Sodium in PDB 7xft: Mucp PDZ2 Domain
Protein crystallography data
The structure of Mucp PDZ2 Domain, PDB code: 7xft
was solved by
X.Lou,
S.Li,
Q.Zhang,
M.Bartlam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
24.66 /
1.21
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.312,
70.66,
50.376,
90,
90,
90
|
|
R / Rfree (%)
|
16.7 /
18.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Mucp PDZ2 Domain
(pdb code 7xft). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Mucp PDZ2 Domain, PDB code: 7xft:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 7xft
Go back to
Sodium Binding Sites List in 7xft
Sodium binding site 1 out
of 5 in the Mucp PDZ2 Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Mucp PDZ2 Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:30.2
occ:1.00
|
HG
|
A:LEU277
|
2.0
|
19.5
|
1.0
|
|
H
|
A:GLY280
|
2.2
|
14.9
|
1.0
|
|
HD21
|
A:LEU277
|
2.6
|
21.9
|
1.0
|
|
CG
|
A:LEU277
|
2.8
|
16.2
|
1.0
|
|
CD2
|
A:LEU277
|
3.0
|
18.2
|
1.0
|
|
N
|
A:GLY280
|
3.0
|
12.4
|
1.0
|
|
HD11
|
A:LEU277
|
3.1
|
21.7
|
1.0
|
|
HD23
|
A:LEU277
|
3.1
|
21.9
|
1.0
|
|
O
|
A:HOH586
|
3.2
|
32.1
|
1.0
|
|
O
|
A:HOH538
|
3.2
|
20.2
|
1.0
|
|
H
|
A:ASP279
|
3.4
|
13.2
|
1.0
|
|
CD1
|
A:LEU277
|
3.4
|
18.1
|
1.0
|
|
HA2
|
A:GLY280
|
3.4
|
15.9
|
1.0
|
|
N
|
A:ASP279
|
3.6
|
10.9
|
1.0
|
|
HA
|
A:ASP279
|
3.7
|
13.8
|
1.0
|
|
HD12
|
A:LEU277
|
3.7
|
21.7
|
1.0
|
|
O
|
A:HOH530
|
3.7
|
23.3
|
1.0
|
|
CA
|
A:GLY280
|
3.8
|
13.2
|
1.0
|
|
HD22
|
A:LEU277
|
3.9
|
21.9
|
1.0
|
|
CA
|
A:ASP279
|
4.0
|
11.5
|
1.0
|
|
C
|
A:ASP279
|
4.0
|
12.2
|
1.0
|
|
CB
|
A:LEU277
|
4.0
|
12.2
|
1.0
|
|
HB3
|
A:LEU277
|
4.1
|
14.7
|
1.0
|
|
C
|
A:ARG278
|
4.2
|
9.9
|
1.0
|
|
HD13
|
A:LEU277
|
4.3
|
21.7
|
1.0
|
|
C
|
A:LEU277
|
4.3
|
10.1
|
1.0
|
|
N
|
A:ARG278
|
4.3
|
10.0
|
1.0
|
|
HA
|
A:ARG278
|
4.5
|
11.7
|
1.0
|
|
HA3
|
A:GLY280
|
4.5
|
15.9
|
1.0
|
|
H
|
A:GLU281
|
4.6
|
14.3
|
1.0
|
|
O
|
A:LEU277
|
4.6
|
10.7
|
1.0
|
|
H
|
A:ARG278
|
4.6
|
12.0
|
1.0
|
|
CA
|
A:ARG278
|
4.6
|
9.7
|
1.0
|
|
HE
|
A:ARG245
|
4.6
|
18.4
|
1.0
|
|
C
|
