Calcium in PDB 4kdw: 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: 4kdw 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)	29.19 / 1.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.640, 28.620, 32.250, 97.02, 112.93, 96.88
R / Rfree (%)	13 / 16.5

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 4kdw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 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: 4kdw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 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:10.4 occ:1.00 O A:VAL18 2.3 9.3 1.0 OG1 A:THR14 2.4 8.8 1.0 OD1 A:ASP16 2.4 13.1 1.0 O A:HOH400 2.4 20.0 1.0 O A:HOH323 2.5 16.7 1.0 OE2 A:GLU23 2.5 12.0 1.0 OE1 A:GLU23 2.5 11.8 1.0 CD A:GLU23 2.9 12.2 1.0 CG A:ASP16 3.4 15.2 1.0 CB A:THR14 3.4 10.1 1.0 C A:VAL18 3.5 8.4 1.0 OD2 A:ASP16 3.7 15.6 1.0 CG2 A:THR14 4.1 10.6 1.0 N A:VAL18 4.3 7.9 1.0 CA A:VAL18 4.3 7.5 1.0 CG A:GLU23 4.4 11.7 1.0 N A:ILE19 4.5 7.6 1.0 CB A:VAL18 4.5 9.2 1.0 N A:ASN20 4.5 9.6 1.0 N A:ASP16 4.5 11.2 1.0 CA A:ILE19 4.6 7.9 1.0 ND2 A:ASN20 4.6 16.9 1.0 O A:ILE13 4.6 8.2 1.0 CA A:THR14 4.7 10.7 1.0 O A:HOH377 4.7 23.8 1.0 CB A:ASP16 4.8 11.4 1.0 N A:SER15 4.8 14.1 1.0 CG A:ASN20 4.8 14.3 1.0 C A:THR14 4.9 10.9 1.0 OG A:SER15 5.0 21.0 1.0

Calcium binding site 2 out of 7 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:6.6 occ:1.00 O A:ALA78 2.3 7.4 1.0 O A:HOH431 2.3 9.2 1.0 O A:HOH349 2.3 21.8 1.0 O A:HOH327 2.4 14.5 1.0 O A:HOH324 2.4 8.1 1.0 OD1 A:ASP76 2.5 6.7 1.0 OD2 A:ASP76 2.5 5.3 1.0 CG A:ASP76 2.8 5.6 1.0 C A:ALA78 3.5 6.7 1.0 O A:HOH308 4.2 9.6 1.0 CA A:PHE79 4.3 5.9 1.0 CB A:ASP76 4.4 5.5 1.0 N A:PHE79 4.4 5.9 1.0 CA A:ALA78 4.4 6.3 1.0 N A:ALA78 4.4 6.3 1.0 CB A:PHE79 4.5 6.3 1.0 CB A:ALA78 4.6 7.2 1.0 O A:HOH343 4.6 15.0 0.5 O A:HOH343 4.6 7.9 0.5 O A:GLU48 4.8 6.6 1.0

Calcium binding site 3 out of 7 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:8.0 occ:1.00 O A:THR100 2.3 7.7 1.0 O A:HOH335 2.3 10.6 1.0 O A:HOH317 2.4 7.4 1.0 OD2 A:ASP17 2.4 8.5 1.0 O A:HOH339 2.4 16.5 1.0 O A:HOH302 2.4 8.0 1.0 OD1 A:ASP17 2.5 7.2 1.0 CG A:ASP17 2.8 6.6 1.0 C A:THR100 3.5 6.6 1.0 N A:THR100 4.1 7.0 1.0 CB A:ASP17 4.3 8.7 1.0 OG A:SER99 4.3 7.6 1.0 CA A:THR100 4.4 7.2 1.0 N A:HIS101 4.4 6.3 1.0 OG1 A:THR100 4.5 11.3 1.0 O A:HOH306 4.5 10.5 1.0 CA A:HIS101 4.5 6.4 1.0 CA A:ALA12 4.5 8.2 1.0 O A:HOH438 4.6 14.1 1.0 CB A:HIS101 4.7 6.0 1.0 N A:ILE13 4.7 7.3 1.0 CG1 A:ILE13 4.8 6.9 1.0 O A:ASN11 4.8 7.1 1.0

Calcium binding site 4 out of 7 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:8.4 occ:1.00 O A:ASP104 2.3 14.4 0.9 O A:HOH433 2.4 8.0 1.0 OD1 A:ASP104 2.5 9.3 0.9 O A:HOH432 2.5 12.0 1.0 C A:ASP104 3.3 13.1 0.9 CG A:ASP104 3.6 9.1 0.9 CA A:ASP104 3.9 9.9 0.9 CA A:CA205 4.0 9.2 0.8 OXT A:ASP104 4.2 14.8 0.9 CB A:ASP104 4.4 9.6 0.9 O A:HOH338 4.4 12.0 1.0 O A:HOH419 4.5 24.2 1.0 OD2 A:ASP104 4.5 11.1 0.9

Calcium binding site 5 out of 7 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:9.2 occ:0.80 OD2 A:ASP104 2.4 11.1 0.9 OD1 A:ASP104 2.6 9.3 0.9 CG A:ASP104 2.8 9.1 0.9 CA A:CA204 4.0 8.4 1.0 CB A:ASP104 4.4 9.6 0.9 O A:HOH433 4.5 8.0 1.0 O A:HOH368 4.7 23.1 1.0 O A:HOH419 5.0 24.2 1.0

Calcium binding site 6 out of 7 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 6 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:Ca206 b:12.7 occ:0.50 O A:HOH307 2.1 26.5 1.0 O A:GLY51 2.2 8.8 1.0 O A:HOH341 2.3 14.8 1.0 O A:HOH301 2.5 37.3 1.0 O A:HOH410 3.1 29.1 1.0 C A:GLY51 3.3 7.1 1.0 CA A:GLY51 3.9 6.4 1.0 OE1 A:GLU48 4.2 18.8 0.5 CD A:GLU48 4.3 14.2 0.5 OG1 A:THR53 4.3 10.6 1.0 N A:GLU52 4.3 5.5 1.0 CG A:GLU48 4.6 10.7 0.5 OE2 A:GLU48 4.6 17.9 0.5 CA A:GLU52 4.7 6.0 1.0 N A:THR53 4.9 5.8 1.0 C A:GLU52 5.0 5.1 1.0

Calcium binding site 7 out of 7 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 7 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:Ca207 b:15.4 occ:0.50 O A:HOH434 1.8 29.0 0.5 O A:HOH383 2.4 29.7 1.0 O A:HOH315 2.5 9.4 1.0 O A:SER86 2.7 13.1 1.0 OG A:SER86 2.8 21.3 1.0 O A:HOH402 2.9 29.7 1.0 C A:SER86 3.6 11.4 1.0 CB A:SER86 3.9 13.9 1.0 N A:SER86 4.0 9.8 1.0 CA A:SER86 4.0 11.2 1.0 CB A:ALA40 4.3 11.9 1.0 O A:HOH345 4.4 21.2 1.0 OD1 A:ASP43 4.5 10.9 1.0 O A:ASP38 4.5 8.2 1.0 N A:ASP87 4.6 10.3 1.0 O A:ASP87 4.7 11.2 1.0 CA A:ASP87 4.9 11.1 1.0 C A:ASP87 5.0 10.8 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