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Fluorine in PDB 6lwp: Crystal Structure of Human NEIL1(R242, Y244R) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

Enzymatic activity of Crystal Structure of Human NEIL1(R242, Y244R) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

All present enzymatic activity of Crystal Structure of Human NEIL1(R242, Y244R) 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, Y244R) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwp 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) 36.17 / 2.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.938, 109.635, 171.944, 90, 90, 90
R / Rfree (%) 20.3 / 23.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human NEIL1(R242, Y244R) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine (pdb code 6lwp). 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, Y244R) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6lwp

Go back to Fluorine Binding Sites List in 6lwp
Fluorine binding site 1 out of 3 in the Crystal Structure of Human NEIL1(R242, Y244R) 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, Y244R) 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:68.4
occ:1.00
 F2 B:EW37 0.0 68.4 1.0
C2' B:EW37 1.3 72.3 1.0
N A:PRO2 2.1 58.7 1.0
C1' B:EW37 2.4 77.3 1.0
C3' B:EW37 2.4 68.5 1.0
O3' B:EW37 2.8 66.2 1.0
CD A:PRO2 3.0 56.9 1.0
N1 B:EW37 3.2 84.0 1.0
CA A:PRO2 3.4 55.2 1.0
O4' B:EW37 3.5 71.8 1.0
C4' B:EW37 3.6 68.0 1.0
O B:HOH110 3.6 77.7 1.0
C6 B:EW37 3.8 86.1 1.0
O A:MET81 3.8 54.8 1.0
C5' B:DG8 3.8 64.5 1.0
SD A:MET81 3.9 68.8 1.0
C A:PRO2 4.0 50.2 1.0
O5' B:DG8 4.0 62.8 1.0
C2 B:EW37 4.0 86.7 1.0
O2 B:EW37 4.1 84.7 1.0
P B:DG8 4.1 61.4 1.0
O A:PRO2 4.1 48.2 1.0
CG A:PRO2 4.2 55.4 1.0
CA A:MET81 4.2 57.8 1.0
O A:GLY80 4.3 47.7 1.0
C A:MET81 4.3 58.2 1.0
C5' B:EW37 4.4 66.5 1.0
CB A:PRO2 4.5 53.2 1.0
OP1 B:DG8 4.9 61.4 1.0
N A:GLU3 4.9 46.5 1.0
O5' B:EW37 4.9 64.1 1.0

Fluorine binding site 2 out of 3 in 6lwp

Go back to Fluorine Binding Sites List in 6lwp
Fluorine binding site 2 out of 3 in the Crystal Structure of Human NEIL1(R242, Y244R) 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, Y244R) 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:73.3
occ:1.00
 F2 E:EW37 0.0 73.3 1.0
C2' E:EW37 1.3 78.8 1.0
C3' E:EW37 2.4 77.0 1.0
N D:PRO2 2.4 54.8 1.0
C1' E:EW37 2.4 84.6 1.0
O3' E:EW37 2.9 72.8 1.0
CD D:PRO2 3.0 54.1 1.0
N1 E:EW37 3.2 90.5 1.0
C4' E:EW37 3.6 81.0 1.0
O4' E:EW37 3.6 83.2 1.0
O D:MET81 3.6 56.3 1.0
C6 E:EW37 3.7 97.0 1.0
SD D:MET81 3.8 65.4 1.0
CA D:PRO2 3.8 54.1 1.0
C5' E:DG8 3.8 66.5 1.0
O5' E:DG8 4.0 67.8 1.0
C2 E:EW37 4.0 90.8 1.0
CA D:MET81 4.0 50.5 1.0
O2 E:EW37 4.0 88.3 1.0
C D:MET81 4.1 50.9 1.0
P E:DG8 4.1 68.4 1.0
C5' E:EW37 4.3 81.6 1.0
O D:GLY80 4.3 47.1 1.0
CG D:PRO2 4.4 52.1 1.0
C D:PRO2 4.4 52.8 1.0
O D:PRO2 4.5 51.7 1.0
CB D:PRO2 4.8 51.9 1.0
CB D:MET81 4.8 55.4 1.0
O5' E:EW37 4.9 79.2 1.0
OP1 E:DG8 4.9 66.2 1.0
CG D:MET81 5.0 60.7 1.0

Fluorine binding site 3 out of 3 in 6lwp

Go back to Fluorine Binding Sites List in 6lwp
Fluorine binding site 3 out of 3 in the Crystal Structure of Human NEIL1(R242, Y244R) 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, Y244R) 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:116.9
occ:1.00
 F2 H:EW37 0.0 116.9 1.0
C2' H:EW37 1.4 117.6 1.0
N G:PRO2 2.0 105.0 1.0
C1' H:EW37 2.4 122.1 1.0
C3' H:EW37 2.4 116.8 1.0
CD G:PRO2 2.7 105.4 1.0
O3' H:EW37 2.8 118.0 1.0
N1 H:EW37 3.2 124.9 1.0
CA G:PRO2 3.3 101.9 1.0
O4' H:EW37 3.5 121.1 1.0
C4' H:EW37 3.6 118.1 1.0
O G:MET81 3.7 103.9 1.0
C6 H:EW37 3.7 124.2 1.0
C5' H:DG8 3.9 114.1 1.0
C G:PRO2 4.0 98.7 1.0
CG G:PRO2 4.0 103.9 1.0
O5' H:DG8 4.0 113.6 1.0
C2 H:EW37 4.0 127.2 1.0
O2 H:EW37 4.1 126.9 1.0
O G:GLY80 4.1 105.0 1.0
O G:PRO2 4.1 95.9 1.0
P H:DG8 4.1 116.0 1.0
CA G:MET81 4.1 104.5 1.0
SD G:MET81 4.2 118.1 1.0
C G:MET81 4.2 102.0 1.0
CB G:PRO2 4.4 102.7 1.0
C5' H:EW37 4.4 116.8 1.0
CE G:MET81 4.6 118.3 1.0
O5' H:EW37 4.9 115.2 1.0
OP1 H:DG8 4.9 117.6 1.0
N G:GLU3 4.9 97.1 1.0
C G:GLY80 5.0 101.8 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 13:02:36 2025

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