Calcium in PDB 8gyr: Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga

The structure of Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga, PDB code: 8gyr was solved by P.Kumar, M.Akif, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.92 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.219, 63.905, 171.839, 90, 90, 90
R / Rfree (%)	20.8 / 23.4

The structure of Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Potassium	(K)	5 atoms
Iodine	(I)	2 atoms
Sodium	(Na)	5 atoms

The binding sites of Calcium atom in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga (pdb code 8gyr). 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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga, PDB code: 8gyr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca209 b:22.4 occ:1.00 O A:VAL10 2.6 14.4 1.0 O A:HOH399 2.6 20.7 1.0 O A:HOH441 2.7 25.4 1.0 O A:HOH401 2.8 13.2 1.0 OG1 A:THR13 2.9 21.5 1.0 O A:LYS84 3.0 15.1 1.0 OG1 A:THR85 3.3 13.3 1.0 CB A:THR85 3.6 12.4 1.0 C A:VAL10 3.8 14.9 1.0 CB A:THR13 3.9 22.0 1.0 CA A:THR13 3.9 20.9 1.0 CA A:THR85 4.1 13.3 1.0 C A:LYS84 4.1 13.3 1.0 N A:VAL10 4.3 14.9 1.0 CG2 A:THR13 4.3 22.9 1.0 CA A:VAL10 4.5 12.9 1.0 O A:PRO12 4.5 17.2 1.0 N A:THR85 4.6 12.3 1.0 OE1 A:GLU9 4.7 25.2 1.0 N A:THR13 4.7 17.7 1.0 CB A:VAL10 4.7 13.2 1.0 I A:IOD210 4.8 20.8 0.8 N A:SER11 4.9 14.4 1.0 C A:PRO12 4.9 15.8 1.0 O A:THR13 4.9 22.9 1.0 C A:THR13 4.9 22.6 1.0 CG2 A:THR85 5.0 13.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:21.6 occ:1.00 O B:VAL10 2.6 13.9 1.0 O B:HOH439 2.7 19.3 1.0 O B:HOH425 2.8 26.1 1.0 O B:HOH385 2.9 15.7 1.0 O B:LYS84 3.1 15.1 1.0 OG1 B:THR85 3.2 14.9 1.0 OG1 B:THR13 3.2 25.4 1.0 CB B:THR85 3.4 16.6 1.0 C B:VAL10 3.8 13.7 1.0 CA B:THR85 3.9 16.9 1.0 O B:HOH441 4.1 14.8 1.0 C B:LYS84 4.1 16.5 1.0 CB B:THR13 4.3 25.9 1.0 N B:VAL10 4.3 15.2 1.0 N B:THR85 4.4 16.5 1.0 CA B:VAL10 4.5 14.7 1.0 O B:HOH368 4.5 33.8 1.0 CA B:THR13 4.5 23.4 1.0 CG2 B:THR13 4.6 27.3 1.0 O B:PRO12 4.6 19.3 1.0 CB B:VAL10 4.7 15.3 1.0 N B:THR13 4.8 20.1 1.0 OE1 B:GLU9 4.9 20.6 1.0 I B:IOD202 4.9 14.3 0.8 N B:SER11 4.9 13.7 1.0 CG2 B:THR85 4.9 15.8 1.0 C B:PRO12 4.9 17.4 1.0

P.Kumar, P.Vyas, S.M.Faisal, Y.F.Chang, M.Akif. Crystal Structure of A Variable Region Segment of Leptospira Host-Interacting Outer Surface Protein, Liga, Reveals the Orientation of Ig-Like Domains. Int.J.Biol.Macromol. 25445 2023.
ISSN: ISSN 0141-8130
PubMed: 37336372
DOI: 10.1016/J.IJBIOMAC.2023.125445