Sodium in PDB 8gkm: A1 Leu Graft + Leu: Adenylation Domain 1 Core Construct From Teicoplanin Biosynthesis, Leucine Selection Pocket Graft; Leucine Bound

The structure of A1 Leu Graft + Leu: Adenylation Domain 1 Core Construct From Teicoplanin Biosynthesis, Leucine Selection Pocket Graft; Leucine Bound, PDB code: 8gkm was solved by M.H.Hansen, M.J.Cryle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.79 / 1.89
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.805, 123.415, 175.171, 90, 90, 90
R / Rfree (%)	18.9 / 22

The binding sites of Sodium atom in the A1 Leu Graft + Leu: Adenylation Domain 1 Core Construct From Teicoplanin Biosynthesis, Leucine Selection Pocket Graft; Leucine Bound (pdb code 8gkm). 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 A1 Leu Graft + Leu: Adenylation Domain 1 Core Construct From Teicoplanin Biosynthesis, Leucine Selection Pocket Graft; Leucine Bound, PDB code: 8gkm:

Sodium binding site 1 out of 1 in the A1 Leu Graft + Leu: Adenylation Domain 1 Core Construct From Teicoplanin Biosynthesis, Leucine Selection Pocket Graft; Leucine Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A1 Leu Graft + Leu: Adenylation Domain 1 Core Construct From Teicoplanin Biosynthesis, Leucine Selection Pocket Graft; Leucine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:43.7 occ:1.00 OH A:TYR375 2.3 26.4 1.0 O A:HOH636 2.3 39.4 1.0 HE2 A:TYR375 2.6 31.3 1.0 CZ A:TYR375 3.1 26.7 1.0 CE2 A:TYR375 3.2 25.3 1.0 HB3 A:PRO290 3.4 31.8 1.0 O A:HOH611 3.5 47.5 1.0 HB2 A:PRO290 3.5 31.8 1.0 OE1 A:GLU292 3.7 27.4 1.0 O A:THR377 3.8 28.0 1.0 HA A:THR377 3.8 33.0 1.0 OE2 A:GLU292 3.8 31.5 1.0 CB A:PRO290 3.9 25.7 1.0 HH21 A:ARG362 3.9 43.2 1.0 CD A:GLU292 3.9 28.5 1.0 HE A:ARG362 3.9 50.0 1.0 HG3 A:PRO290 4.0 32.9 1.0 CE1 A:TYR375 4.4 25.9 1.0 CG A:PRO290 4.5 26.6 1.0 C A:THR377 4.5 27.5 1.0 HH12 A:ARG394 4.5 50.7 1.0 O A:ARG376 4.5 27.0 1.0 HB2 A:GLU292 4.5 31.0 1.0 HH A:TYR352 4.5 31.0 1.0 CD2 A:TYR375 4.5 22.4 1.0 NH2 A:ARG362 4.6 35.2 1.0 CA A:THR377 4.6 26.8 1.0 NE A:ARG362 4.6 40.9 1.0 HE1 A:TYR375 4.8 32.0 1.0 HG2 A:GLU292 4.8 32.5 1.0 CG A:GLU292 4.9 26.3 1.0 HG2 A:PRO290 4.9 32.9 1.0 HD2 A:TYR375 4.9 27.8 1.0 OH A:TYR352 5.0 25.1 1.0

M.H.Hansen, M.Adamek, D.Iftime, D.Petras, F.Schuseil, S.Grond, E.Stegmann, M.J.Cryle, N.Ziemert. Resurrecting Ancestral Antibiotics: Unveiling the Origins of Modern Lipid II Targeting Glycopeptides. Nat Commun V. 14 7842 2023.
ISSN: ESSN 2041-1723
PubMed: 38030603
DOI: 10.1038/S41467-023-43451-4