Calcium in PDB 5irb: Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin

The structure of Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin, PDB code: 5irb was solved by S.Guo, S.Phippen, R.Campbell, P.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.79 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	85.601, 247.023, 84.255, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24

The structure of Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium atom in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin (pdb code 5irb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin, PDB code: 5irb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:38.5 occ:1.00 OE2 A:GLU206 2.4 43.2 1.0 O A:VAL201 2.4 39.3 1.0 OD1 A:ASP199 2.5 47.7 1.0 O A:HOH766 2.5 50.0 1.0 OG1 A:THR197 2.6 41.5 1.0 OE1 A:GLU206 2.6 41.7 1.0 O A:HOH830 2.8 39.2 1.0 CD A:GLU206 2.8 42.4 1.0 O A:HOH951 2.9 44.1 1.0 OD2 A:ASP199 3.1 50.4 1.0 CG A:ASP199 3.1 49.2 1.0 CB A:THR197 3.4 42.3 1.0 C A:VAL201 3.6 38.7 1.0 O A:THR197 4.1 46.2 1.0 CG2 A:THR197 4.1 41.3 1.0 CG A:GLU206 4.3 42.7 1.0 CA A:VAL201 4.4 39.5 1.0 N A:VAL201 4.4 40.1 1.0 CB A:VAL201 4.5 41.4 1.0 CB A:ASP199 4.6 49.7 1.0 O A:HOH794 4.6 55.1 1.0 N A:ILE202 4.6 37.5 1.0 CA A:THR197 4.7 42.3 1.0 C A:THR197 4.7 44.4 1.0 O A:VAL196 4.7 39.8 1.0 CA A:ILE202 4.8 37.5 1.0 N A:ASP199 5.0 47.7 1.0 N A:ASN203 5.0 40.0 1.0

Calcium binding site 2 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:34.8 occ:1.00 O A:HOH877 2.1 30.4 1.0 OD2 A:ASP477 2.2 34.6 1.0 O A:HOH769 2.3 43.7 1.0 O A:SER392 2.4 44.8 1.0 OD1 A:ASP390 2.4 39.8 1.0 O A:HOH711 2.5 26.5 1.0 OD2 A:ASP390 2.5 40.0 1.0 CG A:ASP390 2.8 39.9 1.0 CG A:ASP477 3.4 36.1 1.0 C A:SER392 3.5 43.6 1.0 CB A:ASP477 4.0 35.8 1.0 O A:HOH781 4.1 34.9 1.0 CA A:ALA393 4.2 42.5 1.0 O A:HOH817 4.2 36.7 1.0 N A:ALA393 4.2 43.9 1.0 ND2 A:ASN481 4.2 37.9 1.0 CB A:ASP390 4.3 38.5 1.0 OD1 A:ASP477 4.4 36.3 1.0 O A:HOH935 4.4 54.9 1.0 N A:SER392 4.5 41.4 1.0 CA A:SER392 4.6 42.4 1.0 O A:HOH956 4.6 58.2 1.0 O A:HOH786 4.7 29.4 1.0 OD2 A:ASP428 4.7 37.8 1.0 OD2 A:ASP394 4.9 47.5 1.0 O A:HOH727 5.0 56.7 1.0

Calcium binding site 3 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:42.0 occ:1.00 O A:THR490 2.3 46.6 1.0 OD2 A:ASP407 2.4 48.5 1.0 OD1 A:ASP407 2.4 49.1 1.0 O A:HOH842 2.5 39.8 1.0 O A:HOH893 2.5 37.7 1.0 O A:HOH705 2.5 34.4 1.0 O A:HOH945 2.5 31.1 1.0 CG A:ASP407 2.7 49.4 1.0 C A:THR490 3.5 47.5 1.0 N A:THR490 4.2 45.6 1.0 CB A:ASP407 4.2 51.6 1.0 OG A:SER489 4.2 44.2 1.0 O A:HOH823 4.2 36.7 1.0 OG1 A:THR490 4.4 49.2 1.0 O A:HOH932 4.4 48.7 1.0 N A:HIS491 4.4 48.2 1.0 CA A:HIS491 4.4 50.0 1.0 CA A:THR490 4.4 47.3 1.0 O A:HOH967 4.4 43.5 1.0 CA A:ALA402 4.5 42.9 1.0 CB A:HIS491 4.6 50.0 1.0 CG1 A:ILE403 4.6 45.4 1.0 N A:ILE403 4.6 45.0 1.0 O A:HOH866 4.8 29.8 1.0 O A:ASN401 4.8 39.2 1.0