A:GLY280
|
4.7
|
12.6
|
1.0
|
|
HB2
|
A:LEU277
|
4.7
|
14.7
|
1.0
|
|
CA
|
A:LEU277
|
4.7
|
10.1
|
1.0
|
|
O
|
A:ARG278
|
4.8
|
9.9
|
1.0
|
|
N
|
A:GLU281
|
4.9
|
11.9
|
1.0
|
|
HA
|
A:LEU277
|
5.0
|
12.2
|
1.0
|
|
Sodium binding site 2 out
of 5 in 7xft
Go back to
Sodium Binding Sites List in 7xft
Sodium binding site 2 out
of 5 in the Mucp PDZ2 Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Mucp PDZ2 Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:42.5
occ:1.00
|
OE1
|
A:GLN273
|
2.3
|
24.0
|
1.0
|
|
HB3
|
A:ASP284
|
2.7
|
14.4
|
1.0
|
|
HB3
|
A:GLN273
|
3.2
|
18.5
|
1.0
|
|
H
|
A:VAL285
|
3.4
|
13.2
|
1.0
|
|
CD
|
A:GLN273
|
3.5
|
20.1
|
1.0
|
|
N
|
A:VAL285
|
3.6
|
11.0
|
1.0
|
|
C
|
A:VAL285
|
3.6
|
11.4
|
1.0
|
|
HA
|
A:GLN273
|
3.6
|
16.6
|
1.0
|
|
CB
|
A:ASP284
|
3.6
|
12.0
|
1.0
|
|
O
|
A:VAL285
|
3.6
|
13.2
|
1.0
|
|
HB2
|
A:ALA286
|
3.7
|
17.0
|
1.0
|
|
N
|
A:ALA286
|
3.8
|
11.2
|
1.0
|
|
H
|
A:LEU274
|
3.9
|
15.9
|
1.0
|
|
HA
|
A:ALA286
|
3.9
|
14.4
|
1.0
|
|
CB
|
A:GLN273
|
3.9
|
15.4
|
1.0
|
|
HB2
|
A:ASP284
|
4.0
|
14.4
|
1.0
|
|
C
|
A:ASP284
|
4.0
|
11.2
|
1.0
|
|
O
|
A:LEU274
|
4.1
|
13.5
|
1.0
|
|
HA
|
A:ASP284
|
4.1
|
13.5
|
1.0
|
|
H
|
A:ALA286
|
4.1
|
13.4
|
1.0
|
|
CA
|
A:VAL285
|
4.2
|
11.9
|
1.0
|
|
CA
|
A:GLN273
|
4.2
|
13.8
|
1.0
|
|
CA
|
A:ASP284
|
4.2
|
11.3
|
1.0
|
|
CG
|
A:GLN273
|
4.3
|
17.5
|
1.0
|
|
CA
|
A:ALA286
|
4.3
|
12.0
|
1.0
|
|
N
|
A:LEU274
|
4.3
|
13.2
|
1.0
|
|
HA
|
A:VAL285
|
4.4
|
14.2
|
1.0
|
|
CB
|
A:ALA286
|
4.5
|
14.2
|
1.0
|
|
HG3
|
A:GLN273
|
4.5
|
21.0
|
1.0
|
|
NE2
|
A:GLN273
|
4.6
|
20.7
|
1.0
|
|
OD1
|
A:ASP284
|
4.6
|
15.5
|
1.0
|
|
HE22
|
A:GLN273
|
4.6
|
24.9
|
1.0
|
|
CG
|
A:ASP284
|
4.6
|
13.8
|
1.0
|
|
C
|
A:GLN273
|
4.6
|
13.9
|
1.0
|
|
HB2
|
A:GLN273
|
4.8
|
18.5
|
1.0
|
|
O
|
A:ASP284
|
4.8
|
12.5
|
1.0
|
|
Sodium binding site 3 out
of 5 in 7xft
Go back to
Sodium Binding Sites List in 7xft
Sodium binding site 3 out
of 5 in the Mucp PDZ2 Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Mucp PDZ2 Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na404
b:39.6
