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Fluorine in PDB 4dtc: Crystal Structure of Dpp-IV with Compound C5

Enzymatic activity of Crystal Structure of Dpp-IV with Compound C5

All present enzymatic activity of Crystal Structure of Dpp-IV with Compound C5:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Dpp-IV with Compound C5, PDB code: 4dtc was solved by B.Xiong, L.R.Zhu, D.Q.Chen, Y.L.Zhao, F.Jiang, J.K.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 3.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 80.466, 80.466, 290.901, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 26.8

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Dpp-IV with Compound C5 (pdb code 4dtc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Dpp-IV with Compound C5, PDB code: 4dtc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4dtc

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Fluorine binding site 1 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


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 Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:0.8
occ:1.00
 FBE A:D5C801 0.0 0.8 1.0
CBD A:D5C801 1.4 0.6 1.0
FBG A:D5C801 2.2 0.4 1.0
FBF A:D5C801 2.3 0.7 1.0
CBB A:D5C801 2.3 0.5 1.0
CBA A:D5C801 3.1 0.8 1.0
CBC A:D5C801 3.3 0.5 1.0
OE2 A:GLU361 3.5 0.8 1.0
CD A:GLU361 4.1 0.9 1.0
OE1 A:GLU361 4.3 0.2 1.0
CAZ A:D5C801 4.3 0.5 1.0
CAX A:D5C801 4.5 0.1 1.0
CA A:SER360 4.5 0.4 1.0
N A:GLU361 4.5 0.8 1.0
CAY A:D5C801 4.9 0.3 1.0
CB A:SER360 4.9 0.0 1.0

Fluorine binding site 2 out of 12 in 4dtc

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Fluorine binding site 2 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


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 Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:0.7
occ:1.00
 FBF A:D5C801 0.0 0.7 1.0
CBD A:D5C801 1.4 0.6 1.0
FBG A:D5C801 2.2 0.4 1.0
FBE A:D5C801 2.3 0.8 1.0
CBB A:D5C801 2.3 0.5 1.0
CBC A:D5C801 2.7 0.5 1.0
O A:ARG358 3.6 96.0 1.0
CBA A:D5C801 3.6 0.8 1.0
O A:PRO359 3.7 94.2 1.0
CG A:ARG358 3.7 94.8 1.0
CA A:SER360 3.9 0.4 1.0
CAX A:D5C801 4.1 0.1 1.0
C A:PRO359 4.1 99.2 1.0
C A:ARG358 4.3 98.2 1.0
N A:SER360 4.3 92.6 1.0
NE A:ARG358 4.5 0.7 1.0
CB A:SER360 4.7 0.0 1.0
CAZ A:D5C801 4.7 0.5 1.0
N A:ARG358 4.7 96.6 1.0
CD A:ARG358 4.7 0.7 1.0
CB A:ARG358 4.9 96.5 1.0
CA A:ARG358 4.9 92.4 1.0
C A:SER360 4.9 1.0 1.0
CAY A:D5C801 4.9 0.3 1.0
CAU A:D5C801 4.9 0.0 1.0
N A:GLU361 4.9 0.8 1.0

Fluorine binding site 3 out of 12 in 4dtc

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Fluorine binding site 3 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


