Fluorine in PDB 6qba: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold
Protein crystallography data
The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold, PDB code: 6qba
was solved by
G.Mlynek,
C.U.Brey,
K.Djinovic-Carugo,
D.Puehringer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.25 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.456,
77.614,
80.509,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.8 /
22.1
|
Other elements in 6qba:
The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold
(pdb code 6qba). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold, PDB code: 6qba:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6qba
Go back to
Fluorine Binding Sites List in 6qba
Fluorine binding site 1 out
of 3 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:33.1
occ:1.00
|
F1
|
A:2T1201
|
0.0
|
33.1
|
1.0
|
C12
|
A:2T1201
|
1.3
|
33.2
|
1.0
|
F3
|
A:2T1201
|
2.1
|
35.1
|
1.0
|
F2
|
A:2T1201
|
2.2
|
34.4
|
1.0
|
H11
|
A:2T1201
|
2.2
|
28.2
|
1.0
|
C4
|
A:2T1201
|
2.4
|
30.7
|
1.0
|
H7
|
A:2T1201
|
2.7
|
23.4
|
1.0
|
HE2
|
A:PHE135
|
2.9
|
26.6
|
1.0
|
C11
|
A:2T1201
|
3.0
|
23.5
|
1.0
|
C3
|
A:2T1201
|
3.0
|
26.4
|
1.0
|
C7
|
A:2T1201
|
3.1
|
19.5
|
1.0
|
C5
|
A:2T1201
|
3.4
|
31.7
|
1.0
|
HZ
|
A:PHE137
|
3.5
|
32.7
|
1.0
|
CE2
|
A:PHE135
|
3.5
|
22.1
|
1.0
|
H5
|
A:2T1201
|
3.6
|
38.0
|
1.0
|
H10
|
A:2T1201
|
3.7
|
33.3
|
1.0
|
H11A
|
A:2T1201
|
3.7
|
28.2
|
1.0
|
HD2
|
A:PHE135
|
3.7
|
28.7
|
1.0
|
HB2
|
A:ALA57
|
3.9
|
32.3
|
1.0
|
C10
|
A:2T1201
|
3.9
|
27.7
|
1.0
|
HE1
|
A:HIS104
|
3.9
|
35.7
|
1.0
|
CD2
|
A:PHE135
|
4.0
|
23.9
|
1.0
|
H10A
|
A:2T1201
|
4.3
|
33.3
|
1.0
|
HE1
|
A:TYR133
|
4.3
|
29.3
|
1.0
|
HB1
|
A:ALA57
|
4.3
|
32.3
|
1.0
|
C2
|
A:2T1201
|
4.3
|
29.0
|
1.0
|
CZ
|
A:PHE137
|
4.4
|
27.2
|
1.0
|
HE1
|
A:MET88
|
4.4
|
38.3
|
1.0
|
HB2
|
A:ALA43
|
4.4
|
33.5
|
1.0
|
CB
|
A:ALA57
|
4.5
|
26.9
|
1.0
|
C8
|
A:2T1201
|
4.5
|
22.3
|
1.0
|
CZ
|
A:PHE135
|
4.5
|
21.2
|
1.0
|
C6
|
A:2T1201
|
4.6
|
31.1
|
1.0
|
HZ
|
A:PHE135
|
4.7
|
25.4
|
1.0
|
CE1
|
A:HIS104
|
4.7
|
29.8
|
1.0
|
HB3
|
A:ALA57
|
4.8
