Sodium in PDB 4k7t: Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate

The structure of Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate, PDB code: 4k7t was solved by N.J.Economou, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.01 / 1.10
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	35.980, 35.980, 16.120, 90.00, 90.00, 120.00
R / Rfree (%)	12.7 / 14.9

The structure of Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate (pdb code 4k7t). 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 Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate, PDB code: 4k7t:

Sodium binding site 1 out of 1 in the Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Ternary Complex of Bacitracin, Zinc, and Geranyl- Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:6.1 occ:1.00 O A:ILE8 2.2 8.6 1.0 O A:ILE5 2.3 7.5 1.0 O2B A:GPP101 2.4 5.8 1.0 OD2 A:DAS11 2.4 8.0 1.0 O2A A:GPP101 2.4 7.1 1.0 HZ2 A:LYS6 3.0 8.1 1.0 O3A A:GPP101 3.1 6.1 1.0 PB A:GPP101 3.3 6.3 1.0 PA A:GPP101 3.3 7.0 1.0 C A:ILE5 3.4 7.2 1.0 C A:ILE8 3.4 8.9 1.0 H12 A:GPP101 3.5 13.0 1.0 HA A:DPN9 3.5 9.1 1.0 H A:DAS11 3.5 8.1 1.0 CG A:DAS11 3.5 8.8 1.0 H A:ILE8 3.5 12.0 1.0 HA A:LYS6 3.6 9.5 1.0 H A:ILE5 3.7 9.2 1.0 H A:ASN12 3.7 7.6 1.0 NZ A:LYS6 3.7 6.7 1.0 HE2 A:LYS6 3.7 9.0 1.0 H11 A:GPP101 3.8 13.0 1.0 C1 A:GPP101 4.0 10.8 1.0 N A:ILE5 4.1 7.7 1.0 H A:ORD7 4.1 10.7 1.0 HB3 A:DGL4 4.1 9.5 1.0 OD1 A:DAS11 4.1 10.9 1.0 N A:ASN12 4.1 6.3 1.0 O1 A:GPP101 4.2 8.4 1.0 CA A:DPN9 4.2 7.6 1.0 HB A:ILE5 4.2 11.5 1.0 N A:ILE8 4.2 10.0 1.0 O1B A:GPP101 4.2 5.9 1.0 CE A:LYS6 4.2 7.5 1.0 N A:DPN9 4.3 8.2 1.0 N A:DAS11 4.3 6.8 1.0 CA A:ILE5 4.3 7.9 1.0 N A:LYS6 4.3 7.8 1.0 CA A:LYS6 4.3 7.9 1.0 HB2 A:ASN12 4.4 7.7 1.0 O3B A:GPP101 4.4 6.5 1.0 CA A:ILE8 4.4 10.6 1.0 C A:DPN9 4.6 7.8 1.0 HB A:ILE8 4.6 16.3 1.0 H A:HIS10 4.6 8.8 1.0 N A:ORD7 4.6 8.9 1.0 O1A A:GPP101 4.6 6.5 1.0 HD3 A:LYS6 4.6 9.6 1.0 CB A:DAS11 4.7 8.1 1.0 C A:ASN12 4.7 6.5 1.0 CA A:DAS11 4.7 6.8 1.0 C A:DAS11 4.7 6.7 1.0 N A:HIS10 4.7 7.3 1.0 C A:LYS6 4.8 8.5 1.0 CB A:ILE5 4.8 9.6 1.0 CA A:ASN12 4.8 6.6 1.0 HE3 A:LYS6 5.0 9.0 1.0

N.J.Economou, S.Cocklin, P.J.Loll. High-Resolution Crystal Structure Reveals Molecular Details of Target Recognition By Bacitracin. Proc.Natl.Acad.Sci.Usa V. 110 14207 2013.
ISSN: ISSN 0027-8424
PubMed: 23940351
DOI: 10.1073/PNAS.1308268110