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Magnesium in PDB 5uz0: Crystal Structure of Aicarft Bound to An Antifolate

Enzymatic activity of Crystal Structure of Aicarft Bound to An Antifolate

All present enzymatic activity of Crystal Structure of Aicarft Bound to An Antifolate:
2.1.2.3; 3.5.4.10;

Protein crystallography data

The structure of Crystal Structure of Aicarft Bound to An Antifolate, PDB code: 5uz0 was solved by S.Atwell, Y.Wang, K.R.Fales, D.Clawson, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.04 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.797, 105.121, 105.646, 113.48, 99.42, 95.52
R / Rfree (%) 20.2 / 22.5

Other elements in 5uz0:

The structure of Crystal Structure of Aicarft Bound to An Antifolate also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Aicarft Bound to An Antifolate (pdb code 5uz0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Aicarft Bound to An Antifolate, PDB code: 5uz0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5uz0

Go back to Magnesium Binding Sites List in 5uz0
Magnesium binding site 1 out of 4 in the Crystal Structure of Aicarft Bound to An Antifolate


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 Aicarft Bound to An Antifolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:15.8
occ:1.00
 O A:VAL425 2.4 9.2 1.0
O A:THR428 2.5 10.7 1.0
OD1 A:ASP539 2.7 19.6 1.0
O A:LEU589 2.7 10.3 1.0
OG A:SER432 3.1 19.9 1.0
OG A:SER430 3.2 5.8 1.0
CB A:ASP539 3.5 10.8 1.0
CG A:ASP539 3.5 16.7 1.0
C A:VAL425 3.6 9.9 1.0
C A:THR428 3.7 8.7 1.0
CB A:HIS591 3.7 6.7 1.0
N A:HIS591 3.8 7.0 1.0
C A:LEU589 3.9 9.7 1.0
CB A:SER432 4.1 12.4 1.0
C A:PHE590 4.1 10.1 1.0
N A:THR428 4.2 5.2 1.0
CA A:PHE590 4.2 5.1 1.0
CA A:THR428 4.3 4.9 1.0
CA A:HIS591 4.4 5.5 1.0
N A:SER430 4.4 3.6 1.0
CB A:SER430 4.4 3.2 1.0
CB A:THR428 4.4 9.8 1.0
CA A:VAL425 4.4 7.6 1.0
N A:PHE590 4.5 6.1 1.0
C A:LYS426 4.5 8.7 1.0
N A:LYS426 4.5 5.7 1.0
O A:LYS426 4.5 9.1 1.0
C A:GLN429 4.6 7.5 1.0
CB A:VAL425 4.6 11.6 1.0
CA A:LYS426 4.6 5.3 1.0
CA A:SER430 4.6 3.0 1.0
N A:GLN429 4.7 5.9 1.0
OD2 A:ASP539 4.7 16.7 1.0
O A:PHE590 4.8 11.7 1.0
O A:GLN429 4.9 6.3 1.0
CB A:LEU589 4.9 5.9 1.0
CG A:HIS591 4.9 8.8 1.0
O A:HIS591 4.9 7.6 1.0
CA A:GLN429 5.0 5.6 1.0
N A:TYR427 5.0 5.1 1.0

Magnesium binding site 2 out of 4 in 5uz0

Go back to Magnesium Binding Sites List in 5uz0
Magnesium binding site 2 out of 4 in the Crystal Structure of Aicarft Bound to An Antifolate


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 Aicarft Bound to An Antifolate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:16.5
occ:1.00
 O B:VAL425 2.4 8.6 1.0
O B:THR428 2.6 11.0 1.0
O B:LEU589 2.6 7.1 1.0
OD1 B:ASP539 2.8 20.4 1.0
OG B:SER432 3.2 17.9 1.0
OG B:SER430 3.2 9.0 1.0
CB B:ASP539 3.5 10.3 1.0
C B:VAL425 3.6 10.1 1.0
CB B:HIS591 3.6 4.8 1.0
CG B:ASP539 3.6 18.6 1.0
C B:THR428 3.7 8.9 1.0
N B:HIS591 3.7 7.5 1.0
C B:LEU589 3.8 6.7 1.0
C B:PHE590 4.1 9.6 1.0
CA B:PHE590 4.2 5.2 1.0
N B:THR428 4.2 5.2 1.0
CB B:SER432 4.2 14.3 1.0
CA B:HIS591 4.3 5.4 1.0
CA B:THR428 4.4 4.9 1.0
N B:PHE590 4.4 5.5 1.0
CA B:VAL425 4.4 8.8 1.0
O B:LYS426 4.4 9.3 1.0
C B:LYS426 4.4 7.3 1.0
N B:LYS426 4.4 5.5 1.0
CA B:LYS426 4.5 4.6 1.0
CB B:THR428 4.5 11.3 1.0
CB B:SER430 4.5 5.3 1.0
N B:SER430 4.5 5.1 1.0
CB B:VAL425 4.6 14.4 1.0
C B:GLN429 4.7 8.2 1.0
CA B:SER430 4.7 3.2 1.0
CB B:LEU589 4.8 4.8 1.0
N B:GLN429 4.8 5.2 1.0
O B:PHE590 4.8 9.3 1.0
CG B:HIS591 4.8 6.5 1.0
OD2 B:ASP539 4.8 19.3 1.0
CA B:LEU589 4.9 3.8 1.0
O B:HIS591 4.9 7.4 1.0
N B:TYR427 5.0 6.0 1.0
O B:GLN429 5.0 8.0 1.0

Magnesium binding site 3 out of 4 in 5uz0

Go back to Magnesium Binding Sites List in 5uz0
Magnesium binding site 3 out of 4 in the Crystal Structure of Aicarft Bound to An Antifolate