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 Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:0.4
occ:1.00
 FBG A:D5C801 0.0 0.4 1.0
CBD A:D5C801 1.3 0.6 1.0
FBF A:D5C801 2.2 0.7 1.0
FBE A:D5C801 2.2 0.8 1.0
CBB A:D5C801 2.3 0.5 1.0
CBA A:D5C801 2.7 0.8 1.0
O A:PRO359 3.3 94.2 1.0
CBC A:D5C801 3.5 0.5 1.0
N A:GLU361 3.6 0.8 1.0
CA A:SER360 3.7 0.4 1.0
NE A:ARG358 3.7 0.7 1.0
CZ A:ARG358 3.7 0.1 1.0
NH2 A:ARG358 3.8 0.2 1.0
C A:SER360 3.9 1.0 1.0
CG A:ARG358 4.0 94.8 1.0
CAZ A:D5C801 4.1 0.5 1.0
C A:PRO359 4.2 99.2 1.0
OE2 A:GLU361 4.3 0.8 1.0
NH1 A:ARG358 4.3 0.5 1.0
CD A:ARG358 4.4 0.7 1.0
CB A:GLU361 4.4 1.0 1.0
N A:SER360 4.4 92.6 1.0
CD A:GLU361 4.5 0.9 1.0
CA A:GLU361 4.5 0.8 1.0
CAX A:D5C801 4.6 0.1 1.0
OE1 A:GLU361 4.7 0.2 1.0
CB A:SER360 4.8 0.0 1.0
O A:SER360 4.8 0.5 1.0
CAY A:D5C801 4.9 0.3 1.0
O A:ARG358 4.9 96.0 1.0

Fluorine binding site 4 out of 12 in 4dtc

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Fluorine binding site 4 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


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 Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:0.1
occ:1.00
 FAG A:D5C801 0.0 0.1 1.0
CAE A:D5C801 1.2 85.4 1.0
CAD A:D5C801 2.2 79.2 1.0
CAF A:D5C801 2.3 92.9 1.0
CAJ A:D5C801 2.7 90.7 1.0
NH2 A:ARG125 3.2 82.0 1.0
ND2 A:ASN710 3.2 61.9 1.0
OE2 A:GLU205 3.3 78.1 1.0
OH A:TYR662 3.4 83.5 1.0
NAM A:D5C801 3.4 77.4 1.0
CAC A:D5C801 3.5 93.4 1.0
CAA A:D5C801 3.5 89.1 1.0
CAK A:D5C801 3.7 80.6 1.0
OG A:SER630 3.8 81.7 1.0
CG A:ASN710 3.9 70.2 1.0
CAB A:D5C801 4.0 90.5 1.0
OD1 A:ASN710 4.0 84.4 1.0
CD2 A:HIS740 4.0 77.3 1.0
NE2 A:HIS740 4.0 83.2 1.0
CD A:GLU205 4.4 80.7 1.0
CZ A:ARG125 4.5 81.6 1.0
CZ A:TYR662 4.6 74.3 1.0
FAH A:D5C801 4.7 74.9 1.0
CAL A:D5C801 4.8 85.4 1.0

Fluorine binding site 5 out of 12 in 4dtc

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Fluorine binding site 5 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


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 Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:74.9
occ:1.00
 FAH A:D5C801 0.0 74.9 1.0
CAA A:D5C801 1.4 89.1 1.0
CAB A:D5C801 2.4 90.5 1.0
CAF A:D5C801 2.4 92.9 1.0
FAI A:D5C801 2.7 83.5 1.0
CG2 A:VAL656 3.1 77.0 1.0
CG2 A:VAL711 3.2 60.4 1.0
OG A:SER630 3.6 81.7 1.0
CAC A:D5C801 3.7 93.4 1.0
CAE A:D5C801 3.7 85.4 1.0
N A:TYR631 3.8 64.5 1.0
CZ A:TYR662 3.9 74.3 1.0
CE1 A:TYR662 4.0 72.3 1.0
C A:SER630 4.2 69.6 1.0
OH A:TYR662 4.2 83.5 1.0
CAD A:D5C801 4.2 79.2 1.0
CE2 A:TYR662 4.3 71.8 1.0
CA A:TYR631 4.4 71.0 1.0
CB A:VAL656 4.4 65.2 1.0
CA A:SER630 4.4 70.8 1.0
CD1 A:TYR662 4.5 68.8 1.0
CB A:SER630 4.5 71.6 1.0
CB A:VAL711 4.6 72.8 1.0
FAG A:D5C801 4.7 0.1 1.0
NE2 A:HIS740 4.7 83.2 1.0
CD2 A:TYR662 4.7 80.7 1.0
CG A:TYR662 4.8 72.4 1.0
CE1 A:HIS740 4.9 92.6 1.0
O A:SER630 4.9 69.6 1.0
CB A:TYR631 4.9 69.2 1.0
N A:VAL656 4.9 68.5 1.0

