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Fluorine in PDB 1w4q: Binding of Nonnatural 3'-Nucleotides to Ribonuclease A

Enzymatic activity of Binding of Nonnatural 3'-Nucleotides to Ribonuclease A

All present enzymatic activity of Binding of Nonnatural 3'-Nucleotides to Ribonuclease A:
3.1.27.5;

Protein crystallography data

The structure of Binding of Nonnatural 3'-Nucleotides to Ribonuclease A, PDB code: 1w4q was solved by C.L.Jenkins, N.Thiyagarajan, R.Y.Sweeney, M.P.Guy, B.R.Kelemen, K.R.Acharya, R.T.Raines, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.0 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.101, 32.925, 72.787, 90.00, 90.39, 90.00
R / Rfree (%) 20.9 / 24.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Binding of Nonnatural 3'-Nucleotides to Ribonuclease A (pdb code 1w4q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Binding of Nonnatural 3'-Nucleotides to Ribonuclease A, PDB code: 1w4q:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 1w4q

Go back to Fluorine Binding Sites List in 1w4q
Fluorine binding site 1 out of 2 in the Binding of Nonnatural 3'-Nucleotides to Ribonuclease A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Binding of Nonnatural 3'-Nucleotides to Ribonuclease A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1125

b:20.3
occ:1.00
F2' A:UMF1125 0.0 20.3 1.0
C2' A:UMF1125 1.3 14.8 1.0
C3' A:UMF1125 2.2 12.4 1.0
O3' A:UMF1125 2.2 13.1 1.0
C1' A:UMF1125 2.6 14.1 1.0
CE1 A:HIS12 2.7 7.0 1.0
NZ A:LYS41 2.8 20.5 1.0
O3P A:UMF1125 2.8 10.8 1.0
NE2 A:HIS12 2.8 6.7 1.0
P A:UMF1125 3.1 12.5 1.0
C4' A:UMF1125 3.3 13.7 1.0
CE A:LYS41 3.5 17.4 1.0
O4' A:UMF1125 3.6 11.8 1.0
OD1 A:ASN44 3.6 9.8 1.0
O2 A:UMF1125 3.6 11.2 1.0
N1 A:UMF1125 3.7 13.8 1.0
O2P A:UMF1125 3.8 10.8 1.0
ND1 A:HIS12 4.0 7.1 1.0
C2 A:UMF1125 4.1 12.9 1.0
CD2 A:HIS12 4.2 6.9 1.0
O A:PHE120 4.4 7.0 1.0
NE2 A:GLN11 4.4 10.4 1.0
O1P A:UMF1125 4.4 11.9 1.0
CB A:PHE120 4.4 7.1 1.0
O A:VAL43 4.5 13.8 1.0
CG A:ASN44 4.6 9.3 1.0
CG A:HIS12 4.8 7.3 1.0
CA A:ASN44 4.8 9.9 1.0
C5' A:UMF1125 4.8 14.5 1.0
CD A:GLN11 4.8 12.0 1.0
N A:PHE120 4.8 6.3 1.0
C6 A:UMF1125 4.9 14.9 1.0
CD A:LYS41 4.9 14.9 1.0
O A:HOH2149 4.9 34.0 1.0
OE1 A:GLN11 5.0 13.7 1.0

Fluorine binding site 2 out of 2 in 1w4q

Go back to Fluorine Binding Sites List in 1w4q
Fluorine binding site 2 out of 2 in the Binding of Nonnatural 3'-Nucleotides to Ribonuclease A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Binding of Nonnatural 3'-Nucleotides to Ribonuclease A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1125

b:22.3
occ:1.00
F2' B:UMF1125 0.0 22.3 1.0
C2' B:UMF1125 1.3 15.5 1.0
O3' B:UMF1125 2.1 13.0 1.0
C3' B:UMF1125 2.3 15.2 1.0
C1' B:UMF1125 2.6 15.0 1.0
O3P B:UMF1125 2.8 13.0 1.0
CE1 B:HIS12 2.8 8.3 1.0
NE2 B:HIS12 2.9 7.5 1.0
P B:UMF1125 3.1 13.3 1.0
C4' B:UMF1125 3.2 15.8 1.0
NZ B:LYS41 3.2 21.2 1.0
O4' B:UMF1125 3.5 16.8 1.0
O2 B:UMF1125 3.6 12.1 1.0
N1 B:UMF1125 3.7 14.0 1.0
CE B:LYS41 3.8 19.1 1.0
O2P B:UMF1125 3.8 15.8 1.0
OD1 B:ASN44 3.9 11.0 1.0
NE2 B:GLN11 4.0 8.3 1.0
C2 B:UMF1125 4.1 13.4 1.0
ND1 B:HIS12 4.1 7.5 1.0
CD2 B:HIS12 4.2 7.4 1.0
O B:PHE120 4.3 7.3 1.0
O1P B:UMF1125 4.3 16.2 1.0
CB B:PHE120 4.5 7.2 1.0
C5' B:UMF1125 4.6 17.6 1.0
O B:VAL43 4.6 9.8 1.0
CD B:GLN11 4.6 11.5 1.0
OE1 B:GLN11 4.7 14.6 1.0
CG B:HIS12 4.9 7.6 1.0
C6 B:UMF1125 4.9 15.1 1.0
N B:PHE120 4.9 6.8 1.0
O B:HOH2156 4.9 10.4 1.0
O5' B:UMF1125 5.0 21.1 1.0

Reference:

C.L.Jenkins, N.Thiyagarajan, R.Y.Sweeney, M.P.Guy, B.R.Kelemen, K.R.Acharya, R.T.Raines. Binding of Non-Natural 3'-Nucleotides to Ribonuclease A Febs J. V. 272 744 2005.
ISSN: ISSN 1742-464X
PubMed: 15670155
DOI: 10.1111/J.1742-4658.2004.04511.X
Page generated: Sun Dec 13 11:33:34 2020

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