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Magnesium 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:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3fuc

Go back to Magnesium Binding Sites List in 3fuc
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg302

b:19.3
occ:1.00
O A:HOH425 2.0 21.4 1.0
OE2 A:GLU186 2.0 21.5 1.0
O A:HOH549 2.0 19.7 1.0
O A:HOH503 2.3 24.6 1.0
CD A:GLU186 3.0 22.7 1.0
OE1 A:GLU186 3.3 23.0 1.0
NE2 A:GLN188 4.2 24.0 1.0
OE1 A:GLN188 4.2 18.4 1.0
O A:HOH519 4.3 23.4 1.0
CG A:GLU186 4.3 18.3 1.0
O A:ASN123 4.6 16.1 1.0
CD A:GLN188 4.7 15.5 1.0
CB A:ASN123 4.9 14.3 1.0

Magnesium binding site 2 out of 3 in 3fuc

Go back to Magnesium Binding Sites List in 3fuc
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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
C:Mg302

b:14.6
occ:0.50
O C:HOH530 2.0 15.4 0.5
OD1 C:ASP9 2.0 16.4 1.0
O C:HOH511 2.1 14.6 0.5
O C:HOH407 2.1 14.9 1.0
CG C:ASP9 3.3 16.4 1.0
OD2 C:ASP12 3.9 14.9 1.0
O C:HOH438 4.0 16.9 1.0
OD2 C:ASP9 4.0 16.7 1.0
OD1 C:ASN55 4.0 16.4 1.0
ND2 C:ASN55 4.1 14.9 1.0
CA C:ASP9 4.2 14.6 1.0
CB C:ASP9 4.3 14.3 1.0
CG C:ASN55 4.5 15.0 1.0
N C:ASP9 4.6 15.6 1.0
CG C:ASP12 4.9 14.0 1.0
OG1 C:THR6 5.0 17.5 1.0

Magnesium binding site 3 out of 3 in 3fuc

Go back to Magnesium Binding Sites List in 3fuc
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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
C:Mg303

b:26.9
occ:0.50
O C:HOH516 2.0 18.8 0.0
O C:HOH504 2.2 17.4 0.5
OE2 C:GLU186 2.2 27.3 1.0
O C:HOH505 2.3 22.8 0.5
CD C:GLU186 3.1 27.7 1.0
OE1 C:GLU186 3.5 30.5 1.0
OE1 C:GLN188 4.3 18.5 1.0
NE2 C:GLN188 4.3 23.8 1.0
CG C:GLU186 4.4 24.1 1.0
O C:ASN123 4.7 19.1 1.0
CD C:GLN188 4.8 18.3 1.0
CB C:ASN123 4.8 18.6 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: Mon Dec 14 08:09:18 2020

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