Sodium in PDB 6kgh: Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form)

The structure of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form), PDB code: 6kgh was solved by Z.K.Lu, A.L.Zhang, X.Liu, L.Guddat, H.T.Yang, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.04 / 2.11
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.710, 84.220, 90.500, 90.00, 111.60, 90.00
R / Rfree (%)	18.9 / 22.2

The structure of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) also contains other interesting chemical elements:

Cobalt

(Co)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) (pdb code 6kgh). 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 Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form), PDB code: 6kgh:

Sodium binding site 1 out of 1 in the Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Penicillin Binding Protein 3 (PBP3) From Mycobacterium Tuerculosis (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:37.9 occ:1.00 N A:GLY468 2.4 30.9 1.0 OE1 A:GLN509 2.9 29.4 1.0 O A:SER504 3.0 30.9 1.0 C A:LEU467 3.3 34.8 1.0 CA A:LEU467 3.3 30.6 1.0 CD A:GLN509 3.3 28.4 1.0 NE2 A:GLN509 3.4 30.4 1.0 CA A:GLY468 3.4 29.3 1.0 CB A:LEU467 3.6 28.2 1.0 O A:ALA480 3.6 33.1 1.0 CB A:MET505 3.6 27.6 1.0 CA A:MET505 3.7 24.9 1.0 CD2 A:LEU467 3.9 27.2 1.0 CA A:GLY481 4.0 30.2 1.0 C A:SER504 4.0 29.4 1.0 N A:LEU482 4.1 35.5 1.0 CG2 A:VAL483 4.2 33.1 1.0 CG A:LEU467 4.3 31.1 1.0 N A:MET505 4.4 27.3 1.0 C A:GLY481 4.4 36.1 1.0 O A:LEU467 4.5 34.0 1.0 C A:GLY468 4.5 34.8 1.0 C A:ALA480 4.6 33.0 1.0 CG A:GLN509 4.6 27.1 1.0 N A:GLN469 4.7 29.6 1.0 N A:LEU467 4.7 29.2 1.0 N A:GLY481 4.7 30.0 1.0 CB A:GLN509 4.7 26.8 1.0 O A:LEU482 4.9 34.5 1.0 O A:GLY466 4.9 33.3 1.0 C A:LEU482 5.0 37.3 1.0

Z.Lu, H.Wang, A.Zhang, X.Liu, W.Zhou, C.Yang, L.Guddat, H.Yang, C.J.Schofield, Z.Rao. Structures Ofmycobacterium Tuberculosispenicillin-Binding Protein 3 in Complex with Fivebeta-Lactam Antibiotics Reveal Mechanism of Inactivation. Mol.Pharmacol. V. 97 287 2020.
ISSN: ESSN 1521-0111
PubMed: 32086254
DOI: 10.1124/MOL.119.118042