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Fluorine in PDB 1v48: Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine

Enzymatic activity of Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine

All present enzymatic activity of Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine:
2.4.2.1;

Protein crystallography data

The structure of Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine, PDB code: 1v48 was solved by M.Luic, G.Koellner, T.Yokomatsu, S.Shibuya, A.Bzowska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 93.183, 93.183, 93.183, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24.2

Other elements in 1v48:

The structure of Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine (pdb code 1v48). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine, PDB code: 1v48:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 1v48

Go back to Fluorine Binding Sites List in 1v48
Fluorine binding site 1 out of 2 in the Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F290

b:27.2
occ:1.00
 F15 A:HA1290 0.0 27.2 1.0
C14 A:HA1290 1.3 26.5 1.0
F16 A:HA1290 2.2 26.2 1.0
P A:HA1290 2.4 25.4 1.0
C13 A:HA1290 2.4 25.3 1.0
O3P A:HA1290 2.7 22.7 1.0
O2P A:HA1290 3.0 24.2 1.0
O A:HOH646 3.0 35.4 1.0
O A:HOH645 3.0 23.6 1.0
C12 A:HA1290 3.1 25.7 1.0
NE2 A:HIS86 3.3 19.2 1.0
OG A:SER33 3.6 47.9 1.0
O1P A:HA1290 3.6 24.7 1.0
CD2 A:HIS86 4.0 19.4 1.0
CE1 A:HIS86 4.0 19.9 1.0
OH A:TYR88 4.1 20.1 1.0
CB A:SER33 4.3 47.8 1.0
C11 A:HA1290 4.3 24.2 1.0
N A:SER33 4.7 45.1 1.0
CE2 A:TYR88 4.8 18.5 1.0
ND1 A:HIS86 5.0 17.3 1.0
CZ A:TYR88 5.0 19.3 1.0
CG A:HIS86 5.0 18.4 1.0

Fluorine binding site 2 out of 2 in 1v48

Go back to Fluorine Binding Sites List in 1v48
Fluorine binding site 2 out of 2 in the Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Calf Spleen Purine Nucleoside Phosphorylase (Pnp) Binary Complex with 9-(5,5-Difluoro-5-Phosphonopenthyl)Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F290

b:26.2
occ:1.00
 F16 A:HA1290 0.0 26.2 1.0
C14 A:HA1290 1.3 26.5 1.0
F15 A:HA1290 2.2 27.2 1.0
P A:HA1290 2.3 25.4 1.0
C13 A:HA1290 2.4 25.3 1.0
O1P A:HA1290 2.7 24.7 1.0
C12 A:HA1290 2.8 25.7 1.0
O3P A:HA1290 2.9 22.7 1.0
NE2 A:HIS86 3.2 19.2 1.0
CD2 A:HIS86 3.2 19.4 1.0
O2P A:HA1290 3.6 24.2 1.0
O A:HOH475 3.8 17.1 1.0
CB A:MET219 3.9 18.0 1.0
OG A:SER220 3.9 12.7 1.0
C A:MET219 4.1 17.4 1.0
CB A:SER220 4.1 16.1 1.0
O A:MET219 4.2 18.8 1.0
N A:MET219 4.2 17.5 1.0
C11 A:HA1290 4.3 24.2 1.0
CA A:MET219 4.3 17.9 1.0
CE1 A:HIS86 4.4 19.9 1.0
CE2 A:TYR88 4.4 18.5 1.0
CG A:HIS86 4.4 18.4 1.0
N A:SER220 4.5 16.8 1.0
O A:HOH645 4.6 23.6 1.0
OH A:TYR88 4.7 20.1 1.0
CG A:MET219 4.8 18.9 1.0
O A:HOH646 4.9 35.4 1.0
C10 A:HA1290 4.9 25.1 1.0
CA A:SER220 4.9 16.5 1.0
ND1 A:HIS86 5.0 17.3 1.0

Reference:

M.Luic, G.Koellner, T.Yokomatsu, S.Shibuya, A.Bzowska. Calf Spleen Purine-Nucleoside Phosphorylase: Crystal Structure of the Binary Complex with A Potent Multisubstrate Analogue Inhibitor. Acta Crystallogr.,Sect.D V. 60 1417 2004.
ISSN: ISSN 0907-4449
PubMed: 15272165
DOI: 10.1107/S0907444904013861
Page generated: Sun Dec 13 11:33:28 2020

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