou,
X.C.Ni,
J.Lei,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.91 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.783,
116.992,
127.039,
90,
90,
90
|
R / Rfree (%)
|
17.8 /
23.2
|
Other elements in 7xxk:
The structure of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
(pdb code 7xxk). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the
Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Potassium binding site 1 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 1 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K404
b:32.0
occ:1.00
|
O
|
B:HOH583
|
3.3
|
28.0
|
1.0
|
N
|
A:SER312
|
3.4
|
20.8
|
1.0
|
CB
|
A:SER312
|
3.6
|
20.8
|
1.0
|
N
|
A:ALA311
|
3.7
|
21.8
|
1.0
|
CB
|
A:SER310
|
3.8
|
23.1
|
1.0
|
O
|
A:HOH578
|
3.8
|
27.3
|
1.0
|
OG
|
A:SER310
|
3.9
|
24.4
|
1.0
|
OG1
|
B:THR263
|
3.9
|
32.3
|
1.0
|
CB
|
A:ALA311
|
4.1
|
22.2
|
1.0
|
CA
|
A:SER312
|
4.1
|
20.1
|
1.0
|
CA
|
A:ALA311
|
4.2
|
22.0
|
1.0
|
C
|
A:ALA311
|
4.3
|
21.6
|
1.0
|
O
|
B:HOH630
|
4.3
|
45.4
|
1.0
|
CG2
|
B:THR296
|
4.3
|
30.6
|
1.0
|
CG2
|
B:THR263
|
4.3
|
30.5
|
1.0
|
C
|
A:SER310
|
4.4
|
21.9
|
1.0
|
CB
|
B:THR263
|
4.5
|
30.2
|
1.0
|
CA
|
A:SER310
|
4.6
|
21.9
|
1.0
|
CA
|
B:THR263
|
4.7
|
28.0
|
1.0
|
O
|
B:ARG262
|
4.8
|
26.1
|
1.0
|
OG
|
A:SER312
|
4.8
|
22.9
|
1.0
|
|
Potassium binding site 2 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 2 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K405
b:29.8
occ:1.00
|
O
|
A:HOH545
|
2.9
|
33.4
|
1.0
|
OE1
|
A:GLN303
|
3.0
|
31.9
|
1.0
|
CB
|
A:ASP348
|
3.6
|
23.5
|
1.0
|
CD
|
A:GLN303
|
3.7
|
29.8
|
1.0
|
O
|
A:HOH501
|
3.7
|
32.4
|
1.0
|
CG
|
A:GLN303
|
3.8
|
24.6
|
1.0
|
CG
|
A:GLN349
|
3.9
|
21.1
|
1.0
|
N
|
A:GLN349
|
4.0
|
20.0
|
1.0
|
CB
|
A:ASN345
|
4.1
|
23.6
|
1.0
|
C
|
A:ASP348
|
4.1
|
19.5
|
1.0
|
CB
|
A:GLN303
|
4.2
|
20.1
|
1.0
|
O
|
A:ASN345
|
4.4
|
24.5
|
1.0
|
CA
|
A:GLN349
|
4.4
|
20.6
|
1.0
|
O
|
A:ASP348
|
4.5
|
18.7
|
1.0
|
CG
|
A:ASN345
|
4.5
|
24.7
|
1.0
|
CA
|
A:ASP348
|
4.5
|
21.1
|
1.0
|
O
|
A:HOH594
|
4.6
|
38.7
|
1.0
|
OD2
|
A:ASP348
|
4.6
|
33.5
|
1.0
|
CG
|
A:ASP348
|
4.7
|
29.2
|
1.0
|
OD1
|
A:ASN345
|
4.8
|
25.9
|
1.0
|
CB
|
A:GLN349
|
4.8
|
21.0
|
1.0
|
NE2
|
A:GLN303
|
4.8
|
29.1
|
1.0
|
CD
|
A:GLN349
|
5.0
|
22.1
|
1.0
|
NE2
|
A:GLN349
|
5.0
|
20.0
|
1.0
|
|
Potassium binding site 3 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 3 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K406
b:24.0
occ:1.00
|
O
|
A:HOH642
|
3.3
|
36.8
|
1.0
|
N
|
A:ARG277
|
3.3
|
25.6
|
1.0
|
CB
|
A:ARG276
|
3.7
|
28.0
|
1.0
|
CG2
|
A:THR271
|
3.8
|
29.3
|
1.0
|
CG
|
A:ARG277
|
3.8
|
25.9
|
1.0
|
CA
|
A:ARG276
|
3.8
|
25.9
|
1.0
|
C
|
A:ARG276
|
4.0
|
25.9
|
1.0
|
CB
|
A:ARG277
|
4.2
|
25.6
|
1.0
|
CA
|
A:ARG277
|
4.3
|
25.8
|
1.0
|
CD1
|