Calcium binding site 4 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:30.1 occ:1.00 O A:HOH703 2.0 24.2 1.0 O A:VAL305 2.2 30.0 1.0 OD1 A:ASP303 2.4 35.3 1.0 OG1 A:THR301 2.4 32.2 1.0 OE2 A:GLU310 2.5 35.6 1.0 O A:HOH715 2.5 24.4 1.0 OE1 A:GLU310 2.5 34.8 1.0 CD A:GLU310 2.9 35.3 1.0 CG A:ASP303 3.3 38.3 1.0 C A:VAL305 3.4 31.3 1.0 CB A:THR301 3.4 33.2 1.0 OD2 A:ASP303 3.5 39.7 1.0 CG2 A:THR301 4.0 32.2 1.0 N A:VAL305 4.1 32.3 1.0 CA A:VAL305 4.1 32.4 1.0 N A:VAL306 4.4 31.8 1.0 N A:ASP303 4.4 37.4 1.0 CB A:VAL305 4.4 34.6 1.0 CG A:GLU310 4.4 36.2 1.0 N A:ASN307 4.4 34.7 1.0 CA A:VAL306 4.5 32.4 1.0 N A:SER302 4.6 36.3 1.0 O A:ILE300 4.6 32.0 1.0 CB A:ASP303 4.6 40.5 1.0 CA A:THR301 4.7 33.1 1.0 C A:THR301 4.8 34.7 1.0 ND2 A:ASN307 4.9 38.4 1.0 O A:ALA479 4.9 39.1 1.0 N A:ASP304 4.9 32.7 1.0 C A:VAL306 4.9 34.4 1.0 CG A:ASN307 4.9 37.5 1.0 CA A:ASP303 5.0 37.9 1.0 O A:HOH802 5.0 42.2 1.0 O A:HOH708 5.0 49.6 1.0

Calcium binding site 5 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:41.9 occ:1.00 O A:HOH939 2.3 31.3 1.0 OD2 A:ASP304 2.4 33.9 1.0 O A:THR386 2.4 34.5 1.0 OD1 A:ASP304 2.5 31.2 1.0 O A:HOH756 2.6 39.6 1.0 O A:HOH920 2.7 36.0 1.0 CG A:ASP304 2.7 32.5 1.0 O A:HOH707 2.8 42.8 1.0 C A:THR386 3.6 37.0 1.0 CB A:ASP304 4.2 33.5 1.0 N A:THR386 4.3 36.6 1.0 CA A:SER299 4.3 31.9 1.0 O A:HOH801 4.4 31.9 1.0 O A:HOH749 4.5 48.8 1.0 O A:HOH761 4.5 32.3 1.0 N A:HIS387 4.5 37.7 1.0 OG1 A:THR386 4.6 42.9 1.0 CA A:HIS387 4.6 37.4 1.0 OG A:SER385 4.6 34.1 1.0 CA A:THR386 4.6 38.1 1.0 O A:HOH928 4.6 45.0 1.0 N A:ILE300 4.6 31.8 1.0 CB A:HIS387 4.7 35.8 1.0 O A:ASN298 4.7 28.3 1.0 O A:HOH937 4.8 65.9 1.0 CG1 A:ILE300 4.9 30.4 1.0 CB A:SER299 4.9 34.0 1.0

