Calcium in PDB 5dl7: Crystal Structure of Acinetobacter Baumannii OCCAB3

The structure of Crystal Structure of Acinetobacter Baumannii OCCAB3, PDB code: 5dl7 was solved by M.Zahn, A.Basle, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.14 / 1.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.563, 125.717, 137.459, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.1

The binding sites of Calcium atom in the Crystal Structure of Acinetobacter Baumannii OCCAB3 (pdb code 5dl7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Acinetobacter Baumannii OCCAB3, PDB code: 5dl7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Acinetobacter Baumannii OCCAB3


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 Acinetobacter Baumannii OCCAB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:23.4 occ:1.00 O A:HOH646 2.4 31.1 1.0 O A:HOH667 2.4 24.5 1.0 O A:HOH792 2.4 27.4 1.0 OE2 A:GLU246 2.4 25.8 1.0 O A:HOH784 2.5 31.4 1.0 OE1 A:GLU238 2.5 25.9 1.0 OE1 A:GLU246 2.5 23.8 1.0 OE2 A:GLU238 2.5 22.7 1.0 CD A:GLU246 2.8 24.0 1.0 CD A:GLU238 3.0 23.8 1.0 O A:VAL247 4.2 21.0 1.0 CG A:GLU246 4.3 22.3 1.0 CG A:GLU238 4.4 22.6 1.0 O A:HOH623 4.6 24.2 1.0 O A:HOH614 4.7 37.6 1.0 CG A:GLU237 4.7 35.6 1.0 O A:HOH699 4.7 28.2 1.0 OE1 A:GLU237 4.8 47.8 1.0 O A:HOH812 4.9 32.8 1.0 O A:HOH678 4.9 41.3 1.0 N A:VAL247 5.0 19.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Acinetobacter Baumannii OCCAB3


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 Acinetobacter Baumannii OCCAB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:52.8 occ:1.00 O A:HOH763 2.3 53.4 1.0 OD1 A:ASN82 2.4 42.7 1.0 OD2 A:ASP88 2.6 42.4 1.0 OD1 A:ASP88 2.7 40.8 1.0 CG A:ASP88 2.9 39.2 1.0 CG A:ASN82 3.3 43.9 1.0 ND2 A:ASN82 3.5 43.7 1.0 O A:HOH619 4.5 37.4 1.0 CB A:ASP88 4.5 36.7 1.0 CB A:ASN82 4.7 42.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Acinetobacter Baumannii OCCAB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Acinetobacter Baumannii OCCAB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:35.6 occ:1.00 OD1 A:ASP20 2.2 33.4 1.0 O A:HOH683 2.3 41.5 1.0 OD1 A:ASP24 2.3 45.0 1.0 O A:TYR21 2.4 33.5 1.0 O A:THR29 2.4 36.1 1.0 OG1 A:THR29 2.6 50.8 1.0 CG A:ASP20 3.4 36.4 1.0 CG A:ASP24 3.4 52.7 1.0 C A:THR29 3.5 35.8 1.0 C A:TYR21 3.5 31.8 1.0 N A:TYR21 3.8 28.9 1.0 OD2 A:ASP24 3.8 52.6 1.0 CB A:THR29 3.9 41.0 1.0 CA A:THR29 3.9 38.3 1.0 CA A:TYR21 4.1 28.7 1.0 OD2 A:ASP20 4.1 40.6 1.0 C A:ASP20 4.1 27.2 1.0 CB A:TYR21 4.4 30.5 1.0 CA A:ASP20 4.5 28.0 1.0 CB A:ASP20 4.6 31.1 1.0 O A:ASP20 4.6 27.5 1.0 N A:LYS22 4.6 31.2 1.0 CG2 A:THR29 4.7 38.2 1.0 N A:ALA30 4.7 33.0 1.0 CB A:ASP24 4.7 49.5 1.0 N A:ASP24 4.8 46.5 1.0 CA A:ASP24 4.9 49.2 1.0 CA A:LYS22 4.9 35.7 1.0 C A:LYS22 5.0 40.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Acinetobacter Baumannii OCCAB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Acinetobacter Baumannii OCCAB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:54.9 occ:1.00 O A:HOH727 2.2 52.0 1.0 O A:ARG87 2.5 35.7 1.0 O A:HOH624 2.5 42.8 1.0 OD1 A:ASP89 2.6 41.5 1.0 OD2 A:ASP89 2.7 49.0 1.0 CG A:ASP89 3.0 45.3 1.0 C A:ARG87 3.6 36.7 1.0 O A:HOH760 3.9 47.0 1.0 N A:ARG87 4.1 38.8 1.0 CB A:ARG87 4.3 36.2 1.0 CA A:ARG87 4.3 35.1 1.0 OD1 A:ASP71 4.3 43.8 1.0 CB A:ASP89 4.4 42.3 1.0 N A:ASP89 4.5 37.3 1.0 OD2 A:ASP71 4.5 47.3 1.0 ND2 A:ASN64 4.7 40.3 1.0 N A:ASP88 4.7 33.4 1.0 C A:ASP88 4.7 36.3 1.0 CA A:ASP88 4.8 36.5 1.0 CB A:SER86 4.8 42.9 1.0 CA A:ASP89 4.8 38.0 1.0 CG A:ASP71 4.9 45.2 1.0 O A:GLY67 4.9 46.3 1.0 C A:SER86 5.0 38.7 1.0

M.Zahn, S.P.Bhamidimarri, A.Basle, M.Winterhalter, B.Van Den Berg. Structural Insights Into Outer Membrane Permeability of Acinetobacter Baumannii. Structure V. 24 221 2016.
ISSN: ISSN 0969-2126
PubMed: 26805524
DOI: 10.1016/J.STR.2015.12.009