Sodium in PDB 7xbe: Co-Crystal Structure of Ccpe-Rd with Citrate
Protein crystallography data
The structure of Co-Crystal Structure of Ccpe-Rd with Citrate, PDB code: 7xbe
was solved by
L.F.Lan,
F.F.Chen,
J.H.Gan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.65
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.935,
38.799,
54.504,
90,
118.01,
90
|
R / Rfree (%)
|
18.9 /
22.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Co-Crystal Structure of Ccpe-Rd with Citrate
(pdb code 7xbe). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Co-Crystal Structure of Ccpe-Rd with Citrate, PDB code: 7xbe:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 7xbe
Go back to
Sodium Binding Sites List in 7xbe
Sodium binding site 1 out
of 2 in the Co-Crystal Structure of Ccpe-Rd with Citrate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Co-Crystal Structure of Ccpe-Rd with Citrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:25.6
occ:1.00
|
O
|
A:GLN183
|
2.3
|
22.5
|
1.0
|
O
|
A:ASP211
|
2.3
|
24.4
|
1.0
|
O
|
A:HOH465
|
2.3
|
38.2
|
1.0
|
OG1
|
A:FLC301
|
2.5
|
29.2
|
1.0
|
OHB
|
A:FLC301
|
2.7
|
29.2
|
1.0
|
C
|
A:GLN183
|
3.4
|
23.1
|
1.0
|
CGC
|
A:FLC301
|
3.4
|
32.5
|
1.0
|
C
|
A:ASP211
|
3.5
|
23.4
|
1.0
|
CG
|
A:FLC301
|
3.6
|
34.3
|
1.0
|
CB
|
A:FLC301
|
3.9
|
34.6
|
1.0
|
O
|
A:HOH419
|
3.9
|
35.2
|
1.0
|
N
|
A:GLN183
|
3.9
|
22.8
|
1.0
|
CA
|
A:GLN183
|
4.0
|
24.0
|
1.0
|
O
|
A:HOH446
|
4.0
|
36.1
|
1.0
|
CB
|
A:GLN183
|
4.0
|
27.0
|
1.0
|
CA
|
A:GLN212
|
4.1
|
22.7
|
1.0
|
N
|
A:GLN212
|
4.2
|
22.7
|
1.0
|
CA
|
A:FLC301
|
4.3
|
34.0
|
1.0
|
N
|
A:VAL213
|
4.3
|
20.6
|
1.0
|
CD1
|
A:PHE182
|
4.4
|
20.2
|
1.0
|
N
|
A:ALA184
|
4.5
|
22.1
|
1.0
|
OB1
|
A:FLC301
|
4.5
|
34.0
|
1.0
|
C
|
A:GLN212
|
4.5
|
21.4
|
1.0
|
OG2
|
A:FLC301
|
4.6
|
28.7
|
1.0
|
CG
|
A:GLN183
|
4.6
|
30.3
|
1.0
|
CA
|
A:ASP211
|
4.6
|
24.1
|
1.0
|
CB
|
A:PHE182
|
4.6
|
20.4
|
1.0
|
CG2
|
A:VAL213
|
4.6
|
21.2
|
1.0
|
CBC
|
A:FLC301
|
4.7
|
36.9
|
1.0
|
OE1
|
A:GLN183
|
4.7
|
39.1
|
1.0
|
CA
|
A:ALA184
|
4.8
|
22.2
|
1.0
|
C
|
A:PHE182
|
4.8
|
21.5
|
1.0
|
OA1
|
A:FLC301
|
4.9
|
29.9
|
1.0
|
CG
|
A:PHE182
|
4.9
|
19.9
|
1.0
|
CB
|
A:ALA184
|
5.0
|
21.5
|
1.0
|
|
Sodium binding site 2 out
of 2 in 7xbe
Go back to
Sodium Binding Sites List in 7xbe
Sodium binding site 2 out
of 2 in the Co-Crystal Structure of Ccpe-Rd with Citrate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Co-Crystal Structure of Ccpe-Rd with Citrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na303
b:29.4
occ:1.00
|
O
|
A:HOH464
|
2.7
|
21.6
|
1.0
|
O
|
A:ILE228
|
3.0
|
22.2
|
1.0
|
OG1
|
A:THR227
|
3.1
|
21.5
|
1.0
|
O
|
A:ILE180
|
3.3
|
21.8
|
1.0
|
N
|
A:ILE228
|
3.5
|
21.0
|
1.0
|
CE2
|
A:PHE182
|
3.6
|
20.3
|
1.0
|
CD2
|
A:PHE182
|
3.7
|
19.9
|
1.0
|
CZ
|
A:PHE179
|
3.7
|
22.3
|
1.0
|
CE2
|
A:PHE179
|
3.8
|
22.8
|
1.0
|
C
|
A:ILE228
|
3.9
|
20.5
|
1.0
|
CA
|
A:ILE228
|
4.0
|
21.1
|
1.0
|
CB
|
A:ILE228
|
4.0
|
21.2
|
1.0
|
CB
|
A:THR227
|
4.3
|
21.6
|
1.0
|
CA
|
A:GLU181
|
4.3
|
21.5
|
1.0
|
N
|
A:PHE182
|
4.3
|
20.6
|
1.0
|
CD1
|
A:ILE192
|
4.3
|
19.4
|
1.0
|
CG2
|
A:ILE192
|
4.4
|
18.9
|
1.0
|
C
|
A:ILE180
|
4.4
|
21.0
|
1.0
|
CZ
|
A:PHE182
|
4.4
|
20.1
|
1.0
|
SG
|
A:CYS216
|
4.5
|
26.0
|
1.0
|
C
|
A:THR227
|
4.5
|
21.7
|
1.0
|
CA
|
A:THR227
|
4.6
|
21.3
|
1.0
|
CG
|
A:PHE182
|
4.6
|
19.9
|
1.0
|
C
|
A:GLU181
|
4.8
|
21.8
|
1.0
|
N
|
A:GLU181
|
4.8
|
21.4
|
1.0
|
CE1
|
A:PHE179
|
4.9
|
22.9
|
1.0
|
CD2
|
A:PHE179
|
4.9
|
22.3
|
1.0
|
CG2
|
A:ILE228
|
4.9
|
21.5
|
1.0
|
|
Reference:
L.F.Lan,
F.F.Chen,
J.H.Gan.
Co-Crystal Structure of Ccpe-Rd with Citrate To Be Published.
Page generated: Tue Apr 11 17:36:52 2023
|