|
32.3
|
1.0
|
H8
|
A:2T1201
|
4.9
|
26.7
|
1.0
|
HE2
|
A:PHE137
|
4.9
|
32.4
|
1.0
|
H2
|
A:2T1201
|
5.0
|
34.8
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6qba
Go back to
Fluorine Binding Sites List in 6qba
Fluorine binding site 2 out
of 3 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:35.1
occ:1.00
|
F3
|
A:2T1201
|
0.0
|
35.1
|
1.0
|
C12
|
A:2T1201
|
1.4
|
33.2
|
1.0
|
F1
|
A:2T1201
|
2.1
|
33.1
|
1.0
|
F2
|
A:2T1201
|
2.2
|
34.4
|
1.0
|
H5
|
A:2T1201
|
2.3
|
38.0
|
1.0
|
C4
|
A:2T1201
|
2.4
|
30.7
|
1.0
|
HE1
|
A:HIS104
|
2.6
|
35.7
|
1.0
|
C5
|
A:2T1201
|
2.6
|
31.7
|
1.0
|
HZ
|
A:PHE45
|
3.2
|
34.9
|
1.0
|
CE1
|
A:HIS104
|
3.4
|
29.8
|
1.0
|
C3
|
A:2T1201
|
3.7
|
26.4
|
1.0
|
HZ
|
A:PHE137
|
3.8
|
32.7
|
1.0
|
CZ
|
A:PHE45
|
3.9
|
29.1
|
1.0
|
HZ
|
A:PHE77
|
3.9
|
41.7
|
1.0
|
C6
|
A:2T1201
|
4.0
|
31.1
|
1.0
|
H7
|
A:2T1201
|
4.0
|
23.4
|
1.0
|
ND1
|
A:HIS104
|
4.1
|
28.0
|
1.0
|
HE1
|
A:PHE45
|
4.1
|
34.3
|
1.0
|
H11
|
A:2T1201
|
4.2
|
28.2
|
1.0
|
HB2
|
A:ALA57
|
4.2
|
32.3
|
1.0
|
HB2
|
A:ALA43
|
4.2
|
33.5
|
1.0
|
HB1
|
A:ALA43
|
4.2
|
33.5
|
1.0
|
NE2
|
A:HIS104
|
4.4
|
29.3
|
1.0
|
CE1
|
A:PHE45
|
4.4
|
28.6
|
1.0
|
SD
|
A:MET88
|
4.4
|
30.6
|
1.0
|
C7
|
A:2T1201
|
4.4
|
19.5
|
1.0
|
HE2
|
A:PHE137
|
4.5
|
32.4
|
1.0
|
HE2
|
A:HIS104
|
4.5
|
35.2
|
1.0
|
H6
|
A:2T1201
|
4.5
|
37.3
|
1.0
|
HE1
|
A:MET88
|
4.5
|
38.3
|
1.0
|
CZ
|
A:PHE137
|
4.5
|
27.2
|
1.0
|
HB3
|
A:ALA55
|
4.6
|
33.6
|
1.0
|
HG3
|
A:GLN117
|
4.7
|
31.6
|
1.0
|
CB
|
A:ALA43
|
4.7
|
27.9
|
1.0
|
HB1
|
A:ALA55
|
4.8
|
33.6
|
1.0
|
C2
|
A:2T1201
|
4.8
|
29.0
|
1.0
|
C11
|
A:2T1201
|
4.8
|
23.5
|
1.0
|
CZ
|
A:PHE77
|
4.8
|
34.7
|
1.0
|
HE2
|
A:PHE135
|
4.8
|
26.6
|
1.0
|
CE2
|
A:PHE45
|
4.9
|
30.7
|
1.0
|
HD2
|
A:PHE135
|
4.9
|
28.7
|
1.0
|
C1
|
A:2T1201
|
4.9
|
25.5
|
1.0
|
CE2
|
A:PHE137
|
4.9
|
27.0
|
1.0
|
HE2
|
A:PHE77
|
4.9
|
42.3
|
1.0
|
HE2
|
A:PHE45
|
5.0
|
36.9
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6qba
Go back to
Fluorine Binding Sites List in 6qba
Fluorine binding site 3 out
