Sodium in PDB 7zp2: Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04

All present enzymatic activity of Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04:
2.1.3.2;

The structure of Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04, PDB code: 7zp2 was solved by C.Wang, B.Zhang, M.R.Groves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.19 / 2.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	87.065, 87.36, 104.636, 89.98, 90.04, 117.72
R / Rfree (%)	16.4 / 19.1

The binding sites of Sodium atom in the Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04 (pdb code 7zp2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04, PDB code: 7zp2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:36.8 occ:1.00 O A:HOH524 2.4 23.1 1.0 O C:HOH519 2.5 36.6 1.0 O C:HOH507 3.1 37.5 1.0 O C:HOH523 3.2 35.9 1.0 HD22 A:LEU119 3.3 40.2 1.0 O B:VAL125 3.3 38.5 1.0 HD12 A:LEU119 3.3 39.8 1.0 HD21 A:LEU119 3.5 40.9 1.0 HG13 A:VAL125 3.6 43.0 1.0 O A:VAL125 3.7 39.1 1.0 HG11 A:VAL125 3.8 42.8 1.0 CD2 A:LEU119 3.8 40.5 1.0 HD13 A:LEU119 3.9 40.4 1.0 CD1 A:LEU119 4.0 39.7 1.0 H A:VAL125 4.1 42.4 1.0 H B:VAL125 4.2 41.1 1.0 CG1 A:VAL125 4.2 42.6 1.0 HD21 A:ASN127 4.2 46.9 1.0 O3 C:SO4401 4.3 53.0 1.0 HA B:LEU126 4.4 44.0 1.0 C B:VAL125 4.4 42.9 1.0 CG A:LEU119 4.6 39.6 1.0 HD22 A:ASN127 4.6 47.1 1.0 HD23 A:LEU119 4.6 40.3 1.0 O4 C:SO4401 4.7 48.9 1.0 HG12 A:VAL125 4.7 42.4 1.0 ND2 A:ASN127 4.8 46.0 1.0 HG A:LEU119 4.8 38.5 1.0 HD11 A:LEU119 4.8 39.7 1.0 C A:VAL125 4.8 42.9 1.0 N A:VAL125 4.8 42.5 1.0 O2 C:SO4401 4.9 42.6 1.0 O C:HOH503 4.9 40.4 1.0 S C:SO4401 4.9 41.9 1.0 N B:VAL125 5.0 40.0 1.0 HD22 B:ASN127 5.0 49.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Truncated Aspartate Transcarbamoylase From Plasmodium Falciparum in Complex with Bda-04 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na401 b:43.2 occ:1.00 O D:HOH530 2.8 32.4 1.0 O D:HOH515 2.9 34.5 1.0 O E:HOH413 2.9 36.8 1.0 HD22 E:LEU119 3.1 35.0 1.0 O F:VAL125 3.1 37.9 1.0 HD21 E:LEU119 3.2 35.5 1.0 O F:HOH506 3.3 34.1 1.0 HD12 E:LEU119 3.3 39.7 1.0 HG11 E:VAL125 3.4 38.6 1.0 HG13 E:VAL125 3.5 38.9 1.0 O D:HOH535 3.5 28.2 1.0 CD2 E:LEU119 3.6 34.3 1.0 HD13 E:LEU119 3.7 40.1 1.0 O E:HOH403 3.7 38.5 1.0 O E:HOH423 3.8 37.6 1.0 CD1 E:LEU119 3.9 41.2 1.0 CG1 E:VAL125 3.9 39.0 1.0 O E:VAL125 4.0 39.6 1.0 H F:VAL125 4.1 41.0 1.0 HD21 E:ASN127 4.1 49.1 1.0 H E:VAL125 4.2 37.2 1.0 HA F:LEU126 4.2 40.8 1.0 CG E:LEU119 4.3 36.0 1.0 C F:VAL125 4.3 43.4 1.0 HG12 E:VAL125 4.4 38.1 1.0 HD23 E:LEU119 4.4 34.9 1.0 O3 D:SO4401 4.5 55.2 1.0 HG E:LEU119 4.5 36.2 1.0 HD22 E:ASN127 4.6 49.6 1.0 ND2 E:ASN127 4.7 49.8 1.0 O D:HOH502 4.7 36.4 1.0 O4 D:SO4401 4.8 44.1 1.0 HD11 E:LEU119 4.8 39.4 1.0 N F:VAL125 4.8 40.9 1.0 N E:VAL125 4.9 36.0 1.0 HB3 F:LEU126 4.9 40.9 1.0 C E:VAL125 4.9 35.5 1.0 O1 D:SO4401 4.9 53.7 1.0 HB3 F:LYS124 5.0 39.3 1.0 S D:SO4401 5.0 41.2 1.0

C.Wang, B.Zhang, A.Kruger, X.Du, L.Visser, A.S.S.Domling, C.Wrenger, M.R.Groves. Discovery of Small-Molecule Allosteric Inhibitors of Pf Atc As Antimalarials. J.Am.Chem.Soc. V. 144 19070 2022.
ISSN: ESSN 1520-5126
PubMed: 36195578
DOI: 10.1021/JACS.2C08128