Calcium binding site 6 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:38.8 occ:1.00 OD1 A:ASP260 2.4 38.8 1.0 O A:ILE262 2.4 33.2 1.0 OD1 A:ASP258 2.4 39.6 1.0 O A:HOH739 2.5 32.6 1.0 O A:HOH915 2.5 24.2 0.5 O A:HOH821 2.6 32.0 1.0 OD2 A:ASP258 2.6 39.4 1.0 CG A:ASP258 2.8 40.0 1.0 CG A:ASP260 3.4 40.0 1.0 C A:ILE262 3.5 33.5 1.0 OD2 A:ASP260 3.7 41.0 1.0 N A:ILE262 3.9 35.2 1.0 CA A:ILE262 4.1 34.6 1.0 O A:HOH785 4.1 39.9 1.0 OD2 A:ASP264 4.2 40.5 1.0 CB A:ILE262 4.2 35.7 1.0 O A:HOH915 4.3 31.2 0.5 CB A:ASP258 4.3 39.8 1.0 N A:ASP260 4.5 41.3 1.0 N A:VAL263 4.6 32.9 1.0 CB A:ASP260 4.7 41.0 1.0 CG A:ASP264 4.8 38.6 1.0 N A:ARG261 4.8 37.3 1.0 O A:VAL230 4.8 35.2 1.0 N A:ASN232 4.9 39.1 1.0 CA A:ASP260 4.9 40.5 1.0 CA A:VAL263 5.0 32.7 1.0

Calcium binding site 7 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial 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 Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:57.5 occ:0.50 O A:HOH972 2.2 47.3 1.0 O A:GLN372 2.2 38.0 1.0 O A:HOH710 2.4 47.6 1.0 O A:HOH744 2.4 30.9 1.0 O A:HOH953 2.5 53.6 1.0 O A:HOH948 2.6 45.0 1.0 C A:GLN372 3.4 37.0 1.0 O A:HOH833 3.8 60.9 1.0 N A:GLN372 4.0 35.6 1.0 CA A:GLN372 4.2 38.5 1.0 O A:HOH973 4.4 57.3 1.0 OH A:TYR379 4.4 29.3 1.0 N A:ASP373 4.4 35.9 1.0 CB A:GLN372 4.4 43.2 1.0 CA A:ASP373 4.5 35.1 1.0 O A:HOH721 4.5 32.9 1.0 OG A:SER326 4.6 34.8 1.0 C A:ASP373 4.6 36.5 1.0 O A:ASP373 4.6 37.4 1.0 OD1 A:ASP329 4.7 29.3 1.0 O A:HOH774 4.8 37.5 1.0 CB A:SER326 5.0 33.0 1.0

Calcium binding site 8 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:66.5 occ:1.00 O A:HOH881 2.3 41.6 1.0 OD1 A:ASP362 2.3 71.5 1.0 O A:SER364 2.3 66.8 1.0 O A:HOH861 2.4 15.6 0.5 O A:HOH889 2.4 62.3 1.0 O A:HOH765 2.5 40.9 1.0 CG A:ASP362 3.3 68.4 1.0 C A:SER364 3.5 64.8 1.0 O A:HOH861 3.6 33.2 0.5 OD2 A:ASP362 3.6 70.7 1.0 N A:SER364 4.2 64.6 1.0 CA A:SER364 4.3 65.5 1.0 N A:PHE365 4.5 63.5 1.0 O A:HOH813 4.6 53.7 1.0 CB A:SER364 4.6 70.4 1.0 CB A:ASP362 4.6 65.5 1.0 CA A:PHE365 4.6 65.2 1.0 O A:HOH904 4.7 51.8 1.0 CA A:ASP362 4.8 65.6 1.0 CB A:PHE365 4.8 61.8 1.0 C A:ASP362 5.0 63.7 1.0

