Atomistry » Fluorine » PDB 6lub-6mii » 6lwo
Atomistry »
  Fluorine »
    PDB 6lub-6mii »
      6lwo »

Fluorine in PDB 6lwo: Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

Enzymatic activity of Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

All present enzymatic activity of Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine:
4.2.99.18;

Protein crystallography data

The structure of Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwo was solved by M.H.Liu, J.Zhang, C.X.Zhu, X.X.Zhang, Y.Q.Gao, C.Q.Yi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.15 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.926, 109.447, 170.603, 90, 90, 90
R / Rfree (%) 20.3 / 24.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine (pdb code 6lwo). 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 Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwo:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6lwo

Go back to Fluorine Binding Sites List in 6lwo
Fluorine binding site 1 out of 3 in the Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine


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 NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F7

b:78.5
occ:1.00
 F2 B:EW37 0.0 78.5 1.0
C2' B:EW37 1.3 76.6 1.0
N A:PRO2 2.2 56.0 1.0
C3' B:EW37 2.4 70.5 1.0
C1' B:EW37 2.4 82.8 1.0
O3' B:EW37 2.8 63.5 1.0
CD A:PRO2 2.9 55.8 1.0
N1 B:EW37 3.2 91.0 1.0
O4' B:EW37 3.5 76.6 1.0
CA A:PRO2 3.5 51.5 1.0
C4' B:EW37 3.5 72.5 1.0
O A:HOH399 3.7 75.9 1.0
O A:MET81 3.8 51.5 1.0
C5' B:DG8 3.8 58.2 1.0
C6 B:EW37 3.9 93.6 1.0
O2 B:EW37 3.9 94.3 1.0
C A:PRO2 4.0 50.8 1.0
O5' B:DG8 4.0 56.9 1.0
C2 B:EW37 4.0 92.7 1.0
O A:PRO2 4.0 47.1 1.0
SD A:MET81 4.1 61.8 1.0
P B:DG8 4.1 54.9 1.0
CG A:PRO2 4.1 53.5 1.0
CA A:MET81 4.2 53.8 1.0
O A:GLY80 4.3 52.1 1.0
C5' B:EW37 4.3 71.3 1.0
C A:MET81 4.3 53.8 1.0
CB A:PRO2 4.5 50.6 1.0
CE A:MET81 4.7 62.5 1.0
N A:GLU3 4.9 47.6 1.0
OP1 B:DG8 4.9 55.0 1.0
O5' B:EW37 4.9 66.5 1.0
CB A:MET81 5.0 58.1 1.0

Fluorine binding site 2 out of 3 in 6lwo

Go back to Fluorine Binding Sites List in 6lwo
Fluorine binding site 2 out of 3 in the Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine


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 NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F7

b:74.0
occ:1.00
 F2 E:EW37 0.0 74.0 1.0
C2' E:EW37 1.3 77.3 1.0
N D:PRO2 2.3 56.5 1.0
C3' E:EW37 2.4 74.0 1.0
C1' E:EW37 2.4 82.4 1.0
O3' E:EW37 2.8 65.3 1.0
CD D:PRO2 2.9 54.8 1.0
N1 E:EW37 3.2 90.2 1.0
O4' E:EW37 3.5 78.6 1.0
C4' E:EW37 3.6 76.3 1.0
CA D:PRO2 3.6 52.2 1.0
O D:MET81 3.7 47.9 1.0
C5' E:DG8 3.8 57.6 1.0
C6 E:EW37 3.9 93.2 1.0
O2 E:EW37 3.9 92.7 1.0
C2 E:EW37 4.0 92.9 1.0
O5' E:DG8 4.0 57.9 1.0
SD D:MET81 4.0 60.2 1.0
C D:PRO2 4.1 51.5 1.0
P E:DG8 4.1 59.3 1.0
O D:PRO2 4.1 46.2 1.0
CA D:MET81 4.1 46.2 1.0
O D:GLY80 4.2 46.0 1.0
CG D:PRO2 4.2 52.7 1.0
C D:MET81 4.3 45.5 1.0
C5' E:EW37 4.3 76.5 1.0
CB D:PRO2 4.6 53.0 1.0
OP1 E:DG8 4.9 59.0 1.0
O5' E:EW37 4.9 73.6 1.0
CE D:MET81 4.9 64.1 1.0
CB D:MET81 5.0 51.0 1.0
N D:GLU3 5.0 49.4 1.0

Fluorine binding site 3 out of 3 in 6lwo

Go back to Fluorine Binding Sites List in 6lwo
Fluorine binding site 3 out of 3 in the Crystal Structure of Human NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine


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 NEIL1(R242, Y244H) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F7

b:108.0
occ:1.00
 F2 H:EW37 0.0 108.0 1.0
C2' H:EW37 1.4 106.6 1.0
N G:PRO2 2.1 97.9 1.0
C3' H:EW37 2.4 104.1 1.0
C1' H:EW37 2.4 110.7 1.0
CD G:PRO2 2.7 100.2 1.0
O3' H:EW37 2.8 103.2 1.0
N1 H:EW37 3.2 114.9 1.0
CA G:PRO2 3.5 96.2 1.0
O4' H:EW37 3.5 108.5 1.0
C4' H:EW37 3.6 105.1 1.0
CE G:MET81 3.6 97.7 1.0
O G:MET81 3.7 85.1 1.0
C5' H:DG8 3.9 99.8 1.0
C6 H:EW37 3.9 116.0 1.0
O2 H:EW37 3.9 119.5 1.0
O G:PRO2 3.9 88.7 1.0
CA G:MET81 4.0 87.3 1.0
C G:PRO2 4.0 92.3 1.0
O G:GLY80 4.0 86.1 1.0
O5' H:DG8 4.0 99.1 1.0
C2 H:EW37 4.0 118.7 1.0
CG G:PRO2 4.1 100.8 1.0
P H:DG8 4.1 100.2 1.0
C G:MET81 4.1 85.9 1.0
SD G:MET81 4.2 101.0 1.0
C5' H:EW37 4.4 103.2 1.0
CB G:PRO2 4.4 100.1 1.0
C G:GLY80 4.8 85.5 1.0
N G:MET81 4.9 88.4 1.0
CB G:MET81 4.9 92.0 1.0
O5' H:EW37 4.9 101.7 1.0
N G:GLU3 4.9 90.4 1.0
OP1 H:DG8 4.9 101.5 1.0
OP2 H:DG8 5.0 99.9 1.0

Reference:

M.Liu, J.Zhang, C.Zhu, X.Zhang, W.Xiao, Y.Yan, L.Liu, H.Zhang, Y.Q.Gao, C.Yi. Dna Repair Glycosylase HNEIL1 Triages Damaged Bases Via Competing Interaction Modes. To Be Published.
Page generated: Tue Jul 15 13:02:17 2025

Last articles

Mg in 6YHN
Mg in 6YHM
Mg in 6YF4
Mg in 6YEM
Mg in 6YE9
Mg in 6YDM
Mg in 6YDL
Mg in 6YDJ
Mg in 6YDK
Mg in 6YCZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy