Fluorine in PDB 6pt2: Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07

Protein crystallography data

The structure of Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07, PDB code: 6pt2 was solved by T.Claff, J.Yu, V.Blais, N.Patel, C.Martin, L.Wu, G.W.Han, B.J.Holleran, O.Vander Poorten, M.A.Hanson, P.Sarret, L.Gendron, V.Cherezov, V.Katritch, S.Ballet, Z.Liu, C.E.Muller, R.C.Stevens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.51 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.960, 140.880, 158.640, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 28.2

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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 (pdb code 6pt2). 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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07, PDB code: 6pt2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6pt2

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Fluorine binding site 1 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F5

b:89.8
occ:1.00
 FCA C:OXJ5 0.0 89.8 1.0
CBY C:OXJ5 1.4 88.2 1.0
FCB C:OXJ5 2.2 87.4 1.0
FCC C:OXJ5 2.2 88.6 1.0
CBW C:OXJ5 2.3 86.1 1.0
CBX C:OXJ5 2.9 83.6 1.0
CG2 A:VAL281 3.3 91.9 1.0
CE3 A:TRP284 3.4 95.7 1.0
CD C:DAR2 3.5 96.5 1.0
CBV C:OXJ5 3.5 87.0 1.0
NH1 C:DAR2 3.8 97.9 1.0
CD2 A:TRP284 3.9 93.9 1.0
CB C:DAR2 3.9 88.6 1.0
CA A:VAL281 4.0 89.1 1.0
CZ3 A:TRP284 4.0 97.6 1.0
CB A:VAL281 4.1 92.6 1.0
CBS C:OXJ5 4.2 82.8 1.0
CB A:TRP284 4.3 93.2 1.0
CG A:TRP284 4.3 94.0 1.0
CG1 A:VAL281 4.3 92.0 1.0
CG C:DAR2 4.3 91.1 1.0
O C:DAR2 4.4 80.2 1.0
NE C:DAR2 4.6 98.8 1.0
N A:VAL281 4.6 89.1 1.0
CZ C:DAR2 4.7 99.1 1.0
CBU C:OXJ5 4.7 89.8 1.0
CE2 A:TRP284 4.9 97.3 1.0
CBT C:OXJ5 4.9 85.6 1.0
CH2 A:TRP284 4.9 98.0 1.0

Fluorine binding site 2 out of 12 in 6pt2

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Fluorine binding site 2 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F5

b:87.4
occ:1.00
 FCB C:OXJ5 0.0 87.4 1.0
CBY C:OXJ5 1.4 88.2 1.0
FCC C:OXJ5 2.2 88.6 1.0
FCA C:OXJ5 2.2 89.8 1.0
CBW C:OXJ5 2.4 86.1 1.0
CBX C:OXJ5 3.0 83.6 1.0
CD1 A:LEU300 3.3 84.2 1.0
CB C:DAR2 3.3 88.6 1.0
CBV C:OXJ5 3.4 87.0 1.0
CD1 A:ILE277 3.5 82.6 1.0
O C:DAR2 3.7 80.2 1.0
CG2 A:VAL281 3.9 91.9 1.0
CA C:DAR2 4.0 86.1 1.0
CD C:DAR2 4.2 96.5 1.0
C C:DAR2 4.3 82.2 1.0
CBS C:OXJ5 4.3 82.8 1.0
CG C:DAR2 4.4 91.1 1.0
CG A:LEU300 4.6 83.6 1.0
CBU C:OXJ5 4.6 89.8 1.0
CG1 A:ILE277 4.6 81.5 1.0
CD1 A:ILE304 4.7 71.2 1.0
CD2 A:LEU300 4.8 84.3 1.0
CG1 A:ILE304 4.9 76.3 1.0
CBT C:OXJ5 4.9 85.6 1.0
CD1 A:PHE280 5.0 93.8 1.0

Fluorine binding site 3 out of 12 in 6pt2

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Fluorine binding site 3 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F5

