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Fluorine in PDB 2vkq: Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride

Enzymatic activity of Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride

All present enzymatic activity of Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride, PDB code: 2vkq was solved by K.Wallden, M.Moche, C.H.Arrowsmith, H.Berglund, R.Busam, R.Collins, L.G.Dahlgren, A.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, M.D.Herman, A.Johansson, I.Johansson, A.Kallas, T.Karlberg, T.Kotenyova, L.Lehtio, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, P.Nordlund, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.5
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.265, 99.388, 78.041, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.2

Other elements in 2vkq:

The structure of Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride (pdb code 2vkq). 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 Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride, PDB code: 2vkq:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2vkq

Go back to Fluorine Binding Sites List in 2vkq
Fluorine binding site 1 out of 3 in the Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride


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 Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1287

b:55.5
occ:1.00
 F1 A:BEF1287 0.0 55.5 1.0
BE A:BEF1287 1.4 57.2 1.0
MG A:MG1288 2.0 42.3 1.0
F3 A:BEF1287 2.3 56.3 1.0
F2 A:BEF1287 2.3 58.6 1.0
OD1 A:ASP38 2.6 53.0 1.0
OD2 A:ASP38 2.7 50.7 1.0
O A:HOH2003 2.9 60.7 1.0
CG A:ASP38 3.0 52.6 1.0
O A:ASP40 3.2 51.9 1.0
O A:HOH2021 3.2 40.6 1.0
CB A:ASP40 3.2 52.7 1.0
N A:ASP40 3.4 52.3 1.0
CA A:ASP40 3.6 52.2 1.0
C A:ASP40 3.8 52.0 1.0
OD2 A:ASP40 4.0 52.0 1.0
CG A:ASP40 4.1 53.5 1.0
OD1 A:ASP227 4.2 53.6 1.0
C A:PHE39 4.3 52.2 1.0
N A:PHE39 4.3 52.2 1.0
O A:HOH2005 4.4 42.0 1.0
CB A:ASP38 4.5 52.2 1.0
NZ A:LYS202 4.5 58.9 1.0
OG A:SER153 4.7 52.7 1.0
N A:ALA154 4.8 52.4 1.0
CA A:PHE39 4.8 52.2 1.0

Fluorine binding site 2 out of 3 in 2vkq

Go back to Fluorine Binding Sites List in 2vkq
Fluorine binding site 2 out of 3 in the Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride


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 Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1287

b:58.6
occ:1.00
 F2 A:BEF1287 0.0 58.6 1.0
BE A:BEF1287 1.4 57.2 1.0
F3 A:BEF1287 2.3 56.3 1.0
F1 A:BEF1287 2.3 55.5 1.0
OD1 A:ASP38 2.5 53.0 1.0
NZ A:LYS202 2.8 58.9 1.0
N A:ALA154 2.8 52.4 1.0
O A:HOH2003 3.0 60.7 1.0
CA A:SER153 3.4 52.6 1.0
C A:SER153 3.6 52.5 1.0
CE A:LYS202 3.6 59.1 1.0
CG A:ASP38 3.7 52.6 1.0
CB A:ALA154 3.7 52.1 1.0
CA A:ALA154 3.7 52.2 1.0
OG A:SER153 3.9 52.7 1.0
MG A:MG1288 4.1 42.3 1.0
OD2 A:ASP38 4.1 50.7 1.0
O A:PHE152 4.2 52.9 1.0
CB A:SER153 4.2 52.7 1.0
O A:HOH2021 4.2 40.6 1.0
N A:GLY155 4.5 51.9 1.0
C A:ALA154 4.5 52.0 1.0
N A:SER153 4.6 53.0 1.0
OD1 A:ASP231 4.7 55.9 1.0
O A:SER153 4.8 52.9 1.0
C A:PHE152 4.8 53.1 1.0
OD2 A:ASP40 4.9 52.0 1.0
N A:PHE39 4.9 52.2 1.0
CB A:ASP38 4.9 52.2 1.0
N A:ASP40 5.0 52.3 1.0

Fluorine binding site 3 out of 3 in 2vkq

Go back to Fluorine Binding Sites List in 2vkq
Fluorine binding site 3 out of 3 in the Crystal Structure of Human Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride


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 Cytosolic 5'-Nucleotidase III ( Cn-III, NT5C3) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1287

b:56.3
occ:1.00
 F3 A:BEF1287 0.0 56.3 1.0
BE A:BEF1287 1.4 57.2 1.0
F1 A:BEF1287 2.3 55.5 1.0
F2 A:BEF1287 2.3 58.6 1.0
OG A:SER153 2.6 52.7 1.0
OD1 A:ASP38 2.6 53.0 1.0
N A:ASP40 3.0 52.3 1.0
CB A:SER153 3.1 52.7 1.0
N A:PHE39 3.1 52.2 1.0
CA A:SER153 3.2 52.6 1.0
O A:HOH2003 3.4 60.7 1.0
CG A:ASP38 3.4 52.6 1.0
CA A:PHE39 3.6 52.2 1.0
CB A:PHE39 3.7 52.0 1.0
N A:ALA154 3.7 52.4 1.0
C A:PHE39 3.7 52.2 1.0
OD2 A:ASP38 3.8 50.7 1.0
OD2 A:ASP40 3.8 52.0 1.0
CB A:ASP40 3.9 52.7 1.0
C A:SER153 4.0 52.5 1.0
CA A:ASP40 4.0 52.2 1.0
MG A:MG1288 4.1 42.3 1.0
CG A:ASP40 4.1 53.5 1.0
C A:ASP38 4.3 52.3 1.0
NZ A:LYS202 4.3 58.9 1.0
O A:PHE152 4.3 52.9 1.0
N A:SER153 4.4 53.0 1.0
N A:GLY155 4.5 51.9 1.0
CA A:ASP38 4.5 52.4 1.0
CB A:ASP38 4.6 52.2 1.0
O A:ASP40 4.6 51.9 1.0
C A:PHE152 4.8 53.1 1.0
C A:ASP40 4.8 52.0 1.0
O A:PHE39 4.9 51.6 1.0
CG A:PHE39 4.9 52.4 1.0
CA A:ALA154 4.9 52.2 1.0

Reference:

K.Wallden, P.Stenmark, S.Flodin, T.Nyman, M.Moche, M.Ehn, M.Hammarstrom, P.Nilsson-Ehle, P.Nordlund. Crystal Structure of Human Cytosolic 5'- Nucleotidase III To Be Published.
Page generated: Mon Jul 14 14:32:10 2025

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