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Magnesium in PDB 5no1: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G):
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G), PDB code: 5no1 was solved by V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.06 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 158.570, 158.570, 123.060, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 5no1:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G) also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G) (pdb code 5no1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G), PDB code: 5no1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5no1

Go back to Magnesium Binding Sites List in 5no1
Magnesium binding site 1 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:58.8
occ:1.00
 O21 A:XZ4403 1.7 75.7 1.0
OE1 A:GLU221 2.0 64.9 1.0
O D:HOH201 2.0 58.8 1.0
OD2 A:ASP128 2.1 74.8 1.0
OE2 A:GLU221 2.1 78.8 1.0
O19 A:XZ4403 2.1 79.8 1.0
CD A:GLU221 2.3 53.1 1.0
N20 A:XZ4403 2.6 88.3 1.0
C14 A:XZ4403 2.7 83.4 1.0
CG A:ASP128 3.0 64.3 1.0
OD1 A:ASP128 3.4 71.3 1.0
O A:HOH502 3.7 92.0 1.0
MG A:MG402 3.7 61.7 1.0
ND2 A:ASN224 3.8 65.8 1.0
CG A:GLU221 3.9 53.3 1.0
C16 A:XZ4403 3.9 89.7 1.0
C13 A:XZ4403 4.1 82.0 1.0
OP1 D:DA17 4.2 81.8 1.0
O A:TYR129 4.2 65.4 1.0
O A:HOH515 4.3 68.1 1.0
CB A:ASP128 4.3 59.5 1.0
F8 A:XZ4403 4.4 80.9 1.0
N23 A:XZ4403 4.4 74.1 1.0
N10 A:XZ4403 4.5 58.8 1.0
OD2 A:ASP185 4.5 75.6 1.0
CB A:GLU221 4.7 52.3 1.0
C5' D:DA17 4.7 0.0 1.0
C11 A:XZ4403 4.9 75.4 1.0
C17 A:XZ4403 5.0 83.7 1.0
CA A:GLU221 5.0 65.7 1.0

Magnesium binding site 2 out of 3 in 5no1

Go back to Magnesium Binding Sites List in 5no1
Magnesium binding site 2 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:61.7
occ:1.00
 N23 A:XZ4403 1.9 74.1 1.0
OD2 A:ASP185 2.1 75.6 1.0
OD1 A:ASP128 2.1 71.3 1.0
O A:HOH515 2.1 68.1 1.0
O21 A:XZ4403 2.2 75.7 1.0
O A:HOH536 2.3 63.6 1.0
C16 A:XZ4403 2.7 89.7 1.0
N20 A:XZ4403 2.8 88.3 1.0
C24 A:XZ4403 2.9 74.7 1.0
CG A:ASP185 3.1 74.6 1.0
CG A:ASP128 3.2 64.3 1.0
O27 A:XZ4403 3.2 80.4 1.0
OD1 A:ASP185 3.4 83.8 1.0
OD2 A:ASP128 3.6 74.8 1.0
MG A:MG401 3.7 58.8 1.0
O A:HOH502 3.9 92.0 1.0
C17 A:XZ4403 4.0 83.7 1.0
C25 A:XZ4403 4.2 86.7 1.0
C14 A:XZ4403 4.2 83.4 1.0
CB A:ASP185 4.4 60.8 1.0
OE2 A:GLU221 4.4 78.8 1.0
N A:TYR129 4.4 57.4 1.0
O A:TYR129 4.4 65.4 1.0
CB A:ASP128 4.4 59.5 1.0
O A:HOH513 4.5 68.5 1.0
O D:HOH201 4.6 58.8 1.0
C28 A:XZ4403 4.6 76.3 1.0
C26 A:XZ4403 4.6 78.9 1.0
O19 A:XZ4403 4.7 79.8 1.0
CA A:ASP128 4.8 58.9 1.0

Magnesium binding site 3 out of 3 in 5no1

Go back to Magnesium Binding Sites List in 5no1
Magnesium binding site 3 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:0.1
occ:1.00
 OD1 B:ASP128 2.1 0.0 1.0
OD2 B:ASP185 2.1 97.7 1.0
CG B:ASP185 2.8 93.5 1.0
OD1 B:ASP185 2.9 97.5 1.0
CG B:ASP128 3.2 0.6 1.0
OD2 B:ASP128 3.5 0.1 1.0
O B:HOH504 3.9 72.9 1.0
CB B:ASP185 4.3 69.3 1.0
N B:TYR129 4.5 73.6 1.0
CB B:ASP128 4.5 79.9 1.0
CE2 B:PHE190 4.6 72.4 1.0
CA B:ASP128 4.8 78.8 1.0
O B:TYR129 4.8 86.9 1.0

Reference:

X.Z.Zhao, S.J.Smith, D.P.Maskell, M.Metifiot, V.E.Pye, K.Fesen, C.Marchand, Y.Pommier, P.Cherepanov, S.H.Hughes, T.R.Burke. Structure-Guided Optimization of Hiv Integrase Strand Transfer Inhibitors. J. Med. Chem. V. 60 7315 2017.
ISSN: ISSN 1520-4804
PubMed: 28737946
DOI: 10.1021/ACS.JMEDCHEM.7B00596
Page generated: Sun Sep 29 23:21:53 2024

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