Sodium in PDB 8c6g: Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5
Protein crystallography data
The structure of Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5, PDB code: 8c6g
was solved by
K.E.Tsitsanou,
C.E.Drakou,
S.E.Zographos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.73 /
2.05
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.355,
57.03,
67.34,
90,
100.21,
90
|
R / Rfree (%)
|
19.3 /
22.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5
(pdb code 8c6g). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5, PDB code: 8c6g:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 8c6g
Go back to
Sodium Binding Sites List in 8c6g
Sodium binding site 1 out
of 4 in the Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:29.7
occ:1.00
|
O
|
A:PRO119
|
2.3
|
24.3
|
1.0
|
OG1
|
A:THR118
|
2.4
|
21.6
|
1.0
|
OG
|
A:SER35
|
2.4
|
20.6
|
1.0
|
O
|
A:ALA115
|
2.4
|
19.1
|
1.0
|
O
|
A:THR118
|
2.6
|
25.1
|
1.0
|
O
|
A:HOH302
|
2.7
|
26.4
|
1.0
|
C
|
A:THR118
|
3.1
|
25.1
|
1.0
|
CB
|
A:SER35
|
3.1
|
18.8
|
1.0
|
C
|
A:PRO119
|
3.1
|
26.5
|
1.0
|
C
|
A:ALA115
|
3.4
|
18.4
|
1.0
|
CB
|
A:THR118
|
3.4
|
23.1
|
1.0
|
NA
|
A:NA202
|
3.5
|
30.2
|
1.0
|
N
|
A:PRO119
|
3.7
|
27.2
|
1.0
|
CA
|
A:ALA115
|
3.7
|
17.0
|
1.0
|
CA
|
A:THR118
|
3.7
|
24.1
|
1.0
|
CA
|
A:PRO119
|
3.9
|
27.9
|
1.0
|
CB
|
A:PHE122
|
4.0
|
25.1
|
1.0
|
N
|
A:ASP120
|
4.0
|
28.1
|
1.0
|
N
|
A:THR118
|
4.1
|
22.6
|
1.0
|
O
|
A:SER35
|
4.1
|
19.0
|
1.0
|
CA
|
A:ASP120
|
4.2
|
28.7
|
1.0
|
O
|
A:PHE122
|
4.4
|
25.5
|
1.0
|
O
|
A:ALA114
|
4.4
|
19.1
|
1.0
|
CA
|
A:SER35
|
4.4
|
17.7
|
1.0
|
CB
|
A:ALA115
|
4.6
|
15.4
|
1.0
|
N
|
A:PHE122
|
4.6
|
27.5
|
1.0
|
N
|
A:ASP116
|
4.7
|
18.8
|
1.0
|
C
|
A:SER35
|
4.7
|
18.0
|
1.0
|
OD1
|
A:ASP120
|
4.8
|
29.7
|
1.0
|
CA
|
A:PHE122
|
4.8
|
27.0
|
1.0
|
CG2
|
A:THR118
|
4.8
|
22.6
|
1.0
|
C
|
A:ASP120
|
4.8
|
29.4
|
1.0
|
N
|
A:ALA115
|
4.8
|
16.5
|
1.0
|
O
|
A:HOH323
|
4.9
|
29.0
|
1.0
|
CD2
|
A:PHE122
|
4.9
|
22.9
|
1.0
|
CG
|
A:PHE122
|
4.9
|
25.2
|
1.0
|
|
Sodium binding site 2 out
of 4 in 8c6g
Go back to
Sodium Binding Sites List in 8c6g
Sodium binding site 2 out
of 4 in the Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:30.2
occ:1.00
|
O
|
A:THR118
|
2.3
|
25.1
|
1.0
|
O
|
A:HOH343
|
2.4
|
31.9
|
1.0
|
O
|
A:HOH302
|
2.4
|
26.4
|
1.0
|
O
|
A:HOH340
|
2.4
|
48.7
|
1.0
|
O
|
A:ASP116
|
2.8
|
22.8
|
1.0
|
O
|
A:ALA115
|
2.9
|
19.1
|
1.0
|
C
|