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 Aicarft Bound to An Antifolate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:20.8
occ:1.00
 O C:VAL425 2.4 7.5 1.0
O C:THR428 2.6 9.9 1.0
O C:LEU589 2.7 6.8 1.0
OD1 C:ASP539 2.7 16.6 1.0
OG C:SER432 3.1 22.4 1.0
OG C:SER430 3.2 9.7 1.0
CB C:ASP539 3.5 10.8 1.0
CG C:ASP539 3.5 14.2 1.0
C C:VAL425 3.5 11.0 1.0
C C:THR428 3.7 8.4 1.0
CB C:HIS591 3.7 7.2 1.0
N C:HIS591 3.8 6.8 1.0
C C:LEU589 3.8 8.0 1.0
C C:PHE590 4.1 8.6 1.0
CB C:SER432 4.1 11.6 1.0
CA C:PHE590 4.2 5.8 1.0
N C:THR428 4.2 3.0 1.0
CA C:THR428 4.3 3.0 1.0
CA C:HIS591 4.4 6.8 1.0
CA C:VAL425 4.4 9.3 1.0
CB C:SER430 4.4 6.4 1.0
N C:SER430 4.5 5.1 1.0
CB C:THR428 4.5 9.5 1.0
N C:LYS426 4.5 6.0 1.0
N C:PHE590 4.5 7.2 1.0
C C:LYS426 4.5 9.9 1.0
O C:LYS426 4.5 9.9 1.0
CB C:VAL425 4.5 13.5 1.0
CA C:LYS426 4.5 5.6 1.0
C C:GLN429 4.6 8.7 1.0
CA C:SER430 4.6 4.5 1.0
OD2 C:ASP539 4.7 13.2 1.0
N C:GLN429 4.8 5.6 1.0
CB C:LEU589 4.8 4.3 1.0
O C:PHE590 4.8 7.7 1.0
CG C:HIS591 4.9 9.0 1.0
CA C:LEU589 4.9 4.4 1.0
O C:GLN429 4.9 10.3 1.0
O C:HIS591 4.9 7.2 1.0
CA C:ASP539 5.0 7.9 1.0
N C:TYR427 5.0 5.9 1.0

Magnesium binding site 4 out of 4 in 5uz0

Go back to Magnesium Binding Sites List in 5uz0
Magnesium binding site 4 out of 4 in the Crystal Structure of Aicarft Bound to An Antifolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Aicarft Bound to An Antifolate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg605

b:17.6
occ:1.00
 O D:VAL425 2.4 9.4 1.0
O D:THR428 2.5 10.3 1.0
O D:LEU589 2.7 6.9 1.0
OD1 D:ASP539 2.7 19.1 1.0
OG D:SER432 3.2 23.3 1.0
OG D:SER430 3.2 11.4 1.0
CG D:ASP539 3.5 16.4 1.0
CB D:ASP539 3.5 8.4 1.0
C D:VAL425 3.6 9.2 1.0
CB D:HIS591 3.6 7.2 1.0
C D:THR428 3.6 9.4 1.0
N D:HIS591 3.8 8.4 1.0
C D:LEU589 3.8 7.5 1.0
N D:THR428 4.1 5.3 1.0
C D:PHE590 4.1 10.2 1.0
CB D:SER432 4.2 13.4 1.0
CA D:PHE590 4.2 4.9 1.0
CA D:THR428 4.3 4.8 1.0
CA D:HIS591 4.3 6.1 1.0
O D:LYS426 4.4 8.3 1.0
CB D:THR428 4.4 8.1 1.0
C D:LYS426 4.4 7.2 1.0
CA D:VAL425 4.4 8.2 1.0
N D:LYS426 4.5 4.1 1.0
CB D:SER430 4.5 6.2 1.0
N D:SER430 4.5 3.3 1.0
N D:PHE590 4.5 5.2 1.0
CA D:LYS426 4.5 3.0 1.0
CB D:VAL425 4.6 13.0 1.0
C D:GLN429 4.6 7.6 1.0
CA D:SER430 4.7 3.0 1.0
N D:GLN429 4.7 6.0 1.0
OD2 D:ASP539 4.7 16.9 1.0
CG D:HIS591 4.8 9.8 1.0
CB D:LEU589 4.8 4.3 1.0
O D:PHE590 4.8 9.6 1.0
O D:HIS591 4.9 7.0 1.0
N D:TYR427 4.9 4.7 1.0
CA D:LEU589 5.0 5.2 1.0
O D:GLN429 5.0 7.9 1.0
CA D:GLN429 5.0 6.1 1.0

Reference:

K.R.Fales, F.G.Njoroge, H.B.Brooks, S.Thibodeaux, A.Torrado, C.Si, J.L.Toth, J.R.Mc Cowan, K.D.Roth, K.J.Thrasher, K.Frimpong, M.R.Lee, R.D.Dally, T.A.Shepherd, T.B.Durham, B.J.Margolis, Z.Wu, Y.Wang, S.Atwell, J.Wang, Y.H.Hui, T.I.Meier, S.A.Konicek, S.Geeganage. Discovery of N-(6-Fluoro-1-Oxo-1,2-Dihydroisoquinolin-7-Yl)-5-[(3R) -3-Hydroxypyrrolidin-1-Yl]Thiophene-2-Sulfonamide (Lsn 3213128), A Potent and Selective Nonclassical Antifolate Aminoimidazole-4-Carboxamide Ribonucleotide Formyltransferase (Aicarft) Inhibitor Effective at Tumor Suppression in A Cancer Xenograft Model. J. Med. Chem. V. 60 9599 2017.
ISSN: ISSN 1520-4804
PubMed: 29072452
DOI: 10.1021/ACS.JMEDCHEM.7B01046
Page generated: Mon Sep 30 05:56:42 2024

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