Fluorine in PDB 5v88: Structure of DCN1 Bound to Nacm-Cov

All present enzymatic activity of Structure of DCN1 Bound to Nacm-Cov:
3.2.1.17;

The structure of Structure of DCN1 Bound to Nacm-Cov, PDB code: 5v88 was solved by R.K.Guy, B.A.Schulman, D.C.Scott, J.T.Hammill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.52 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.392, 98.677, 59.181, 90.00, 104.83, 90.00
R / Rfree (%)	15.9 / 18.9

The binding sites of Fluorine atom in the Structure of DCN1 Bound to Nacm-Cov (pdb code 5v88). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of DCN1 Bound to Nacm-Cov, PDB code: 5v88:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of DCN1 Bound to Nacm-Cov


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of DCN1 Bound to Nacm-Cov within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:25.1 occ:1.00 FBI A:8ZD401 0.0 25.1 1.0 CBH A:8ZD401 1.4 25.5 1.0 FBK A:8ZD401 2.1 27.7 1.0 FBJ A:8ZD401 2.2 28.1 1.0 CBF A:8ZD401 2.4 22.4 1.0 HB2 A:ALA1106 2.8 25.0 1.0 CBG A:8ZD401 2.9 20.9 1.0 O A:VAL1102 2.9 20.0 1.0 HB A:ILE1105 3.0 26.9 1.0 H A:ALA1106 3.0 23.0 1.0 HG13 A:VAL1102 3.1 27.8 1.0 N A:ALA1106 3.3 19.1 1.0 HG22 A:ILE1105 3.3 27.3 1.0 HA A:ALA1106 3.4 25.0 1.0 CBE A:8ZD401 3.5 23.2 1.0 HG12 A:VAL1102 3.6 27.8 1.0 CB A:ALA1106 3.6 20.9 1.0 CA A:ALA1106 3.6 20.9 1.0 CB A:ILE1105 3.7 22.4 1.0 CG1 A:VAL1102 3.8 23.2 1.0 CG2 A:ILE1105 3.8 22.7 1.0 HG21 A:ILE1105 3.8 27.3 1.0 C A:VAL1102 3.9 21.4 1.0 C A:ILE1105 4.0 19.6 1.0 HE2 A:PHE1089 4.0 36.5 1.0 HA A:VAL1102 4.0 24.2 1.0 HB3 A:ALA1106 4.1 25.0 1.0 HB1 A:ALA1106 4.2 25.0 1.0 CBB A:8ZD401 4.2 20.5 1.0 CA A:ILE1105 4.4 20.8 1.0 CA A:VAL1102 4.4 20.1 1.0 HG11 A:VAL1102 4.4 27.8 1.0 HD12 A:ILE1105 4.6 32.3 1.0 OAZ A:8ZD401 4.6 22.6 1.0 CBD A:8ZD401 4.6 22.8 1.0 H A:ILE1105 4.7 22.7 1.0 CB A:VAL1102 4.7 21.9 1.0 HG23 A:ILE1105 4.7 27.3 1.0 O A:ILE1105 4.7 21.9 1.0 HA A:LEU1103 4.8 24.1 1.0 HD2 A:PHE1089 4.8 27.7 1.0 CE2 A:PHE1089 4.9 30.4 1.0 N A:ILE1105 4.9 18.9 1.0 HD13 A:ILE1105 4.9 32.3 1.0 CBC A:8ZD401 4.9 20.4 1.0 HZ A:PHE1164 5.0 25.6 1.0 CG1 A:ILE1105 5.0 26.9 1.0 N A:LEU1103 5.0 19.6 1.0

Fluorine binding site 2 out of 3 in the Structure of DCN1 Bound to Nacm-Cov


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of DCN1 Bound to Nacm-Cov within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.1 occ:1.00 FBJ A:8ZD401 0.0 28.1 1.0 CBH A:8ZD401 1.4 25.5 1.0 FBK A:8ZD401 2.1 27.7 1.0 FBI A:8ZD401 2.2 25.1 1.0 CBF A:8ZD401 2.3 22.4 1.0 HE2 A:PHE1089 2.7 36.5 1.0 HD2 A:PHE1089 2.8 27.7 1.0 CBG A:8ZD401 2.9 20.9 1.0 CE2 A:PHE1089 3.3 30.4 1.0 CBE A:8ZD401 3.4 23.2 1.0 CD2 A:PHE1089 3.4 23.1 1.0 HE1 A:PHE1117 3.4 29.6 1.0 HG23 A:ILE1086 3.5 30.5 1.0 HG13 A:VAL1102 3.7 27.8 1.0 CE1 A:PHE1117 3.7 24.7 1.0 HG22 A:ILE1105 4.1 27.3 1.0 HG21 A:ILE1105 4.1 27.3 1.0 HD1 A:PHE1117 4.2 29.4 1.0 CD1 A:PHE1117 4.2 24.5 1.0 CBB A:8ZD401 4.2 20.5 1.0 CZ A:PHE1117 4.3 27.3 1.0 CG2 A:ILE1086 4.3 25.4 1.0 HB A:ILE1105 4.4 26.9 1.0 HZ A:PHE1117 4.5 32.8 1.0 CBD A:8ZD401 4.5 22.8 1.0 HG A:CYS1090 4.5 29.4 1.0 HG21 A:ILE1086 4.5 30.5 1.0 CG2 A:ILE1105 4.5 22.7 1.0 CZ A:PHE1089 4.6 23.3 1.0 HG22 A:ILE1086 4.6 30.5 1.0 CG1 A:VAL1102 4.6 23.2 1.0 HB2 A:ALA1106 4.7 25.0 1.0 CG A:PHE1089 4.7 18.8 1.0 HG12 A:VAL1102 4.8 27.8 1.0 HB3 A:PHE1089 4.8 25.0 1.0 CBC A:8ZD401 4.8 20.4 1.0 HZ A:PHE1089 4.9 28.0 1.0 HG11 A:VAL1102 4.9 27.8 1.0 O A:VAL1102 4.9 20.0 1.0 HG12 A:ILE1086 4.9 30.6 1.0 HA A:ALA1106 5.0 25.0 1.0