A:ASP116
|
3.5
|
21.5
|
1.0
|
NA
|
A:NA201
|
3.5
|
29.7
|
1.0
|
C
|
A:THR118
|
3.5
|
25.1
|
1.0
|
CA
|
A:ASP116
|
3.8
|
20.4
|
1.0
|
C
|
A:ALA115
|
3.9
|
18.4
|
1.0
|
O
|
A:HOH301
|
3.9
|
29.2
|
1.0
|
N
|
A:THR118
|
4.2
|
22.6
|
1.0
|
OD1
|
A:ASP120
|
4.2
|
29.7
|
1.0
|
CA
|
A:PRO119
|
4.3
|
27.9
|
1.0
|
N
|
A:ASP116
|
4.3
|
18.8
|
1.0
|
C
|
A:PRO119
|
4.4
|
26.5
|
1.0
|
N
|
A:PRO119
|
4.4
|
27.2
|
1.0
|
N
|
A:PHE117
|
4.5
|
20.5
|
1.0
|
CA
|
A:THR118
|
4.5
|
24.1
|
1.0
|
C
|
A:PHE117
|
4.5
|
23.5
|
1.0
|
O
|
A:PRO119
|
4.6
|
24.3
|
1.0
|
O
|
A:PHE117
|
4.8
|
24.2
|
1.0
|
OG1
|
A:THR118
|
4.9
|
21.6
|
1.0
|
N
|
A:ASP120
|
4.9
|
28.1
|
1.0
|
O
|
A:SER35
|
4.9
|
19.0
|
1.0
|
|
Sodium binding site 3 out
of 4 in 8c6g
Go back to
Sodium Binding Sites List in 8c6g
Sodium binding site 3 out
of 4 in the Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na203
b:46.2
occ:1.00
|
OD2
|
A:ASP116
|
2.3
|
24.6
|
1.0
|
CG
|
A:ASP116
|
3.4
|
22.4
|
1.0
|
CB
|
A:ASP116
|
3.8
|
21.0
|
1.0
|
CE
|
A:LYS112
|
4.2
|
21.1
|
1.0
|
OD1
|
A:ASP116
|
4.4
|
24.1
|
1.0
|
NZ
|
A:LYS112
|
4.6
|
19.3
|
1.0
|
CG
|
A:LYS112
|
4.9
|
16.0
|
1.0
|
CD
|
A:LYS112
|
5.0
|
17.7
|
1.0
|
|
Sodium binding site 4 out
of 4 in 8c6g
Go back to
Sodium Binding Sites List in 8c6g
Sodium binding site 4 out
of 4 in the Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Odorant Binding Protein 4 From Anopheles Gambiae (AGAMOBP4) at pH 6.5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na204
b:51.5
occ:1.00
|
OE1
|
A:GLN6
|
2.3
|
24.9
|
1.0
|
O
|
A:ALA1
|
2.9
|
33.0
|
1.0
|
CD
|
A:GLN6
|
3.3
|
27.4
|
1.0
|
O
|
A:HOH329
|
3.5
|
36.5
|
1.0
|
N
|
A:THR3
|
3.5
|
24.6
|
1.0
|
CA
|
A:MET2
|
3.6
|
28.1
|
1.0
|
NE2
|
A:GLN6
|
3.6
|
27.2
|
1.0
|
C
|
A:MET2
|
3.8
|
26.5
|
1.0
|
C
|
A:ALA1
|
3.9
|
33.8
|
1.0
|
CG2
|
A:THR3
|
3.9
|
25.1
|
1.0
|
N
|
A:MET2
|
4.1
|
31.3
|
1.0
|
CA
|
A:THR3
|
4.6
|
23.5
|
1.0
|
CG
|
A:GLN6
|
4.7
|
24.6
|
1.0
|
CB
|
A:THR3
|
4.7
|
24.1
|
1.0
|
O
|
A:MET2
|
4.7
|
26.0
|
1.0
|
CB
|
A:MET2
|
4.7
|
27.4
|
1.0
|
OG1
|
A:THR3
|
4.9
|
23.9
|
1.0
|
|
Reference:
B.Mam,
K.E.Tsitsanou,
P.G.V.Liggri,
F.Saitta,
E.C.V.Stamati,
J.Mahita,
G.Leonis,
C.E.Drakou,
M.Papadopoulos,
P.Arnaud,
B.Offmann,
D.Fessas,
R.Sowdhamini,
S.E.Zographos.
Influence of pH on Indole-Dependent Heterodimeric Interactions Between Anopheles Gambiae Odorant-Binding Proteins OBP1 and OBP4. To Be Published.
Page generated: Mon Aug 18 13:23:48 2025
|