Sodium in PDB 7rc3: Aeronamide N-Methyltransferase, Aere (Y137F)

The structure of Aeronamide N-Methyltransferase, Aere (Y137F), PDB code: 7rc3 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)	19.52 / 1.53
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.697, 77.697, 152.239, 90, 90, 120
R / Rfree (%)	16.4 / 18.4

The structure of Aeronamide N-Methyltransferase, Aere (Y137F) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Aeronamide N-Methyltransferase, Aere (Y137F) (pdb code 7rc3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Aeronamide N-Methyltransferase, Aere (Y137F), PDB code: 7rc3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Aeronamide N-Methyltransferase, Aere (Y137F)


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 (Y137F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:16.8 occ:1.00 O A:PRO232 2.4 16.0 1.0 OD1 A:ASN231 2.5 14.7 1.0 O A:HOH528 2.6 30.8 1.0 O A:HOH523 2.7 21.8 1.0 O A:HOH749 2.8 20.4 1.0 CE2 A:PHE234 3.1 17.0 1.0 CD2 A:PHE234 3.3 15.1 1.0 C A:PRO232 3.3 14.1 1.0 CG A:ASN231 3.4 15.7 1.0 O A:ASN231 3.7 15.4 1.0 C A:ASN231 3.9 13.8 1.0 CZ A:PHE234 3.9 17.2 1.0 N A:PRO233 4.0 13.2 1.0 ND2 A:ASN231 4.0 13.7 1.0 CA A:PRO233 4.1 13.3 1.0 N A:PRO232 4.1 12.0 1.0 CG A:PHE234 4.1 15.7 1.0 O A:TYR246 4.2 21.0 1.0 OD2 A:ASP141 4.2 21.8 1.0 O A:HOH902 4.3 25.7 1.0 SD A:SAH405 4.3 18.9 1.0 CA A:PRO232 4.3 15.4 1.0 N A:PHE234 4.3 15.8 1.0 CB A:ASN231 4.5 14.2 1.0 C A:PRO233 4.6 16.5 1.0 C5' A:SAH405 4.6 16.1 1.0 CG A:SAH405 4.6 16.9 1.0 CA A:ASN231 4.6 13.1 1.0 CE1 A:PHE234 4.7 15.8 1.0 CD1 A:PHE234 4.8 15.5 1.0 CE2 A:PHE137 4.9 18.1 1.0 CD A:PRO232 4.9 14.4 1.0 CB A:PHE234 5.0 16.2 1.0

Sodium binding site 2 out of 2 in the Aeronamide N-Methyltransferase, Aere (Y137F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Aeronamide N-Methyltransferase, Aere (Y137F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:31.9 occ:1.00 O19 A:P6G404 2.7 22.2 1.0 O13 A:P6G404 2.8 24.0 1.0 O7 A:P6G404 2.9 30.0 1.0 O16 A:P6G404 3.0 21.9 1.0 O10 A:P6G404 3.0 27.8 1.0 CE1 A:HIS50 3.2 15.6 1.0 C6 A:P6G404 3.3 34.3 1.0 O A:HOH814 3.5 34.5 1.0 ND1 A:HIS50 3.5 18.3 1.0 C18 A:P6G404 3.6 18.2 1.0 C11 A:P6G404 3.6 22.0 1.0 O A:HOH651 3.7 24.9 1.0 C8 A:P6G404 3.7 31.1 1.0 C15 A:P6G404 3.7 19.0 1.0 C9 A:P6G404 3.7 32.4 1.0 C17 A:P6G404 3.7 20.0 1.0 C12 A:P6G404 3.8 24.5 1.0 C14 A:P6G404 3.8 19.8 1.0 O4 A:P6G404 4.1 37.5 1.0 C5 A:P6G404 4.2 40.9 1.0 NE2 A:HIS50 4.5 16.4 1.0 CG A:HIS50 4.9 14.4 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