Calcium binding site 9 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:52.9 occ:1.00 O A:VAL408 2.3 61.5 1.0 O A:HOH795 2.3 59.6 1.0 OD1 A:ASP406 2.4 62.0 1.0 OG1 A:THR404 2.5 57.1 1.0 O A:HOH826 2.5 59.6 1.0 OE2 A:GLU413 2.6 62.3 1.0 OE1 A:GLU413 2.6 63.5 1.0 CD A:GLU413 3.0 63.8 1.0 CG A:ASP406 3.2 64.7 1.0 CB A:THR404 3.3 58.3 1.0 OD2 A:ASP406 3.5 69.6 1.0 C A:VAL408 3.5 60.2 1.0 CG2 A:THR404 4.0 59.0 1.0 N A:VAL408 4.1 57.2 1.0 CA A:VAL408 4.2 58.9 1.0 N A:ASP406 4.4 60.7 1.0 O A:ILE403 4.5 51.0 1.0 CB A:VAL408 4.5 61.5 1.0 CG A:GLU413 4.5 66.0 1.0 CB A:ASP406 4.5 63.6 1.0 N A:ILE409 4.5 60.8 1.0 ND2 A:ASN410 4.6 81.3 1.0 CA A:THR404 4.6 55.5 1.0 N A:SER405 4.7 60.0 1.0 CA A:ILE409 4.7 63.0 1.0 N A:ASN410 4.7 70.7 1.0 C A:THR404 4.7 56.6 1.0 N A:ASP407 4.8 56.1 1.0 CA A:ASP406 4.9 60.6 1.0 C A:ASP406 5.0 58.1 1.0

Calcium binding site 10 out of 17 in the Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structural Insight Into Host Cell Surface Retention of A 1.5-Mda Bacterial Ice-Binding Adhesin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:47.8 occ:1.00 OD1 A:ASP466 2.2 49.4 1.0 O B:ALA468 2.3 43.8 1.0 O A:ALA468 2.3 45.7 1.0 OD1 B:ASP466 2.4 49.1 1.0 O A:HOH723 2.5 59.0 1.0 OD2 A:ASP466 2.5 47.0 1.0 O B:HOH704 2.5 54.0 1.0 CG A:ASP466 2.7 49.4 1.0 CG B:ASP466 3.3 47.5 1.0 OD2 B:ASP466 3.4 45.9 1.0 C B:ALA468 3.5 42.0 1.0 C A:ALA468 3.5 45.5 1.0 CB A:ASP466 4.2 51.0 1.0 N B:ALA468 4.2 43.1 1.0 CA B:ALA468 4.2 41.6 1.0 N A:ALA468 4.3 48.8 1.0 CA A:ALA468 4.4 46.3 1.0 CA A:PHE469 4.4 43.0 1.0 N A:PHE469 4.4 43.7 1.0 N B:PHE469 4.5 40.0 1.0 CB B:ALA468 4.5 42.7 1.0 CB A:PHE469 4.5 43.4 1.0 CA B:PHE469 4.6 40.0 1.0 CB B:ASP466 4.7 48.0 1.0 O A:HOH885 4.8 44.7 1.0 CB A:ALA468 4.8 46.4 1.0 CA A:ASP466 4.8 52.6 1.0 CB B:PHE469 4.9 41.3 1.0 C A:ASP466 4.9 51.6 1.0

S.Guo, C.A.Stevens, T.D.R.Vance, L.L.C.Olijve, L.A.Graham, R.L.Campbell, S.R.Yazdi, C.Escobedo, M.Bar-Dolev, V.Yashunsky, I.Braslavsky, D.N.Langelaan, S.P.Smith, J.S.Allingham, I.K.Voets, P.L.Davies. Structure of A 1.5-Mda Adhesin That Binds Its Antarctic Bacterium to Diatoms and Ice. Sci Adv V. 3 01440 2017.
ISSN: ESSN 2375-2548
PubMed: 28808685
DOI: 10.1126/SCIADV.1701440