b:88.6
occ:1.00
 FCC C:OXJ5 0.0 88.6 1.0
CBY C:OXJ5 1.4 88.2 1.0
FCB C:OXJ5 2.2 87.4 1.0
FCA C:OXJ5 2.2 89.8 1.0
CBW C:OXJ5 2.4 86.1 1.0
CBV C:OXJ5 2.7 87.0 1.0
CD1 A:PHE280 3.4 93.8 1.0
C A:PHE280 3.5 91.8 1.0
O A:PHE280 3.6 91.0 1.0
N A:VAL281 3.6 89.1 1.0
CBX C:OXJ5 3.7 83.6 1.0
CB A:TRP284 3.7 93.2 1.0
CA A:VAL281 3.7 89.1 1.0
CG2 A:VAL281 3.8 91.9 1.0
CD1 A:LEU300 3.9 84.2 1.0
CB A:PHE280 3.9 90.1 1.0
CG A:PHE280 4.0 91.1 1.0
CBU C:OXJ5 4.1 89.8 1.0
CG A:TRP284 4.1 94.0 1.0
CE1 A:PHE280 4.2 94.4 1.0
CA A:PHE280 4.3 88.8 1.0
CD1 A:ILE277 4.4 82.6 1.0
CB A:VAL281 4.4 92.6 1.0
CD2 A:TRP284 4.5 93.9 1.0
CE3 A:TRP284 4.6 95.7 1.0
FCE C:OXJ5 4.7 99.7 1.0
CBS C:OXJ5 4.8 82.8 1.0
C A:VAL281 4.9 94.6 1.0
CD1 A:TRP284 4.9 96.7 1.0
CBT C:OXJ5 5.0 85.6 1.0
O A:ILE277 5.0 88.2 1.0
CBZ C:OXJ5 5.0 97.3 1.0

Fluorine binding site 4 out of 12 in 6pt2

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Fluorine binding site 4 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F5

b:98.6
occ:1.00
 FCD C:OXJ5 0.0 98.6 1.0
CBZ C:OXJ5 1.4 97.3 1.0
FCE C:OXJ5 2.2 99.7 1.0
FCF C:OXJ5 2.2 98.6 1.0
CBU C:OXJ5 2.4 89.8 1.0
CBV C:OXJ5 3.2 87.0 1.0
CD2 A:LEU300 3.3 84.3 1.0
CBT C:OXJ5 3.3 85.6 1.0
CG2 A:VAL296 3.8 98.1 1.0
CE1 A:PHE280 4.0 94.4 1.0
CG A:LEU300 4.2 83.6 1.0
CB A:LEU300 4.2 79.7 1.0
CZ A:PHE280 4.4 93.0 1.0
CD1 A:LEU300 4.5 84.2 1.0
CBW C:OXJ5 4.5 86.1 1.0
CG2 A:ILE289 4.5 0.7 1.0
CBS C:OXJ5 4.5 82.8 1.0
O A:VAL296 4.7 0.5 1.0
CD1 A:TRP284 4.9 96.7 1.0
CB A:VAL296 4.9 98.8 1.0
CA A:ARG291 5.0 98.6 1.0
NE1 A:TRP284 5.0 95.6 1.0

Fluorine binding site 5 out of 12 in 6pt2

Go back to Fluorine Binding Sites List in 6pt2
Fluorine binding site 5 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F5

b:99.7
occ:1.00
 FCE C:OXJ5 0.0 99.7 1.0
CBZ C:OXJ5 1.4 97.3 1.0
FCD C:OXJ5 2.2 98.6 1.0
FCF C:OXJ5 2.3 98.6 1.0
CBU C:OXJ5 2.3 89.8 1.0
CBV C:OXJ5 2.8 87.0 1.0
CD1 A:TRP284 2.9 96.7 1.0
NE1 A:TRP284 3.4 95.6 1.0
CG2 A:ILE289 3.5 0.7 1.0
CBT C:OXJ5 3.6 85.6 1.0
CE1 A:PHE280 3.6 94.4 1.0
CG A:TRP284 3.7 94.0 1.0
CB A:ILE289 3.8 0.4 1.0
CD1 A:ILE289 4.0 0.8 1.0
CBW C:OXJ5 4.1 86.1 1.0
CB A:TRP284 4.3 93.2 1.0
CD1 A:PHE280 4.3 93.8 1.0
CE2 A:TRP284 4.4 97.3 1.0
CG1 A:ILE289 4.5 0.7 1.0
CD2 A:TRP284 4.5 93.9 1.0
CZ A:PHE280 4.6 93.0 1.0
CBS C:OXJ5 4.7 82.8 1.0
FCC C:OXJ5 4.7 88.6 1.0
CG2 A:VAL296 4.9 98.1 1.0
CBX C:OXJ5 4.9 83.6 1.0
CA A:TRP284 4.9 95.5 1.0

