Fluorine in PDB 5zid: Crystal Structure of Human Dpp-IV in Complex with HL2

Enzymatic activity of Crystal Structure of Human Dpp-IV in Complex with HL2

All present enzymatic activity of Crystal Structure of Human Dpp-IV in Complex with HL2:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Human Dpp-IV in Complex with HL2, PDB code: 5zid was solved by L.Zhu, H.Li, F.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.82 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.070, 126.190, 118.620, 90.00, 99.30, 90.00
R / Rfree (%) 19.1 / 25.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Dpp-IV in Complex with HL2 (pdb code 5zid). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Dpp-IV in Complex with HL2, PDB code: 5zid:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5zid

Go back to Fluorine Binding Sites List in 5zid
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL2


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 Human Dpp-IV in Complex with HL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:30.8
occ:1.00
F7 A:9EL802 0.0 30.8 1.0
C1 A:9EL802 1.3 25.4 1.0
C2 A:9EL802 2.3 22.9 1.0
C6 A:9EL802 2.4 25.1 1.0
C10 A:9EL802 2.6 21.0 1.0
OE2 A:GLU205 3.0 14.8 1.0
N16 A:9EL802 3.2 20.8 1.0
NH2 A:ARG125 3.2 16.1 1.0
OH A:TYR662 3.5 20.6 1.0
C15 A:9EL802 3.5 20.4 1.0
C3 A:9EL802 3.5 24.0 1.0
ND2 A:ASN710 3.5 19.2 1.0
C5 A:9EL802 3.6 24.5 1.0
O11 A:9EL802 3.8 20.4 1.0
OD1 A:ASN710 4.0 18.7 1.0
NE2 A:HIS740 4.0 22.2 1.0
C4 A:9EL802 4.1 24.0 1.0
CG A:ASN710 4.1 19.1 1.0
CD2 A:HIS740 4.1 21.7 1.0
CD A:GLU205 4.3 15.3 1.0
C14 A:9EL802 4.4 20.2 1.0
CZ A:ARG125 4.5 16.2 1.0
OG A:SER630 4.7 16.6 1.0
CZ A:TYR662 4.8 20.9 1.0
F8 A:9EL802 4.8 25.4 1.0
C12 A:9EL802 4.8 19.1 1.0
OE1 A:GLU205 4.9 14.9 1.0

Fluorine binding site 2 out of 6 in 5zid

Go back to Fluorine Binding Sites List in 5zid
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL2


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 Human Dpp-IV in Complex with HL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:25.4
occ:1.00
F8 A:9EL802 0.0 25.4 1.0
C5 A:9EL802 1.3 24.5 1.0
C4 A:9EL802 2.3 24.0 1.0
C6 A:9EL802 2.4 25.1 1.0
F9 A:9EL802 2.6 25.6 1.0
CG2 A:VAL711 3.3 16.7 1.0
CG2 A:VAL656 3.4 18.9 1.0
C3 A:9EL802 3.6 24.0 1.0
C1 A:9EL802 3.6 25.4 1.0
CB A:SER630 3.7 16.4 1.0
N A:TYR631 3.9 16.1 1.0
CA A:SER630 3.9 16.5 1.0
C A:SER630 4.0 16.2 1.0
CZ A:TYR662 4.0 20.9 1.0
OG A:SER630 4.1 16.6 1.0
C2 A:9EL802 4.1 22.9 1.0
OH A:TYR662 4.1 20.6 1.0
CE1 A:TYR662 4.3 21.2 1.0
NE2 A:HIS740 4.3 22.2 1.0
CE2 A:TYR662 4.4 20.4 1.0
CE1 A:HIS740 4.4 22.0 1.0
CA A:TYR631 4.5 15.3 1.0
O A:SER630 4.7 16.5 1.0
CB A:VAL711 4.7 16.3 1.0
F7 A:9EL802 4.8 30.8 1.0
CB A:VAL656 4.8 18.7 1.0
CD1 A:TYR662 4.9 20.2 1.0
CB A:TYR631 4.9 14.6 1.0
CD2 A:TYR662 4.9 20.0 1.0

Fluorine binding site 3 out of 6 in 5zid

Go back to Fluorine Binding Sites List in 5zid
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL2


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 Human Dpp-IV in Complex with HL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:25.6
occ:1.00
F9 A:9EL802 0.0 25.6 1.0
C4 A:9EL802 1.3 24.0 1.0
C5 A:9EL802 2.3 24.5 1.0
C3 A:9EL802 2.4 24.0 1.0
F8 A:9EL802 2.6 25.4 1.0
CD2 A:TYR631 3.4 14.1 1.0
CB A:TYR631 3.5 14.6 1.0
C6 A:9EL802 3.6 25.1 1.0
C2 A:9EL802 3.6 22.9 1.0
OH A:TYR666 3.8 19.8 1.0
CZ A:TYR666 3.9 18.6 1.0
CG A:TYR631 3.9 14.0 1.0
CA A:TYR631 4.0 15.3 1.0
N A:TYR631 4.0 16.1 1.0
C1 A:9EL802 4.1 25.4 1.0
CE1 A:TYR666 4.2 18.0 1.0
CE2 A:TYR662 4.2 20.4 1.0
CH2 A:TRP659 4.3 15.2 1.0
CG2 A:VAL656 4.4 18.9 1.0
CE2 A:TYR666 4.4 17.9 1.0
CZ3 A:TRP659 4.5 15.2 1.0
CE2 A:TYR631 4.5 14.1 1.0
CZ A:TYR662 4.6 20.9 1.0
CD2 A:TYR662 4.7 20.0 1.0
OH A:TYR662 4.8 20.6 1.0
C10 A:9EL802 4.8 21.0 1.0
CD1 A:TYR666 4.9 17.0 1.0
C A:SER630 4.9 16.2 1.0
CB A:SER630 4.9 16.4 1.0
OH A:TYR547 4.9 19.1 1.0

