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Fluorine in PDB 3fuc: Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit

Enzymatic activity of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit

All present enzymatic activity of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit:
2.4.2.1;

Protein crystallography data

The structure of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit, PDB code: 3fuc was solved by M.Bochtler, K.Breer, A.Bzowska, G.Chojnowski, M.Hashimoto, S.Hikishima, M.Narczyk, B.Wielgus-Kutrowska, T.Yokomatsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.795, 78.253, 94.901, 90.00, 97.19, 90.00
R / Rfree (%) 18 / 19.9

Other elements in 3fuc:

The structure of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit (pdb code 3fuc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit, PDB code: 3fuc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3fuc

Go back to Fluorine Binding Sites List in 3fuc
Fluorine binding site 1 out of 6 in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:16.4
occ:1.00
 F1 A:9D9301 0.0 16.4 1.0
C14 A:9D9301 1.4 14.7 1.0
F2 A:9D9301 2.2 15.1 1.0
C13 A:9D9301 2.4 13.4 1.0
P A:9D9301 2.6 12.1 1.0
O1P A:9D9301 2.9 12.6 1.0
C12 A:9D9301 3.0 14.5 1.0
O2P A:9D9301 3.3 14.0 1.0
O A:HOH555 3.3 44.1 1.0
NE2 A:HIS86 3.4 14.2 1.0
OH A:TYR88 3.5 17.0 1.0
OG A:SER33 3.6 18.7 1.0
O A:HOH556 3.8 26.6 1.0
O3P A:9D9301 3.9 13.6 1.0
CE1 A:HIS86 3.9 13.6 1.0
CD2 A:HIS86 4.1 14.2 1.0
C11 A:9D9301 4.4 14.7 1.0
CZ A:TYR88 4.6 13.9 1.0
CE2 A:TYR88 4.7 13.4 1.0
ND1 A:HIS86 4.8 14.6 1.0
CZ B:PHE159 4.9 12.6 1.0
CG A:HIS86 5.0 12.8 1.0
CB A:SER33 5.0 16.4 1.0

Fluorine binding site 2 out of 6 in 3fuc

Go back to Fluorine Binding Sites List in 3fuc
Fluorine binding site 2 out of 6 in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:15.1
occ:1.00
 F2 A:9D9301 0.0 15.1 1.0
C14 A:9D9301 1.3 14.7 1.0
F1 A:9D9301 2.2 16.4 1.0
C13 A:9D9301 2.4 13.4 1.0
P A:9D9301 2.6 12.1 1.0
C12 A:9D9301 2.7 14.5 1.0
O3P A:9D9301 2.9 13.6 1.0
NE2 A:HIS86 3.1 14.2 1.0
O1P A:9D9301 3.1 12.6 1.0
CD2 A:HIS86 3.1 14.2 1.0
CE2 A:TYR88 3.8 13.4 1.0
OH A:TYR88 3.8 17.0 1.0
O2P A:9D9301 3.9 14.0 1.0
O A:HOH428 4.0 10.3 1.0
CE1 A:HIS86 4.1 13.6 1.0
CB A:MET219 4.1 9.7 1.0
CB A:SER220 4.2 11.1 1.0
C11 A:9D9301 4.2 14.7 1.0
CG A:HIS86 4.2 12.8 1.0
CZ A:TYR88 4.3 13.9 1.0
OG A:SER220 4.4 11.4 1.0
C A:MET219 4.5 9.3 1.0
O A:MET219 4.5 9.8 1.0
C10 A:9D9301 4.7 11.9 1.0
ND1 A:HIS86 4.7 14.6 1.0
CA A:MET219 4.7 9.3 1.0
N A:SER220 4.7 8.9 1.0
N A:MET219 4.8 8.7 1.0
CD2 A:TYR88 4.9 13.2 1.0

Fluorine binding site 3 out of 6 in 3fuc

Go back to Fluorine Binding Sites List in 3fuc
Fluorine binding site 3 out of 6 in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:14.9
occ:1.00
 F1 B:9D9301 0.0 14.9 1.0
C14 B:9D9301 1.3 13.5 1.0
F2 B:9D9301 2.2 13.8 1.0
C13 B:9D9301 2.3 12.1 1.0
P B:9D9301 2.6 10.7 1.0
O1P B:9D9301 3.0 12.0 1.0
C12 B:9D9301 3.0 12.4 1.0
O2P B:9D9301 3.2 12.3 1.0
NE2 B:HIS86 3.4 14.4 1.0
O B:HOH619 3.6 25.3 1.0
OG B:SER33 3.6 17.2 1.0
OH B:TYR88 3.6 16.5 1.0
O3P B:9D9301 3.8 12.9 1.0
CE1 B:HIS86 3.9 15.4 1.0
CD2 B:HIS86 4.2 15.2 1.0
C11 B:9D9301 4.4 10.8 1.0
CZ B:TYR88 4.7 12.1 1.0
CE2 B:TYR88 4.8 11.9 1.0
ND1 B:HIS86 4.8 16.3 1.0
CB B:SER33 4.9 14.9 1.0
CZ C:PHE159 5.0 11.2 1.0