occ:1.00
|
HE22
|
A:GLN247
|
2.3
|
31.1
|
1.0
|
|
O
|
A:HOH628
|
2.9
|
31.6
|
1.0
|
|
NE2
|
A:GLN247
|
3.1
|
25.9
|
1.0
|
|
HG21
|
A:VAL282
|
3.3
|
17.4
|
1.0
|
|
HE21
|
A:GLN247
|
3.4
|
31.1
|
1.0
|
|
HG22
|
A:VAL282
|
3.7
|
17.4
|
1.0
|
|
CG2
|
A:VAL282
|
3.8
|
14.5
|
1.0
|
|
HG23
|
A:VAL282
|
4.0
|
17.4
|
1.0
|
|
CD
|
A:GLN247
|
4.1
|
24.0
|
1.0
|
|
OE1
|
A:GLN247
|
4.3
|
24.9
|
1.0
|
|
HD13
|
A:LEU277
|
4.4
|
21.7
|
1.0
|
|
O
|
A:HOH504
|
4.5
|
32.4
|
1.0
|
|
HD22
|
A:LEU277
|
4.8
|
21.9
|
1.0
|
|
HG11
|
A:VAL282
|
4.9
|
19.6
|
1.0
|
|
Sodium binding site 4 out
of 5 in 7xft
Go back to
Sodium Binding Sites List in 7xft
Sodium binding site 4 out
of 5 in the Mucp PDZ2 Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Mucp PDZ2 Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na405
b:20.9
occ:1.00
|
H
|
A:GLU288
|
2.2
|
16.2
|
1.0
|
|
HB2
|
A:ALA238
|
2.7
|
16.2
|
1.0
|
|
HD12
|
A:LEU287
|
2.8
|
17.9
|
1.0
|
|
O
|
A:PRO234
|
2.9
|
11.0
|
1.0
|
|
HB2
|
A:GLU288
|
2.9
|
24.3
|
1.0
|
|
N
|
A:GLU288
|
3.0
|
13.5
|
1.0
|
|
HB3
|
A:PRO234
|
3.1
|
15.5
|
1.0
|
|
HA
|
A:LEU287
|
3.1
|
15.1
|
1.0
|
|
O
|
A:HOH622
|
3.2
|
37.4
|
1.0
|
|
HA
|
A:PRO234
|
3.3
|
13.7
|
1.0
|
|
HB3
|
A:ALA237
|
3.5
|
17.9
|
1.0
|
|
C
|
A:PRO234
|
3.6
|
10.3
|
1.0
|
|
CB
|
A:ALA238
|
3.6
|
13.5
|
1.0
|
|
CA
|
A:PRO234
|
3.7
|
11.4
|
1.0
|
|
CB
|
A:GLU288
|
3.7
|
20.3
|
1.0
|
|
CD1
|
A:LEU287
|
3.7
|
14.9
|
1.0
|
|
H
|
A:ALA238
|
3.8
|
14.7
|
1.0
|
|
CB
|
A:PRO234
|
3.8
|
12.9
|
1.0
|
|
CA
|
A:GLU288
|
3.8
|
14.4
|
1.0
|
|
O
|
A:GLU288
|
3.8
|
12.8
|
1.0
|
|
N
|
A:ALA238
|
3.9
|
12.2
|
1.0
|
|
CA
|
A:LEU287
|
3.9
|
12.6
|
1.0
|
|
C
|
A:LEU287
|
3.9
|
13.0
|
1.0
|
|
HA
|
A:ALA238
|
4.0
|
15.8
|
1.0
|
|
CA
|
A:ALA238
|
4.1
|
13.1
|
1.0
|
|
HD13
|
A:LEU287
|
4.1
|
17.9
|
1.0
|
|
HB2
|
A:PRO234
|
4.1
|
15.5
|
1.0
|
|
HG2
|
A:GLU288
|
4.1
|
34.2
|
1.0
|
|
HD11
|
A:LEU287
|
4.1
|
17.9
|
1.0
|
|
HB3
|
A:ALA238
|
4.1
|
16.2
|
1.0
|
|
HB1
|
A:ALA238
|
4.2
|
16.2
|
1.0
|
|
C
|
A:GLU288
|
4.2
|
12.5
|
1.0
|
|
CG
|
A:GLU288
|
4.4
|
28.5
|
1.0
|
|
O
|
A:ALA286
|
4.4
|