Fluorine binding site 6 out of 12 in 4dtc

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Fluorine binding site 6 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


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 Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:83.5
occ:1.00
 FAI A:D5C801 0.0 83.5 1.0
CAB A:D5C801 1.3 90.5 1.0
CAA A:D5C801 2.3 89.1 1.0
CAC A:D5C801 2.4 93.4 1.0
FAH A:D5C801 2.7 74.9 1.0
CD2 A:TYR631 3.3 78.9 1.0
CE1 A:TYR666 3.4 73.7 1.0
CZ A:TYR666 3.6 73.0 1.0
CAF A:D5C801 3.6 92.9 1.0
OH A:TYR666 3.6 69.7 1.0
CB A:TYR631 3.6 69.2 1.0
CAD A:D5C801 3.6 79.2 1.0
CH2 A:TRP659 3.8 85.6 1.0
CG A:TYR631 3.9 81.4 1.0
CA A:TYR631 4.0 71.0 1.0
CAE A:D5C801 4.1 85.4 1.0
N A:TYR631 4.1 64.5 1.0
CD1 A:TYR666 4.1 79.8 1.0
CZ3 A:TRP659 4.2 71.4 1.0
CE2 A:TYR662 4.2 71.8 1.0
CE2 A:TYR631 4.4 81.8 1.0
OH A:TYR547 4.5 83.9 1.0
CE2 A:TYR666 4.5 80.9 1.0
CG2 A:VAL656 4.5 77.0 1.0
CZ A:TYR662 4.6 74.3 1.0
CD2 A:TYR662 4.7 80.7 1.0
CAJ A:D5C801 4.8 90.7 1.0
OG A:SER630 4.8 81.7 1.0
OH A:TYR662 4.9 83.5 1.0
CG A:TYR666 5.0 76.0 1.0

Fluorine binding site 7 out of 12 in 4dtc

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Fluorine binding site 7 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.9
occ:1.00
 FBE B:D5C801 0.0 0.9 1.0
CBD B:D5C801 1.4 0.8 1.0
FBF B:D5C801 2.2 0.9 1.0
FBG B:D5C801 2.2 0.6 1.0
CBB B:D5C801 2.3 0.7 1.0
CBA B:D5C801 2.8 0.1 1.0
OE2 B:GLU361 3.4 0.1 1.0
CBC B:D5C801 3.4 0.5 1.0
CD B:GLU361 4.0 0.1 1.0
CAZ B:D5C801 4.1 0.3 1.0
OE1 B:GLU361 4.2 0.7 1.0
N B:GLU361 4.4 89.9 1.0
CA B:SER360 4.5 0.8 1.0
CAX B:D5C801 4.6 0.7 1.0
CAY B:D5C801 4.8 0.6 1.0
CB B:SER360 4.9 0.3 1.0
C B:SER360 5.0 0.7 1.0

Fluorine binding site 8 out of 12 in 4dtc

Go back to Fluorine Binding Sites List in 4dtc
Fluorine binding site 8 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.9
occ:1.00
 FBF B:D5C801 0.0 0.9 1.0
CBD B:D5C801 1.4 0.8 1.0
FBE B:D5C801 2.2 0.9 1.0
FBG B:D5C801 2.2 0.6 1.0
CBB B:D5C801 2.3 0.7 1.0
CBC B:D5C801 2.6 0.5 1.0
CBA B:D5C801 3.6 0.1 1.0
CAX B:D5C801 4.0 0.7 1.0
O B:ARG358 4.0 0.8 1.0
CG B:ARG358 4.2 1.0 1.0
CA B:SER360 4.3 0.8 1.0
O B:PRO359 4.4 0.1 1.0
CAZ B:D5C801 4.7 0.3 1.0
C B:PRO359 4.7 0.5 1.0
N B:SER360 4.8 0.5 1.0
CD B:ARG358 4.8 0.0 1.0
C B:ARG358 4.8 0.7 1.0
CAU B:D5C801 4.8 0.4 1.0
CAY B:D5C801 4.8 0.6 1.0
CB B:SER360 4.9 0.3 1.0
N B:ARG358 5.0 98.4 1.0

