Sodium in PDB 7rc4: Aeronamide N-Methyltransferase, Aere (D141A)

The structure of Aeronamide N-Methyltransferase, Aere (D141A), PDB code: 7rc4 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)	40.41 / 1.66
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.595, 77.595, 151.734, 90, 90, 120
R / Rfree (%)	17 / 18.8

The structure of Aeronamide N-Methyltransferase, Aere (D141A) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Aeronamide N-Methyltransferase, Aere (D141A) (pdb code 7rc4). 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 (D141A), PDB code: 7rc4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Aeronamide N-Methyltransferase, Aere (D141A)


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 (D141A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:32.0 occ:1.00 O A:HOH737 2.3 30.0 1.0 O A:HOH560 2.5 37.4 1.0 OD1 A:ASN231 2.6 20.0 1.0 O A:PRO232 2.6 19.5 1.0 O A:HOH736 2.8 23.5 1.0 CE2 A:PHE234 3.2 22.2 1.0 C A:PRO232 3.4 17.1 1.0 CG A:ASN231 3.5 18.8 1.0 CD2 A:PHE234 3.5 21.4 1.0 O A:ASN231 3.7 18.6 1.0 C A:ASN231 3.9 19.3 1.0 ND2 A:ASN231 4.0 16.5 1.0 CZ A:PHE234 4.0 20.0 1.0 N A:PRO233 4.0 17.0 1.0 SD A:SAH401 4.0 21.4 1.0 O A:TYR246 4.1 25.1 1.0 CA A:PRO233 4.1 16.0 1.0 N A:PRO232 4.2 15.5 1.0 CA A:PRO232 4.3 19.6 1.0 CG A:PHE234 4.4 18.9 1.0 C5' A:SAH401 4.4 21.6 1.0 CG A:SAH401 4.5 21.1 1.0 N A:PHE234 4.5 18.7 1.0 CB A:ASN231 4.5 16.4 1.0 CE2 A:TYR137 4.6 23.7 1.0 CA A:ASN231 4.7 17.5 1.0 C A:PRO233 4.7 18.1 1.0 CE1 A:PHE234 4.8 20.4 1.0 CD2 A:TYR137 4.8 20.5 1.0 CZ A:TYR137 4.9 28.4 1.0 O A:HOH828 4.9 38.1 1.0 CD1 A:PHE234 5.0 18.6 1.0

Sodium binding site 2 out of 2 in the Aeronamide N-Methyltransferase, Aere (D141A)


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 (D141A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:32.6 occ:1.00 O19 A:P6G406 2.6 22.8 1.0 O7 A:P6G406 2.9 30.3 1.0 O13 A:P6G406 2.9 25.3 1.0 O16 A:P6G406 3.0 24.5 1.0 O10 A:P6G406 3.0 26.3 1.0 CE1 A:HIS50 3.2 18.6 1.0 C6 A:P6G406 3.5 30.6 1.0 ND1 A:HIS50 3.5 20.6 1.0 C18 A:P6G406 3.5 22.9 1.0 C5 A:P6G406 3.6 28.5 1.0 C17 A:P6G406 3.6 21.7 1.0 O A:HOH623 3.7 27.9 1.0 C11 A:P6G406 3.7 23.3 1.0 C9 A:P6G406 3.7 32.4 1.0 C15 A:P6G406 3.8 21.6 1.0 C8 A:P6G406 3.8 33.6 1.0 C12 A:P6G406 3.8 25.9 1.0 C14 A:P6G406 3.9 21.6 1.0 O A:HOH797 3.9 43.1 1.0 O4 A:P6G406 4.4 31.7 1.0 NE2 A:HIS50 4.5 18.0 1.0 CG A:HIS50 4.9 16.4 1.0 C3 A:P6G406 5.0 32.4 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