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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:

Zinc (Zn) 3 atoms

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: Tue Jul 15 14:58:57 2025

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