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Fluorine in PDB 6lwn: Crystal Structure of Human NEIL1(R242, G249P) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

Enzymatic activity of Crystal Structure of Human NEIL1(R242, G249P) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

All present enzymatic activity of Crystal Structure of Human NEIL1(R242, G249P) 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, G249P) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwn 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) 45.34 / 2.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.766, 109.988, 172.178, 90, 90, 90
R / Rfree (%) 19.9 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human NEIL1(R242, G249P) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine (pdb code 6lwn). 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, G249P) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6lwn

Go back to Fluorine Binding Sites List in 6lwn
Fluorine binding site 1 out of 3 in the Crystal Structure of Human NEIL1(R242, G249P) 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, G249P) 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:75.5
occ:1.00
 F2 B:EW37 0.0 75.5 1.0
C2' B:EW37 1.3 77.6 1.0
N A:PRO2 2.1 56.8 1.0
C1' B:EW37 2.3 84.6 1.0
C3' B:EW37 2.4 72.1 1.0
O3' B:EW37 2.8 68.6 1.0
CD A:PRO2 3.1 55.7 1.0
N1 B:EW37 3.1 95.7 1.0
CA A:PRO2 3.3 53.1 1.0
O4' B:EW37 3.5 79.4 1.0
O B:HOH112 3.5 66.3 1.0
C4' B:EW37 3.6 73.2 1.0
O A:MET81 3.7 53.4 1.0
O2 B:EW37 3.8 100.9 1.0
C5' B:DG8 3.8 66.0 1.0
C A:PRO2 3.8 48.0 1.0
O A:PRO2 3.8 49.0 1.0
C2 B:EW37 3.9 101.5 1.0
C6 B:EW37 3.9 99.6 1.0
SD A:MET81 4.1 64.6 1.0
O5' B:DG8 4.1 64.7 1.0
P B:DG8 4.1 62.6 1.0
CA A:MET81 4.1 53.9 1.0
C A:MET81 4.2 53.5 1.0
O A:GLY80 4.2 46.5 1.0
CG A:PRO2 4.3 54.8 1.0
C5' B:EW37 4.4 71.8 1.0
CB A:PRO2 4.5 53.0 1.0
OP1 B:DG8 4.8 62.2 1.0
N A:GLU3 4.8 45.0 1.0
O A:HOH403 4.9 50.1 1.0
O5' B:EW37 5.0 67.9 1.0
CB A:MET81 5.0 57.4 1.0

Fluorine binding site 2 out of 3 in 6lwn

Go back to Fluorine Binding Sites List in 6lwn
Fluorine binding site 2 out of 3 in the Crystal Structure of Human NEIL1(R242, G249P) 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, G249P) 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:83.0
occ:1.00
 F2 E:EW37 0.0 83.0 1.0
C2' E:EW37 1.3 84.2 1.0
N D:PRO2 2.2 57.2 1.0
C1' E:EW37 2.3 90.9 1.0
C3' E:EW37 2.4 80.6 1.0
O3' E:EW37 2.8 75.4 1.0
CD D:PRO2 3.0 58.1 1.0
N1 E:EW37 3.1 96.6 1.0
CA D:PRO2 3.4 55.1 1.0
O4' E:EW37 3.5 89.8 1.0
C4' E:EW37 3.6 84.1 1.0
O D:MET81 3.7 50.6 1.0
O2 E:EW37 3.8 99.2 1.0
C5' E:DG8 3.8 69.9 1.0
C2 E:EW37 3.9 101.0 1.0
SD D:MET81 3.9 63.7 1.0
C6 E:EW37 3.9 99.2 1.0
C D:PRO2 4.0 51.9 1.0
O D:PRO2 4.0 53.4 1.0
CA D:MET81 4.1 47.5 1.0
O5' E:DG8 4.1 70.1 1.0
P E:DG8 4.1 70.0 1.0
C D:MET81 4.1 46.5 1.0
O D:HOH348 4.2 79.7 1.0
O D:GLY80 4.2 44.4 1.0
CG D:PRO2 4.3 57.3 1.0
C5' E:EW37 4.4 82.8 1.0
CB D:PRO2 4.6 54.4 1.0
OP1 E:DG8 4.8 68.7 1.0
CB D:MET81 4.9 52.5 1.0
O5' E:EW37 5.0 80.2 1.0
C D:GLY80 5.0 43.4 1.0
N D:GLU3 5.0 48.6 1.0
N D:MET81 5.0 46.2 1.0

Fluorine binding site 3 out of 3 in 6lwn

Go back to Fluorine Binding Sites List in 6lwn
Fluorine binding site 3 out of 3 in the Crystal Structure of Human NEIL1(R242, G249P) 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, G249P) 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:118.7
occ:1.00
 F2 H:EW37 0.0 118.7 1.0
C2' H:EW37 1.4 118.1 1.0
N G:PRO2 1.8 106.4 1.0
C1' H:EW37 2.3 121.5 1.0
C3' H:EW37 2.4 116.9 1.0
CD G:PRO2 2.7 107.7 1.0
O3' H:EW37 2.7 117.6 1.0
CA G:PRO2 3.1 103.7 1.0
N1 H:EW37 3.1 124.2 1.0
O4' H:EW37 3.5 120.5 1.0
C4' H:EW37 3.6 118.2 1.0
O G:MET81 3.6 103.5 1.0
C G:PRO2 3.8 100.4 1.0
O2 H:EW37 3.8 128.4 1.0
O G:PRO2 3.8 99.4 1.0
C2 H:EW37 3.9 127.8 1.0
C6 H:EW37 3.9 123.7 1.0
C5' H:DG8 3.9 116.6 1.0
CG G:PRO2 4.0 106.6 1.0
P H:DG8 4.1 115.5 1.0
O G:GLY80 4.1 105.6 1.0
O5' H:DG8 4.1 115.1 1.0
C G:MET81 4.1 103.5 1.0
CA G:MET81 4.2 107.9 1.0
CB G:PRO2 4.2 104.6 1.0
C5' H:EW37 4.4 117.2 1.0
SD G:MET81 4.4 125.3 1.0
N G:GLU3 4.7 97.4 1.0
OP1 H:DG8 4.8 117.3 1.0
C G:GLY80 5.0 104.4 1.0
O5' H:EW37 5.0 116.2 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: Thu Aug 1 22:08:22 2024

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