Fluorine binding site 4 out of 6 in 5zid

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Fluorine binding site 4 out of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Dpp-IV in Complex with HL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F806

b:22.4
occ:1.00
F7 B:9EL806 0.0 22.4 1.0
C1 B:9EL806 1.4 22.6 1.0
C2 B:9EL806 2.4 21.5 1.0
C6 B:9EL806 2.4 22.2 1.0
C10 B:9EL806 2.7 20.4 1.0
N16 B:9EL806 2.8 20.7 1.0
NH2 B:ARG125 3.2 22.4 1.0
C15 B:9EL806 3.4 20.2 1.0
ND2 B:ASN710 3.4 21.3 1.0
OE2 B:GLU205 3.6 13.7 1.0
C3 B:9EL806 3.7 22.0 1.0
C5 B:9EL806 3.7 21.1 1.0
OH B:TYR662 3.7 20.1 1.0
O11 B:9EL806 3.9 20.7 1.0
OG B:SER630 4.0 19.1 1.0
CG B:ASN710 4.2 21.6 1.0
C4 B:9EL806 4.2 21.6 1.0
OD1 B:ASN710 4.3 24.8 1.0
C14 B:9EL806 4.4 20.7 1.0
CZ B:ARG125 4.5 22.2 1.0
CD2 B:HIS740 4.6 16.3 1.0
NE2 B:HIS740 4.6 16.1 1.0
CD B:GLU205 4.7 14.4 1.0
F8 B:9EL806 4.7 20.0 1.0
C12 B:9EL806 4.9 21.0 1.0

Fluorine binding site 5 out of 6 in 5zid

Go back to Fluorine Binding Sites List in 5zid
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Dpp-IV in Complex with HL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F806

b:20.0
occ:1.00
F8 B:9EL806 0.0 20.0 1.0
C5 B:9EL806 1.3 21.1 1.0
C4 B:9EL806 2.3 21.6 1.0
C6 B:9EL806 2.3 22.2 1.0
F9 B:9EL806 2.7 20.5 1.0
OG B:SER630 3.3 19.1 1.0
CG2 B:VAL711 3.3 16.8 1.0
CG2 B:VAL656 3.5 16.2 1.0
C3 B:9EL806 3.6 22.0 1.0
C1 B:9EL806 3.6 22.6 1.0
CE1 B:TYR662 3.9 22.0 1.0
N B:TYR631 4.0 16.2 1.0
OH B:TYR662 4.0 20.1 1.0
CZ B:TYR662 4.0 21.7 1.0
C2 B:9EL806 4.1 21.5 1.0
C B:SER630 4.1 17.1 1.0
CA B:SER630 4.2 17.9 1.0
CB B:SER630 4.2 18.9 1.0
NE2 B:HIS740 4.5 16.1 1.0
CD1 B:TYR662 4.6 21.3 1.0
CA B:TYR631 4.6 15.3 1.0
CE1 B:HIS740 4.6 16.2 1.0
O B:SER630 4.7 17.5 1.0
F7 B:9EL806 4.7 22.4 1.0
CB B:VAL711 4.8 16.5 1.0
CE2 B:TYR662 4.8 21.3 1.0
CB B:VAL656 4.8 15.9 1.0

Fluorine binding site 6 out of 6 in 5zid

Go back to Fluorine Binding Sites List in 5zid
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Dpp-IV in Complex with HL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F806

b:20.5
occ:1.00
F9 B:9EL806 0.0 20.5 1.0
C4 B:9EL806 1.3 21.6 1.0
C5 B:9EL806 2.4 21.1 1.0
C3 B:9EL806 2.4 22.0 1.0
F8 B:9EL806 2.7 20.0 1.0
CD2 B:TYR631 3.4 14.8 1.0
C6 B:9EL806 3.6 22.2 1.0
C2 B:9EL806 3.7 21.5 1.0
OH B:TYR666 3.7 17.4 1.0
CB B:TYR631 3.8 15.2 1.0
CZ B:TYR666 3.8 16.9 1.0
CE1 B:TYR666 3.9 16.5 1.0
CA B:TYR631 4.0 15.3 1.0
CG B:TYR631 4.0 14.9 1.0
N B:TYR631 4.1 16.2 1.0
CH2 B:TRP659 4.2 14.5 1.0
C1 B:9EL806 4.2 22.6 1.0
CE2 B:TYR631 4.4 14.5 1.0
CE2 B:TYR666 4.5 16.7 1.0
CZ3 B:TRP659 4.6 14.6 1.0
CZ B:TYR662 4.6 21.7 1.0
OG B:SER630 4.7 19.1 1.0
CG2 B:VAL656 4.7 16.2 1.0
OH B:TYR662 4.7 20.1 1.0
CD1 B:TYR666 4.7 16.5 1.0
CE2 B:TYR662 4.7 21.3 1.0
C B:SER630 4.9 17.1 1.0
C10 B:9EL806 4.9 20.4 1.0
O11 B:9EL806 5.0 20.7 1.0

Reference:

L.Zhu, H.Li, F.Wu. Crystal Structure of Human Dpp-IV in Complex with HL2 To Be Published.
Page generated: Sun Dec 13 12:43:45 2020

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