Calcium in PDB 4kdv: Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin

The structure of Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin, PDB code: 4kdv was solved by S.Guo, C.P.Garnham, S.P.Karunan, R.L.Campbell, J.S.Allingham, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.70 / 2.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.690, 43.020, 32.260, 90.00, 96.91, 90.00
R / Rfree (%)	14.4 / 23.4

The binding sites of Calcium atom in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin (pdb code 4kdv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin, PDB code: 4kdv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin


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 Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:30.4 occ:1.00 O A:HOH333 2.2 19.1 1.0 OE2 A:GLU23 2.2 28.4 1.0 OD1 A:ASP16 2.3 34.5 1.0 O A:VAL18 2.4 16.4 1.0 OG1 A:THR14 2.4 25.1 1.0 OE1 A:GLU23 2.6 28.7 1.0 CD A:GLU23 2.8 27.4 1.0 CG A:ASP16 3.3 31.6 1.0 CB A:THR14 3.4 24.4 1.0 C A:VAL18 3.5 16.7 1.0 OD2 A:ASP16 3.6 31.1 1.0 CG2 A:THR14 4.1 23.7 1.0 N A:VAL18 4.2 17.1 1.0 CG A:GLU23 4.2 25.7 1.0 CA A:VAL18 4.3 16.7 1.0 CB A:VAL18 4.4 16.0 1.0 N A:ILE19 4.5 18.4 1.0 O A:ILE13 4.5 23.6 1.0 N A:ASP16 4.5 26.4 1.0 CA A:ILE19 4.7 19.5 1.0 CA A:THR14 4.7 25.3 1.0 CB A:ASP16 4.7 27.9 1.0 C A:THR14 4.8 26.1 1.0 N A:ASN20 4.8 22.9 1.0 N A:SER15 4.8 27.9 1.0 N A:ASP17 4.8 20.7 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin


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 Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:19.9 occ:1.00 O A:HOH327 2.3 19.0 1.0 O A:THR100 2.4 18.3 1.0 O A:HOH331 2.4 14.3 1.0 OD2 A:ASP17 2.4 21.0 1.0 O A:HOH332 2.5 11.6 1.0 OD1 A:ASP17 2.6 19.9 1.0 CG A:ASP17 2.9 19.4 1.0 O A:HOH306 3.0 28.3 1.0 C A:THR100 3.6 17.3 1.0 OG A:SER99 4.2 18.1 1.0 O A:HOH352 4.2 12.2 1.0 O A:HOH342 4.2 5.3 0.5 N A:THR100 4.2 17.4 1.0 O A:HOH341 4.2 29.8 1.0 CB A:ASP17 4.3 19.0 1.0 O A:HOH342 4.4 9.9 0.5 CA A:ALA12 4.4 21.9 1.0 N A:HIS101 4.5 17.7 1.0 CA A:HIS101 4.5 18.2 1.0 CA A:THR100 4.5 17.3 1.0 OG1 A:THR100 4.5 17.9 1.0 N A:ILE13 4.7 21.1 1.0 CB A:HIS101 4.7 18.3 1.0 O A:ASN11 4.7 22.2 1.0 CG1 A:ILE13 4.7 21.9 1.0 O A:HOH340 5.0 27.4 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin


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 A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:34.7 occ:1.00 OD1 A:ASP104 2.2 36.2 1.0 O A:HOH312 2.6 26.9 1.0 OXT A:ASP104 2.8 33.2 1.0 CG A:ASP104 3.4 35.0 1.0 C A:ASP104 3.6 31.9 1.0 CA A:ASP104 4.1 30.0 1.0 OD2 A:ASP104 4.2 35.4 1.0 CA A:CA205 4.2 45.0 1.0 CB A:ASP104 4.4 33.3 1.0 O A:ASP104 4.5 32.2 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin


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 A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:20.5 occ:1.00 OD1 A:ASP76 2.3 19.6 1.0 O A:ALA78 2.4 18.0 1.0 O A:HOH350 2.4 24.6 1.0 OD2 A:ASP76 2.6 19.7 1.0 CG A:ASP76 2.8 18.4 1.0 C A:ALA78 3.5 16.9 1.0 CB A:ASP76 4.3 17.9 1.0 N A:PHE79 4.4 17.9 1.0 CA A:PHE79 4.4 18.1 1.0 O A:HOH314 4.4 10.8 1.0 CA A:ALA78 4.4 17.1 1.0 N A:ALA78 4.4 16.6 1.0 CB A:PHE79 4.6 17.9 1.0 O A:HOH338 4.7 27.0 1.0 CB A:ALA78 4.7 17.0 1.0 O A:GLU48 4.8 22.0 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Bacterial Immunoglobulin-Like Domain From the M. Primoryensis Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:45.0 occ:1.00 OD2 A:ASP104 2.4 35.4 1.0 OD1 A:ASP104 3.0 36.2 1.0 CG A:ASP104 3.1 35.0 1.0 CA A:CA203 4.2 34.7 1.0 CB A:ASP104 4.5 33.3 1.0 O A:HOH312 4.8 26.9 1.0

S.Guo, C.P.Garnham, S.Karunan Partha, R.L.Campbell, J.S.Allingham, P.L.Davies. Role of Ca(2+) in Folding the Tandem Beta-Sandwich Extender Domains of A Bacterial Ice-Binding Adhesin. Febs J. V. 280 5919 2013.
ISSN: ISSN 1742-464X
PubMed: 24024640
DOI: 10.1111/FEBS.12518