Fluorine binding site 3 out of 3 in the Structure of DCN1 Bound to Nacm-Cov


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of DCN1 Bound to Nacm-Cov within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.7 occ:1.00 FBK A:8ZD401 0.0 27.7 1.0 CBH A:8ZD401 1.3 25.5 1.0 FBJ A:8ZD401 2.1 28.1 1.0 FBI A:8ZD401 2.1 25.1 1.0 CBF A:8ZD401 2.3 22.4 1.0 HG22 A:ILE1105 2.7 27.3 1.0 CBE A:8ZD401 2.8 23.2 1.0 HE2 A:PHE1089 3.1 36.5 1.0 HA A:ALA1106 3.2 25.0 1.0 HG21 A:ILE1105 3.4 27.3 1.0 CG2 A:ILE1105 3.5 22.7 1.0 HZ A:PHE1117 3.5 32.8 1.0 CZ A:PHE1117 3.5 27.3 1.0 CBG A:8ZD401 3.6 20.9 1.0 CE1 A:PHE1117 3.6 24.7 1.0 HE1 A:PHE1117 3.7 29.6 1.0 HB2 A:ALA1106 3.8 25.0 1.0 HB A:ILE1105 3.9 26.9 1.0 N A:ALA1106 3.9 19.1 1.0 CA A:ALA1106 3.9 20.9 1.0 CE2 A:PHE1089 3.9 30.4 1.0 HB2 A:PHE1109 4.1 27.7 1.0 CBD A:8ZD401 4.1 22.8 1.0 H A:ALA1106 4.1 23.0 1.0 CE2 A:PHE1117 4.2 26.4 1.0 C A:ILE1105 4.2 19.6 1.0 HG23 A:ILE1105 4.2 27.3 1.0 CB A:ILE1105 4.2 22.4 1.0 CD1 A:PHE1117 4.4 24.5 1.0 CB A:ALA1106 4.4 20.9 1.0 HD2 A:PHE1089 4.4 27.7 1.0 O A:ILE1105 4.4 21.9 1.0 CD2 A:PHE1109 4.5 35.2 1.0 CG A:PHE1109 4.5 26.4 1.0 HE2 A:PHE1117 4.5 31.7 1.0 HD2 A:PHE1109 4.5 42.2 1.0 CD2 A:PHE1089 4.6 23.1 1.0 CB A:PHE1109 4.7 23.1 1.0 CBB A:8ZD401 4.7 20.5 1.0 HB1 A:ALA1106 4.8 25.0 1.0 HZ A:PHE1089 4.8 28.0 1.0 HD1 A:PHE1117 4.8 29.4 1.0 HB2 A:ALA1111 4.8 28.5 1.0 O A:VAL1102 4.8 20.0 1.0 CZ A:PHE1089 4.8 23.3 1.0 CD2 A:PHE1117 4.8 25.6 1.0 HB3 A:PHE1109 4.9 27.7 1.0 CA A:ILE1105 4.9 20.8 1.0 CE2 A:PHE1109 4.9 41.2 1.0 CG A:PHE1117 4.9 23.3 1.0 CD1 A:PHE1109 4.9 48.9 1.0 HG13 A:VAL1102 5.0 27.8 1.0 CBC A:8ZD401 5.0 20.4 1.0

D.C.Scott, J.T.Hammill, J.Min, D.Y.Rhee, M.Connelly, V.O.Sviderskiy, D.Bhasin, Y.Chen, S.S.Ong, S.C.Chai, A.N.Goktug, G.Huang, J.K.Monda, J.Low, H.S.Kim, J.A.Paulo, J.R.Cannon, A.A.Shelat, T.Chen, I.R.Kelsall, A.F.Alpi, V.Pagala, X.Wang, J.Peng, B.Singh, J.W.Harper, B.A.Schulman, R.K.Guy. Blocking An N-Terminal Acetylation-Dependent Protein Interaction Inhibits An E3 Ligase. Nat. Chem. Biol. V. 13 850 2017.
ISSN: ESSN 1552-4469
PubMed: 28581483
DOI: 10.1038/NCHEMBIO.2386