A:ILE292
|
4.4
|
23.9
|
1.0
|
O
|
A:ARG277
|
4.4
|
27.9
|
1.0
|
CG2
|
C:VAL324
|
4.6
|
29.0
|
1.0
|
CE2
|
A:PHE363
|
4.7
|
44.5
|
1.0
|
CB
|
C:VAL324
|
4.8
|
28.6
|
1.0
|
CG1
|
C:VAL324
|
4.9
|
29.8
|
1.0
|
C
|
A:ARG277
|
4.9
|
27.4
|
1.0
|
CG
|
A:ARG276
|
4.9
|
31.7
|
1.0
|
CD
|
A:ARG277
|
5.0
|
24.9
|
1.0
|
CB
|
A:THR271
|
5.0
|
28.1
|
1.0
|
|
Potassium binding site 4 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 4 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K407
b:38.6
occ:1.00
|
OE1
|
A:GLU323
|
2.3
|
49.0
|
1.0
|
N
|
A:VAL324
|
3.4
|
23.9
|
1.0
|
CD
|
A:GLU323
|
3.5
|
44.2
|
1.0
|
CA
|
A:GLU323
|
3.7
|
26.1
|
1.0
|
CB
|
A:GLU323
|
3.7
|
29.6
|
1.0
|
O
|
A:VAL324
|
3.8
|
25.2
|
1.0
|
CG
|
A:GLU323
|
4.0
|
36.1
|
1.0
|
C
|
A:GLU323
|
4.0
|
25.7
|
1.0
|
CG2
|
A:VAL324
|
4.4
|
24.7
|
1.0
|
CA
|
A:VAL324
|
4.5
|
23.6
|
1.0
|
OE2
|
A:GLU323
|
4.5
|
44.6
|
1.0
|
C
|
A:VAL324
|
4.6
|
24.1
|
1.0
|
O
|
A:HOH523
|
4.6
|
33.7
|
1.0
|
O
|
A:MET322
|
4.7
|
24.9
|
1.0
|
N
|
A:GLU323
|
4.9
|
25.5
|
1.0
|
|
Potassium binding site 5 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 5 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K401
b:30.9
occ:1.00
|
O
|
A:HOH601
|
2.9
|
26.0
|
1.0
|
N
|
B:SER312
|
3.3
|
18.2
|
1.0
|
CB
|
B:SER312
|
3.5
|
19.1
|
1.0
|
O
|
B:HOH582
|
3.6
|
26.8
|
1.0
|
N
|
B:ALA311
|
3.7
|
18.4
|
1.0
|
CB
|
B:SER310
|
3.8
|
20.9
|
1.0
|
OG1
|
A:THR263
|
3.8
|
28.6
|
1.0
|
CG2
|
A:THR263
|
3.9
|
27.3
|
1.0
|
CB
|
B:ALA311
|
4.0
|
16.8
|
1.0
|
OG
|
B:SER310
|
4.0
|
20.8
|
1.0
|
CA
|
B:SER312
|
4.0
|
18.4
|
1.0
|
CA
|
B:ALA311
|
4.1
|
17.6
|
1.0
|
C
|
B:ALA311
|
4.2
|
18.1
|
1.0
|
CG2
|
A:THR296
|
4.2
|
22.4
|
1.0
|
C
|
B:SER310
|
4.3
|
18.8
|
1.0
|
CB
|
A:THR263
|
4.4
|
26.9
|
1.0
|
CA
|
B:SER310
|
4.6
|
20.0
|
1.0
|
OG
|
B:SER312
|
4.7
|
20.1
|
1.0
|
CA
|
A:THR263
|
4.8
|
24.7
|
1.0
|
CZ2
|
A:TRP301
|
4.9
|
21.3
|
1.0
|
O
|
A:HOH645
|
4.9
|
51.4
|
1.0
|
NE1
|
A:TRP301
|
4.9
|
21.2
|
1.0
|
|
Potassium binding site 6 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 6 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K403
b:27.2
occ:1.00
|
O
|
D:HOH595
|
3.2
|
24.7
|
1.0
|
N
|
C:SER312
|
3.4
|
17.2
|
1.0
|
CB
|
C:SER312
|
3.6
|
19.6
|
1.0
|
N
|
C:ALA311
|
3.7
|
16.9
|
1.0
|
CL
|
C:CL408
|
3.8
|
48.9
|
1.0
|
CB
|
C:SER310
|
3.8
|
19.8
|
1.0
|
OG1
|
D:THR263
|
3.9
|
24.2
|
1.0
|
CG2
|
D:THR263
|
4.0
|
22.3
|
1.0
|
OG
|
C:SER310
|
4.0
|
20.9
|
1.0
|
CB
|
C:ALA311
|
4.1
|
16.5
|
1.0
|
CA
|
C:SER312
|
4.1
|
17.8
|
1.0
|
CG2
|
D:THR296
|
4.2
|
23.6
|
1.0
|
CA
|
C:ALA311
|
4.2
|
16.9
|
1.0
|
C
|
C:ALA311
|
4.2
|
16.9
|
1.0
|
C
|
C:SER310
|
4.4
|
17.7
|
1.0
|
CB
|
D:THR263
|
4.4
|
22.4
|
1.0
|
CA
|
C:SER310
|
4.6
|
18.5
|
1.0
|
O
|
D:HOH640
|
4.7
|
43.5
|
1.0
|
CA
|
D:THR263
|
4.7
|
20.1
|
1.0
|
OG
|
C:SER312
