Sodium in PDB 8byk: The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases

The structure of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases, PDB code: 8byk was solved by C.V.Knospe, M.Kamel, O.Spitz, A.Hoeppner, S.Galle, J.Reiners, A.Kedrov, S.H.Smits, L.Schmitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.89 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.14, 66.119, 117.258, 90, 90, 90
R / Rfree (%)	19 / 22

The structure of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases (pdb code 8byk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases, PDB code: 8byk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:20.6 occ:1.00 O A:TRP201 2.8 12.2 1.0 N A:ASN223 2.9 10.4 1.0 OH A:TYR151 3.1 10.9 1.0 CG1 A:ILE203 3.5 13.6 1.0 O A:ASN223 3.6 10.0 1.0 CB A:ASN223 3.7 11.9 1.0 C A:PHE222 3.8 9.8 1.0 CA A:ASN223 3.8 10.1 1.0 CD1 A:TRP201 3.8 10.4 1.0 C A:TRP201 3.8 10.6 1.0 CA A:PHE222 3.8 11.4 1.0 CD1 A:ILE203 3.9 16.3 1.0 CB A:TRP201 4.0 10.1 1.0 CZ A:TYR151 4.1 11.1 1.0 C A:ASN223 4.2 10.4 1.0 CG A:TRP201 4.3 10.2 1.0 CA A:TRP201 4.5 10.1 1.0 CE2 A:TYR151 4.5 11.5 1.0 CB A:PHE222 4.6 10.9 1.0 O A:CYS221 4.8 13.1 1.0 CG2 A:VAL230 4.8 11.9 1.0 CA A:GLY229 4.9 10.3 1.0 CB A:ILE203 4.9 12.0 1.0 N A:TYR202 4.9 11.1 1.0 N A:ILE203 5.0 11.2 1.0 O A:PHE222 5.0 12.7 1.0 O A:HIS228 5.0 11.7 1.0

Sodium binding site 2 out of 2 in the The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:29.1 occ:1.00 O A:HOH968 2.6 37.3 1.0 O A:HOH818 2.7 18.3 1.0 OE2 A:GLU219 3.0 38.7 1.0 N A:GLU281 3.1 16.3 1.0 CB A:GLU281 3.4 21.4 1.0 N A:LEU280 3.6 15.2 1.0 CB A:SER279 3.6 16.2 1.0 OG A:SER279 3.8 15.4 1.0 CA A:GLU281 3.8 17.6 1.0 CB A:GLU219 3.8 24.7 1.0 CD A:GLU219 4.0 40.6 1.0 C A:LEU280 4.0 16.4 1.0 CB A:LEU280 4.0 17.2 1.0 CA A:LEU280 4.1 14.8 1.0 CG A:GLU219 4.2 32.5 1.0 C A:SER279 4.3 13.3 1.0 O A:GLY220 4.4 16.9 1.0 CA A:SER279 4.4 13.7 1.0 O A:HOH746 4.5 33.8 1.0 N A:GLU219 4.7 20.4 1.0 CA A:GLU219 4.8 22.8 1.0 NH2 A:ARG284 4.8 36.2 0.7 CG A:GLU281 4.8 25.8 1.0

C.V.Knospe, M.Kamel, O.Spitz, A.Hoeppner, S.Galle, J.Reiners, A.Kedrov, S.H.J.Smits, L.Schmitt. The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases. Front Microbiol V. 13 57217 2022.
ISSN: ESSN 1664-302X
PubMed: 36741885
DOI: 10.3389/FMICB.2022.1057217