of 3 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand A1120 and Engineered Binding Scaffold within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F201
b:34.4
occ:1.00
|
F2
|
A:2T1201
|
0.0
|
34.4
|
1.0
|
C12
|
A:2T1201
|
1.4
|
33.2
|
1.0
|
F1
|
A:2T1201
|
2.2
|
33.1
|
1.0
|
F3
|
A:2T1201
|
2.2
|
35.1
|
1.0
|
C4
|
A:2T1201
|
2.4
|
30.7
|
1.0
|
H7
|
A:2T1201
|
2.4
|
23.4
|
1.0
|
HE1
|
A:MET88
|
2.7
|
38.3
|
1.0
|
HE1
|
A:HIS104
|
2.8
|
35.7
|
1.0
|
C3
|
A:2T1201
|
3.1
|
26.4
|
1.0
|
C7
|
A:2T1201
|
3.1
|
19.5
|
1.0
|
ND1
|
A:HIS104
|
3.3
|
28.0
|
1.0
|
CE1
|
A:HIS104
|
3.4
|
29.8
|
1.0
|
CE
|
A:MET88
|
3.4
|
31.9
|
1.0
|
C5
|
A:2T1201
|
3.4
|
31.7
|
1.0
|
SD
|
A:MET88
|
3.4
|
30.6
|
1.0
|
O
|
A:HOH319
|
3.5
|
32.4
|
1.0
|
H5
|
A:2T1201
|
3.6
|
38.0
|
1.0
|
H11
|
A:2T1201
|
3.7
|
28.2
|
1.0
|
HE1
|
A:TYR133
|
3.7
|
29.3
|
1.0
|
HE2
|
A:MET88
|
3.8
|
38.3
|
1.0
|
C11
|
A:2T1201
|
3.9
|
23.5
|
1.0
|
OH
|
A:TYR133
|
4.0
|
25.5
|
1.0
|
HE2
|
A:PHE135
|
4.1
|
26.6
|
1.0
|
H8
|
A:2T1201
|
4.1
|
26.7
|
1.0
|
HE21
|
A:GLN117
|
4.2
|
31.9
|
1.0
|
HE3
|
A:MET88
|
4.2
|
38.3
|
1.0
|
C8
|
A:2T1201
|
4.2
|
22.3
|
1.0
|
H10
|
A:2T1201
|
4.3
|
33.3
|
1.0
|
C2
|
A:2T1201
|
4.3
|
29.0
|
1.0
|
NE2
|
A:GLN117
|
4.4
|
26.6
|
1.0
|
HE22
|
A:GLN117
|
4.5
|
31.9
|
1.0
|
CE1
|
A:TYR133
|
4.5
|
24.4
|
1.0
|
HG3
|
A:GLN117
|
4.6
|
31.6
|
1.0
|
H9A
|
A:2T1201
|
4.6
|
23.1
|
1.0
|
HH
|
A:TYR133
|
4.6
|
30.6
|
1.0
|
C6
|
A:2T1201
|
4.6
|
31.1
|
1.0
|
NE2
|
A:HIS104
|
4.7
|
29.3
|
1.0
|
CG
|
A:HIS104
|
4.7
|
27.9
|
1.0
|
HD2
|
A:PHE135
|
4.7
|
28.7
|
1.0
|
C10
|
A:2T1201
|
4.7
|
27.7
|
1.0
|
H11A
|
A:2T1201
|
4.7
|
28.2
|
1.0
|
CZ
|
A:TYR133
|
4.7
|
27.5
|
1.0
|
HZ
|
A:PHE77
|
4.8
|
41.7
|
1.0
|
HE2
|
A:PHE77
|
4.9
|
42.3
|
1.0
|
CD
|
A:GLN117
|
4.9
|
26.9
|
1.0
|
CE2
|
A:PHE135
|
4.9
|
22.1
|
1.0
|
H8A
|
A:2T1201
|
4.9
|
26.7
|
1.0
|
C9
|
A:2T1201
|
5.0
|
19.3
|
1.0
|
H2
|
A:2T1201
|
5.0
|
34.8
|
1.0
|
HZ
|
A:PHE45
|
5.0
|
34.9
|
1.0
|
C1
|
A:2T1201
|
5.0
|
25.5
|
1.0
|
HZ
|
A:PHE137
|
5.0
|
32.7
|
1.0
|
|
Reference:
C.Brey,
G.Mlynek,
C.U.Brey,
K.Djinovic-Carugo,
D.Puehringer.
N/A N/A.
Page generated: Fri Aug 2 00:45:41 2024
|