Fluorine binding site 9 out of 12 in 4dtc

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Fluorine binding site 9 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.6
occ:1.00
 FBG B:D5C801 0.0 0.6 1.0
CBD B:D5C801 1.4 0.8 1.0
FBF B:D5C801 2.2 0.9 1.0
FBE B:D5C801 2.2 0.9 1.0
CBB B:D5C801 2.3 0.7 1.0
CBA B:D5C801 2.9 0.1 1.0
O B:PRO359 3.1 0.1 1.0
CBC B:D5C801 3.3 0.5 1.0
CG B:ARG358 3.5 1.0 1.0
CA B:SER360 3.6 0.8 1.0
N B:GLU361 3.8 89.9 1.0
CD B:ARG358 3.9 0.0 1.0
C B:PRO359 3.9 0.5 1.0
NH2 B:ARG358 3.9 0.3 1.0
NE B:ARG358 3.9 0.8 1.0
C B:SER360 4.0 0.7 1.0
CZ B:ARG358 4.0 0.2 1.0
N B:SER360 4.1 0.5 1.0
CAZ B:D5C801 4.2 0.3 1.0
O B:ARG358 4.5 0.8 1.0
CAX B:D5C801 4.5 0.7 1.0
CB B:SER360 4.6 0.3 1.0
OE2 B:GLU361 4.7 0.1 1.0
NH1 B:ARG358 4.7 0.6 1.0
C B:ARG358 4.8 0.7 1.0
CAY B:D5C801 4.8 0.6 1.0
O B:SER360 4.8 0.0 1.0
CA B:GLU361 4.9 0.7 1.0
CB B:GLU361 4.9 0.1 1.0
CD B:GLU361 4.9 0.1 1.0
CB B:ARG358 4.9 99.1 1.0

Fluorine binding site 10 out of 12 in 4dtc

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Fluorine binding site 10 out of 12 in the Crystal Structure of Dpp-IV with Compound C5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Dpp-IV with Compound C5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:0.7
occ:1.00
 FAG B:D5C801 0.0 0.7 1.0
CAE B:D5C801 1.3 88.7 1.0
CAF B:D5C801 2.3 89.8 1.0
CAD B:D5C801 2.3 85.8 1.0
CAJ B:D5C801 2.8 83.1 1.0
NAM B:D5C801 3.1 90.8 1.0
NH2 B:ARG125 3.1 78.0 1.0
OE2 B:GLU205 3.2 79.8 1.0
OH B:TYR662 3.3 82.6 1.0
CAK B:D5C801 3.5 85.9 1.0
ND2 B:ASN710 3.5 78.0 1.0
CAA B:D5C801 3.5 89.2 1.0
CAC B:D5C801 3.5 89.5 1.0
OG B:SER630 3.9 85.9 1.0
CAB B:D5C801 4.0 87.7 1.0
OD1 B:ASN710 4.2 79.3 1.0
CG B:ASN710 4.2 72.3 1.0
CD2 B:HIS740 4.2 65.1 1.0
NE2 B:HIS740 4.3 70.3 1.0
CD B:GLU205 4.4 93.6 1.0
CAL B:D5C801 4.4 80.4 1.0
CZ B:ARG125 4.4 80.7 1.0
CZ B:TYR662 4.6 83.1 1.0
FAH B:D5C801 4.6 96.1 1.0

Reference:

B.Xiong, L.R.Zhu, D.Q.Chen, Y.L.Zhao, F.Jiang, J.K.Shen. Crystal Structure of Dpp-IV with Compound C5 To Be Published.
Page generated: Thu Aug 1 01:05:11 2024

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