14.0
|
1.0
|
|
CB
|
A:ALA237
|
4.4
|
14.9
|
1.0
|
|
O
|
A:HOH518
|
4.4
|
27.1
|
1.0
|
|
HG3
|
A:GLU288
|
4.5
|
34.2
|
1.0
|
|
HB1
|
A:ALA237
|
4.5
|
17.9
|
1.0
|
|
HB3
|
A:GLU288
|
4.5
|
24.3
|
1.0
|
|
C
|
A:ALA237
|
4.5
|
13.6
|
1.0
|
|
HG
|
A:LEU287
|
4.6
|
16.4
|
1.0
|
|
CG
|
A:LEU287
|
4.6
|
13.7
|
1.0
|
|
HA
|
A:GLU288
|
4.7
|
17.3
|
1.0
|
|
N
|
A:ALA235
|
4.7
|
9.8
|
1.0
|
|
CB
|
A:LEU287
|
4.8
|
13.2
|
1.0
|
|
HA
|
A:ALA235
|
4.8
|
11.7
|
1.0
|
|
N
|
A:LEU287
|
4.9
|
12.6
|
1.0
|
|
CA
|
A:ALA237
|
5.0
|
13.4
|
1.0
|
|
HG3
|
A:PRO234
|
5.0
|
16.1
|
1.0
|
|
Sodium binding site 5 out
of 5 in 7xft
Go back to
Sodium Binding Sites List in 7xft
Sodium binding site 5 out
of 5 in the Mucp PDZ2 Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Mucp PDZ2 Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na406
b:23.1
occ:1.00
|
O
|
A:ASP262
|
2.8
|
12.7
|
1.0
|
|
HB2
|
A:ALA266
|
2.8
|
14.6
|
1.0
|
|
O
|
A:HOH571
|
2.9
|
23.7
|
1.0
|
|
HB2
|
A:ARG265
|
3.1
|
15.5
|
1.0
|
|
HA
|
A:ASP262
|
3.2
|
16.0
|
1.0
|
|
H
|
A:ALA266
|
3.5
|
12.3
|
1.0
|
|
C
|
A:ASP262
|
3.6
|
12.0
|
1.0
|
|
N
|
A:ALA266
|
3.7
|
10.2
|
1.0
|
|
CB
|
A:ALA266
|
3.7
|
12.2
|
1.0
|
|
HB3
|
A:ARG265
|
3.7
|
15.5
|
1.0
|
|
CA
|
A:ASP262
|
3.8
|
13.3
|
1.0
|
|
HB3
|
A:ASP262
|
3.8
|
19.3
|
1.0
|
|
CB
|
A:ARG265
|
3.9
|
12.9
|
1.0
|
|
HA
|
A:ALA266
|
4.0
|
12.9
|
1.0
|
|
CA
|
A:ALA266
|
4.0
|
10.8
|
1.0
|
|
HB3
|
A:ALA266
|
4.1
|
14.6
|
1.0
|
|
O
|
A:HOH509
|
4.1
|
33.5
|
1.0
|
|
C
|
A:ARG265
|
4.2
|
10.3
|
1.0
|
|
CB
|
A:ASP262
|
4.3
|
16.1
|
1.0
|
|
HB1
|
A:ALA266
|
4.3
|
14.6
|
1.0
|
|
HE
|
A:ARG265
|
4.4
|
26.8
|
1.0
|
|
HD3
|
A:ARG265
|
4.5
|
22.6
|
1.0
|
|
CA
|
A:ARG265
|
4.6
|
11.0
|
1.0
|
|
H
|
A:ARG265
|
4.7
|
12.1
|
1.0
|
|
OD1
|
A:ASP262
|
4.8
|
21.1
|
1.0
|
|
CG
|
A:ASP262
|
4.8
|
19.6
|
1.0
|
|
N
|
A:SER263
|
4.9
|
11.7
|
1.0
|
|
O
|
A:VAL261
|
4.9
|
12.6
|
1.0
|
|
N
|
A:ARG265
|
4.9
|
10.1
|
1.0
|
|
O
|
A:ARG265
|
5.0
|
11.2
|
1.0
|
|
Reference:
X.Lou,
S.Li,
Q.Zhang,
M.Bartlam.
Mucp PDZ2 Domain To Be Published.
Page generated: Wed Oct 9 09:42:42 2024
|