Fluorine binding site 6 out of 12 in 6pt2

Go back to Fluorine Binding Sites List in 6pt2
Fluorine binding site 6 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F5

b:98.6
occ:1.00
 FCF C:OXJ5 0.0 98.6 1.0
CBZ C:OXJ5 1.4 97.3 1.0
FCD C:OXJ5 2.2 98.6 1.0
FCE C:OXJ5 2.3 99.7 1.0
CBU C:OXJ5 2.3 89.8 1.0
CBT C:OXJ5 2.7 85.6 1.0
CG A:ARG291 3.3 0.6 1.0
NE1 A:TRP284 3.4 95.6 1.0
CBV C:OXJ5 3.6 87.0 1.0
CD A:ARG291 3.7 0.2 1.0
CD1 A:TRP284 3.8 96.7 1.0
NE A:ARG291 3.8 0.4 1.0
CBS C:OXJ5 4.1 82.8 1.0
CA A:ARG291 4.2 98.6 1.0
CB A:ARG291 4.2 0.2 1.0
CE2 A:TRP284 4.3 97.3 1.0
CZ A:ARG291 4.4 0.4 1.0
CG2 A:ILE289 4.6 0.7 1.0
CBW C:OXJ5 4.7 86.1 1.0
CG A:TRP284 4.8 94.0 1.0
N A:ARG291 4.8 99.0 1.0
O A:ILE289 4.9 0.9 1.0
CD2 A:LEU300 4.9 84.3 1.0
CB A:ILE289 4.9 0.4 1.0
NH1 A:ARG291 4.9 0.3 1.0
CBX C:OXJ5 4.9 83.6 1.0
CBR C:OXJ5 4.9 80.2 1.0
CZ2 A:TRP284 5.0 96.8 1.0

Fluorine binding site 7 out of 12 in 6pt2

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Fluorine binding site 7 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F5

b:0.2
occ:1.00
 FCA D:OXJ5 0.0 0.2 1.0
CBY D:OXJ5 1.4 0.1 1.0
FCC D:OXJ5 2.2 0.0 1.0
FCB D:OXJ5 2.2 0.2 1.0
CBW D:OXJ5 2.3 0.2 1.0
CBX D:OXJ5 2.9 97.7 1.0
CE3 B:TRP284 3.2 98.6 1.0
CG2 B:VAL281 3.3 93.0 1.0
NH1 D:DAR2 3.3 94.7 1.0
CBV D:OXJ5 3.5 0.7 1.0
CZ3 B:TRP284 3.7 0.4 1.0
CD2 B:TRP284 3.9 97.5 1.0
CA B:VAL281 3.9 90.7 1.0
CB B:VAL281 3.9 93.5 1.0
CB D:DAR2 3.9 90.4 1.0
CD D:DAR2 4.0 97.3 1.0
CG1 B:VAL281 4.2 93.2 1.0
CBS D:OXJ5 4.2 94.8 1.0
O D:DAR2 4.5 78.2 1.0
CZ D:DAR2 4.5 97.2 1.0
CG B:TRP284 4.5 97.6 1.0
CB B:TRP284 4.5 96.6 1.0
CH2 B:TRP284 4.6 0.5 1.0
CBU D:OXJ5 4.6 0.9 1.0
CG D:DAR2 4.7 94.1 1.0
N B:VAL281 4.7 90.6 1.0
NE D:DAR2 4.7 97.5 1.0
CE2 B:TRP284 4.8 0.7 1.0
O B:VAL281 4.8 95.5 1.0
CBT D:OXJ5 4.9 98.0 1.0
C B:VAL281 4.9 95.2 1.0

Fluorine binding site 8 out of 12 in 6pt2

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Fluorine binding site 8 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F5

b:0.2
occ:1.00
 FCB D:OXJ5 0.0 0.2 1.0
CBY D:OXJ5 1.4 0.1 1.0
FCA D:OXJ5 2.2 0.2 1.0
FCC D:OXJ5 2.2 0.0 1.0
CBW D:OXJ5 2.4 0.2 1.0
CBX D:OXJ5 3.0 97.7 1.0
CD1 B:LEU300 3.4 90.8 1.0
CB D:DAR2 3.4 90.4 1.0
CBV D:OXJ5 3.4 0.7 1.0
O D:DAR2 3.5 78.2 1.0
CD1 B:ILE277 3.6 88.7 1.0
CG2 B:VAL281 3.8 93.0 1.0
CA D:DAR2 3.9 85.0 1.0
C D:DAR2 4.1 81.0 1.0
CBS D:OXJ5 4.3 94.8 1.0
CBU D:OXJ5 4.6 0.9 1.0
CG1 B:ILE277 4.6 86.5 1.0
CG B:LEU300 4.6 91.8 1.0
CG D:DAR2 4.7 94.1 1.0
CD D:DAR2 4.7 97.3 1.0
NH1 D:DAR2 4.8 94.7 1.0
CD2 B:LEU300 4.9 92.7 1.0
CA B:VAL281 4.9 90.7 1.0
CB B:VAL281 4.9 93.5 1.0
CD1 B:ILE304 5.0 85.0 1.0
CBT D:OXJ5 5.0 98.0 1.0