|
4.9
|
21.4
|
1.0
|
O
|
D:ARG262
|
5.0
|
19.2
|
1.0
|
|
Potassium binding site 7 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 7 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K401
b:29.6
occ:1.00
|
O
|
C:HOH561
|
3.2
|
20.5
|
1.0
|
N
|
D:SER312
|
3.2
|
19.7
|
1.0
|
CB
|
D:SER312
|
3.5
|
20.8
|
1.0
|
N
|
D:ALA311
|
3.7
|
16.9
|
1.0
|
O
|
D:HOH576
|
3.7
|
23.4
|
1.0
|
CB
|
D:SER310
|
3.9
|
19.0
|
1.0
|
CG2
|
C:THR263
|
3.9
|
23.4
|
1.0
|
CA
|
D:SER312
|
4.0
|
19.6
|
1.0
|
OG1
|
C:THR263
|
4.0
|
23.5
|
1.0
|
OG
|
D:SER310
|
4.1
|
21.0
|
1.0
|
CB
|
D:ALA311
|
4.1
|
17.4
|
1.0
|
C
|
D:ALA311
|
4.1
|
19.5
|
1.0
|
CA
|
D:ALA311
|
4.1
|
17.6
|
1.0
|
CG2
|
C:THR296
|
4.2
|
20.2
|
1.0
|
C
|
D:SER310
|
4.4
|
17.2
|
1.0
|
CB
|
C:THR263
|
4.5
|
22.6
|
1.0
|
CA
|
D:SER310
|
4.6
|
17.5
|
1.0
|
O
|
C:HOH609
|
4.6
|
36.0
|
1.0
|
OG
|
D:SER312
|
4.8
|
22.0
|
1.0
|
CZ2
|
C:TRP301
|
4.8
|
18.6
|
1.0
|
CA
|
C:THR263
|
4.8
|
21.1
|
1.0
|
NE1
|
C:TRP301
|
4.9
|
18.9
|
1.0
|
|
Potassium binding site 8 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 8 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K402
b:30.8
occ:1.00
|
O
|
D:HOH603
|
3.5
|
20.8
|
1.0
|
NE2
|
D:GLN303
|
3.5
|
22.7
|
1.0
|
O
|
D:HOH630
|
3.6
|
58.2
|
1.0
|
CG
|
D:GLN303
|
4.0
|
21.1
|
1.0
|
CD
|
D:GLN303
|
4.3
|
23.2
|
1.0
|
O
|
D:HOH551
|
4.3
|
44.4
|
1.0
|
O
|
D:HOH561
|
4.4
|
30.2
|
1.0
|
ND2
|
D:ASN345
|
4.6
|
31.6
|
1.0
|
|
Potassium binding site 9 out
of 9 in 7xxk
Go back to
Potassium Binding Sites List in 7xxk
Potassium binding site 9 out
of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp
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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K402
b:28.8
occ:1.00
|
O
|
E:HOH569
|
3.3
|
24.6
|
1.0
|
N
|
F:SER312
|
3.4
|
20.2
|
1.0
|
CB
|
F:SER312
|
3.6
|
21.4
|
1.0
|
O
|
F:HOH551
|
3.6
|
32.5
|
1.0
|
OG1
|
E:THR263
|
3.7
|
29.0
|
1.0
|
N
|
F:ALA311
|
3.7
|
21.0
|
1.0
|
CB
|
F:SER310
|
3.9
|
23.7
|
1.0
|
CA
|
F:SER312
|
4.1
|
20.6
|
1.0
|
CB
|
F:ALA311
|
4.1
|
20.4
|
1.0
|
OG
|
F:SER310
|
4.1
|
25.6
|
1.0
|
O
|
F:HOH602
|
4.1
|
45.6
|
1.0
|
CG2
|
E:THR296
|
4.2
|
25.4
|
1.0
|
CA
|
F:ALA311
|
4.2
|
20.6
|
1.0
|
CG2
|
E:THR263
|
4.2
|
28.1
|
1.0
|
C
|
F:ALA311
|
4.3
|
20.5
|
1.0
|
CB
|
E:THR263
|
4.4
|
27.5
|
1.0
|
C
|
F:SER310
|
4.4
|
21.4
|
1.0
|
CA
|
F:SER310
|
4.7
|
22.4
|
1.0
|
CA
|
E:THR263
|
4.7
|
25.8
|
1.0
|
O
|
E:HOH627
|
4.8
|
55.0
|
1.0
|
OG
|
F:SER312
|
4.8
|
22.7
|
1.0
|
O
|
E:HOH621
|
4.9
|
37.1
|
1.0
|
O
|
E:ARG262
|
5.0
|
24.3
|
1.0
|
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Reference:
R.J.Zhou,
X.C.Ni,
J.Lei.
Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp To Be Published.
Page generated: Mon Aug 12 21:38:43 2024
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