Fluorine binding site 4 out of 6 in 3fuc

Go back to Fluorine Binding Sites List in 3fuc
Fluorine binding site 4 out of 6 in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:13.8
occ:1.00
 F2 B:9D9301 0.0 13.8 1.0
C14 B:9D9301 1.4 13.5 1.0
F1 B:9D9301 2.2 14.9 1.0
C13 B:9D9301 2.4 12.1 1.0
P B:9D9301 2.6 10.7 1.0
C12 B:9D9301 2.8 12.4 1.0
O3P B:9D9301 2.9 12.9 1.0
NE2 B:HIS86 3.0 14.4 1.0
O1P B:9D9301 3.1 12.0 1.0
CD2 B:HIS86 3.2 15.2 1.0
CE2 B:TYR88 3.8 11.9 1.0
OH B:TYR88 3.8 16.5 1.0
O2P B:9D9301 3.9 12.3 1.0
O B:HOH510 4.0 9.3 1.0
CE1 B:HIS86 4.1 15.4 1.0
CB B:SER220 4.1 10.0 1.0
CB B:MET219 4.2 9.1 1.0
C11 B:9D9301 4.2 10.8 1.0
CG B:HIS86 4.2 14.9 1.0
CZ B:TYR88 4.3 12.1 1.0
OG B:SER220 4.5 10.8 1.0
C B:MET219 4.5 8.9 1.0
O B:MET219 4.6 9.5 1.0
ND1 B:HIS86 4.7 16.3 1.0
C10 B:9D9301 4.7 9.5 1.0
CA B:MET219 4.7 9.1 1.0
N B:SER220 4.8 9.0 1.0
N B:MET219 4.9 8.6 1.0
CD2 B:TYR88 4.9 11.8 1.0
O B:HOH619 4.9 25.3 1.0

Fluorine binding site 5 out of 6 in 3fuc

Go back to Fluorine Binding Sites List in 3fuc
Fluorine binding site 5 out of 6 in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:15.4
occ:1.00
 F1 C:9D9301 0.0 15.4 1.0
C14 C:9D9301 1.3 14.6 1.0
F2 C:9D9301 2.2 16.1 1.0
C13 C:9D9301 2.4 13.2 1.0
P C:9D9301 2.6 12.4 1.0
O1P C:9D9301 3.0 12.5 1.0
C12 C:9D9301 3.0 14.5 1.0
O2P C:9D9301 3.3 14.7 1.0
NE2 C:HIS86 3.3 15.2 1.0
O C:HOH486 3.4 25.6 1.0
OH C:TYR88 3.5 17.6 1.0
OG C:SER33 3.7 19.8 1.0
O3P C:9D9301 3.8 14.0 1.0
CE1 C:HIS86 3.9 13.6 1.0
CD2 C:HIS86 4.1 14.7 1.0
C11 C:9D9301 4.4 14.0 1.0
CZ C:TYR88 4.6 12.8 1.0
CE2 C:TYR88 4.6 12.8 1.0
ND1 C:HIS86 4.8 15.4 1.0
CG C:HIS86 4.9 12.6 1.0
CZ A:PHE159 5.0 11.7 1.0
CB C:SER33 5.0 19.7 1.0

Fluorine binding site 6 out of 6 in 3fuc

Go back to Fluorine Binding Sites List in 3fuc
Fluorine binding site 6 out of 6 in the Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Recombinant Calf Purine Nucleoside Phosphorylase in A Binary Complex with Multisubstrate Analogue Inhibitor 9-(5',5'-Difluoro-5'- Phosphonopentyl)-9-Deazaguanine Structure in A New Space Group with One Full Trimer in the Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:16.1
occ:1.00
 F2 C:9D9301 0.0 16.1 1.0
C14 C:9D9301 1.3 14.6 1.0
F1 C:9D9301 2.2 15.4 1.0
C13 C:9D9301 2.4 13.2 1.0
P C:9D9301 2.5 12.4 1.0
C12 C:9D9301 2.8 14.5 1.0
O3P C:9D9301 2.8 14.0 1.0
NE2 C:HIS86 3.0 15.2 1.0
O1P C:9D9301 3.1 12.5 1.0
CD2 C:HIS86 3.1 14.7 1.0
CE2 C:TYR88 3.8 12.8 1.0
O2P C:9D9301 3.8 14.7 1.0
OH C:TYR88 3.9 17.6 1.0
O C:HOH401 4.0 9.7 1.0
CB C:SER220 4.1 10.8 1.0
CE1 C:HIS86 4.1 13.6 1.0
CB C:MET219 4.2 9.6 1.0
CG C:HIS86 4.2 12.6 1.0
C11 C:9D9301 4.3 14.0 1.0
CZ C:TYR88 4.3 12.8 1.0
OG C:SER220 4.4 11.2 1.0
C C:MET219 4.4 9.1 1.0
O C:MET219 4.5 10.7 1.0
N C:SER220 4.7 9.0 1.0
C10 C:9D9301 4.7 11.5 1.0
CA C:MET219 4.7 9.2 1.0
ND1 C:HIS86 4.7 15.4 1.0
N C:MET219 4.8 8.6 1.0
O C:HOH486 4.8 25.6 1.0
CD2 C:TYR88 4.9 11.7 1.0
CA C:SER220 5.0 9.9 1.0

Reference:

G.Chojnowski, K.Breer, M.Narczyk, B.Wielgus-Kutrowska, H.Czapinska, M.Hashimoto, S.Hikishima, T.Yokomatsu, M.Bochtler, A.Girstun, K.Staron, A.Bzowska. 1.45 A Resolution Crystal Structure of Recombinant Pnp in Complex with A Pm Multisubstrate Analogue Inhibitor Bearing One Feature of the Postulated Transition State. Biochem.Biophys.Res.Commun. V. 391 703 2010.
ISSN: ISSN 0006-291X
PubMed: 19944078
DOI: 10.1016/J.BBRC.2009.11.124
Page generated: Wed Jul 31 18:41:29 2024

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