Sodium in PDB 7rc6: Aeronamide N-Methyltransferase, Aere, Bound to Modified Peptide Substrate, Aera-Dl,34

The structure of Aeronamide N-Methyltransferase, Aere, Bound to Modified Peptide Substrate, Aera-Dl,34, PDB code: 7rc6 was solved by D.P.Cogan, R.Reyes, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.78 / 1.71
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.029, 78.029, 153.399, 90, 90, 120
R / Rfree (%)	16.5 / 18.8

The binding sites of Sodium atom in the Aeronamide N-Methyltransferase, Aere, Bound to Modified Peptide Substrate, Aera-Dl,34 (pdb code 7rc6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Aeronamide N-Methyltransferase, Aere, Bound to Modified Peptide Substrate, Aera-Dl,34, PDB code: 7rc6:

Sodium binding site 1 out of 1 in the Aeronamide N-Methyltransferase, Aere, Bound to Modified Peptide Substrate, Aera-Dl,34


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Aeronamide N-Methyltransferase, Aere, Bound to Modified Peptide Substrate, Aera-Dl,34 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:23.0 occ:1.00 OD1 C:DSG1 2.1 41.8 1.0 O A:PRO232 2.3 14.6 1.0 CG C:DSG1 2.4 45.8 1.0 O A:HOH760 2.5 20.5 1.0 OD1 A:ASN231 2.5 15.7 1.0 CE2 A:PHE234 3.0 15.6 1.0 CD2 A:PHE234 3.0 16.3 1.0 ND2 C:DSG1 3.1 43.8 1.0 C A:PRO232 3.2 14.7 1.0 CB C:DSG1 3.5 40.7 1.0 CG A:ASN231 3.5 18.2 1.0 CZ A:PHE234 3.8 15.3 1.0 CA C:DSG1 3.8 37.1 1.0 N A:PRO233 3.9 14.8 1.0 CG A:PHE234 3.9 15.2 1.0 CA A:PRO233 3.9 14.0 1.0 O A:ASN231 4.0 15.3 1.0 C A:ASN231 4.0 16.6 1.0 ND2 A:ASN231 4.1 14.4 1.0 N A:PHE234 4.1 15.4 1.0 N A:PRO232 4.1 15.3 1.0 CA A:PRO232 4.3 16.0 1.0 O A:TYR246 4.3 15.8 1.0 OD2 A:ASP141 4.3 20.9 1.0 SD C:SAH101 4.3 17.1 1.0 C A:PRO233 4.4 15.3 1.0 CE1 A:PHE234 4.5 17.8 1.0 N C:DSG1 4.6 42.1 1.0 CD1 A:PHE234 4.6 15.3 1.0 C5' C:SAH101 4.6 18.5 1.0 CB A:ASN231 4.6 14.0 1.0 CA A:ASN231 4.7 14.5 1.0 CB A:PHE234 4.7 12.4 1.0 CG C:SAH101 4.8 15.8 1.0 CD A:PRO232 4.8 15.7 1.0

D.P.Cogan, A.Bhushan, R.Reyes, L.Zhu, J.Piel, S.K.Nair. Structure and Mechanism For Iterative Amide N -Methylation in the Biosynthesis of Channel-Forming Peptide Cytotoxins. Proc.Natl.Acad.Sci.Usa V. 119 78119 2022.
ISSN: ESSN 1091-6490
PubMed: 35316135
DOI: 10.1073/PNAS.2116578119