Fluorine binding site 9 out of 12 in 6pt2

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Fluorine binding site 9 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F5

b:0.0
occ:1.00
 FCC D:OXJ5 0.0 0.0 1.0
CBY D:OXJ5 1.4 0.1 1.0
FCA D:OXJ5 2.2 0.2 1.0
FCB D:OXJ5 2.2 0.2 1.0
CBW D:OXJ5 2.4 0.2 1.0
CBV D:OXJ5 2.7 0.7 1.0
CD1 B:PHE280 3.5 95.2 1.0
CA B:VAL281 3.5 90.7 1.0
N B:VAL281 3.6 90.6 1.0
CBX D:OXJ5 3.7 97.7 1.0
O B:PHE280 3.7 95.5 1.0
C B:PHE280 3.7 95.0 1.0
CG2 B:VAL281 3.7 93.0 1.0
CB B:TRP284 3.7 96.6 1.0
CD1 B:LEU300 3.9 90.8 1.0
CBU D:OXJ5 4.1 0.9 1.0
CG B:TRP284 4.1 97.6 1.0
CG B:PHE280 4.2 92.5 1.0
CB B:VAL281 4.2 93.5 1.0
CE1 B:PHE280 4.2 96.7 1.0
CB B:PHE280 4.2 91.1 1.0
CE3 B:TRP284 4.3 98.6 1.0
CD2 B:TRP284 4.3 97.5 1.0
CD1 B:ILE277 4.5 88.7 1.0
C B:VAL281 4.6 95.2 1.0
FCE D:OXJ5 4.6 0.5 1.0
CA B:PHE280 4.6 89.8 1.0
O B:VAL281 4.8 95.5 1.0
CBS D:OXJ5 4.8 94.8 1.0
O B:ILE277 4.9 90.8 1.0
CBT D:OXJ5 4.9 98.0 1.0
CBZ D:OXJ5 5.0 0.2 1.0

Fluorine binding site 10 out of 12 in 6pt2

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Fluorine binding site 10 out of 12 in the Crystal Structure of the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07


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 the Active Delta Opioid Receptor in Complex with the Peptide Agonist KGCHM07 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F5

b:0.4
occ:1.00
 FCD D:OXJ5 0.0 0.4 1.0
CBZ D:OXJ5 1.4 0.2 1.0
FCE D:OXJ5 2.2 0.5 1.0
FCF D:OXJ5 2.2 0.4 1.0
CBU D:OXJ5 2.3 0.9 1.0
CBT D:OXJ5 3.1 98.0 1.0
CD2 B:LEU300 3.2 92.7 1.0
CBV D:OXJ5 3.3 0.7 1.0
CBS D:OXJ5 4.3 94.8 1.0
CG B:LEU300 4.3 91.8 1.0
CG1 B:VAL296 4.4 0.8 1.0
CBW D:OXJ5 4.5 0.2 1.0
CG2 B:ILE289 4.5 0.7 1.0
CE1 B:PHE280 4.6 96.7 1.0
CG B:ARG291 4.6 0.6 1.0
CA B:ARG291 4.6 0.0 1.0
CB B:LEU300 4.6 89.1 1.0
CD1 B:TRP284 4.7 0.8 1.0
NE1 B:TRP284 4.7 0.5 1.0
CD1 B:LEU300 4.8 90.8 1.0
CB B:ARG291 4.8 0.6 1.0
CZ B:PHE280 4.8 96.5 1.0
CBX D:OXJ5 4.9 97.7 1.0

Reference:

T.Claff, J.Yu, V.Blais, N.Patel, C.Martin, L.Wu, G.W.Han, B.J.Holleran, O.Van Der Poorten, K.L.White, M.A.Hanson, P.Sarret, L.Gendron, V.Cherezov, V.Katritch, S.Ballet, Z.J.Liu, C.E.Muller, R.C.Stevens. Elucidating the Active Delta-Opioid Receptor Crystal Structure with Peptide and Small-Molecule Agonists. Sci Adv V. 5 X9115 2019.
ISSN: ESSN 2375-2548
PubMed: 31807708
DOI: 10.1126/SCIADV.AAX9115
Page generated: Sun Dec 13 13:07:20 2020

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