Calcium in PDB 6p3j: Crystal Structure of Ligu

The structure of Crystal Structure of Ligu, PDB code: 6p3j was solved by S.A.Cory, T.N.Hogancamp, F.M.Raushel, D.P.Barondeau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.99 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.776, 67.364, 161.072, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.2

The structure of Crystal Structure of Ligu also contains other interesting chemical elements:

Chlorine	(Cl)	9 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Ligu (pdb code 6p3j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Ligu, PDB code: 6p3j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Ligu


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ligu within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:40.6 occ:1.00 OE1 B:GLU359 2.4 48.6 1.0 O B:HOH543 2.5 35.4 1.0 O B:HOH527 2.5 37.9 1.0 O B:ARG6 2.5 47.8 1.0 OE2 B:GLU359 2.5 41.9 1.0 CD B:GLU359 2.7 47.1 1.0 C B:ARG6 3.7 48.8 1.0 CA B:CA402 4.1 38.7 1.0 CG B:GLU359 4.2 44.9 1.0 O B:HOH572 4.3 36.2 1.0 CA B:ASN7 4.3 44.9 1.0 N B:ASN7 4.5 44.4 1.0 NE2 B:HIS361 4.6 83.8 1.0 O B:HOH545 4.6 36.3 1.0 OD1 B:ASN7 4.7 47.0 1.0 CE1 B:HIS361 4.7 81.5 1.0 CA B:ARG6 4.7 49.7 1.0 C B:ASN7 5.0 43.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Ligu


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ligu within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:38.7 occ:1.00 OE2 B:GLU359 2.3 41.9 1.0 OD1 B:ASP9 2.4 46.0 1.0 O B:HOH545 2.4 36.3 1.0 O B:MET8 2.5 38.7 1.0 O B:HOH572 2.6 36.2 1.0 O B:HOH543 2.6 35.4 1.0 CD B:GLU359 3.5 47.1 1.0 C B:MET8 3.5 39.7 1.0 CG B:ASP9 3.6 44.5 1.0 CG B:GLU359 4.0 44.9 1.0 CA B:ASP9 4.0 39.4 1.0 N B:ASP9 4.1 38.1 1.0 CA B:CA401 4.1 40.6 1.0 O B:ARG6 4.2 47.8 1.0 O B:HOH516 4.3 41.5 1.0 CB B:ASP9 4.4 39.8 1.0 N B:MET8 4.5 40.8 1.0 OE1 B:GLU359 4.5 48.6 1.0 OD2 B:ASP9 4.5 46.0 1.0 CA B:MET8 4.6 41.3 1.0 O B:HOH512 4.6 41.5 1.0 O B:ASP5 4.7 41.5 1.0 C B:ARG6 4.7 48.8 1.0 O B:HOH580 4.8 53.2 1.0

T.N.Hogancamp, S.A.Cory, D.P.Barondeau, F.M.Raushel. Structure and Chemical Reaction Mechanism of Ligu, An Enzyme That Catalyzes An Allylic Isomerization in the Bacterial Degradation of Lignin. Biochemistry V. 58 3494 2019.
ISSN: ISSN 0006-2960
PubMed: 31339729
DOI: 10.1021/ACS.BIOCHEM.9B00549