Calcium in PDB 5kiq: Srpa with Sialyl Lewisx

The structure of Srpa with Sialyl Lewisx, PDB code: 5kiq was solved by T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.41 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.911, 46.766, 65.169, 90.00, 102.73, 90.00
R / Rfree (%)	19.3 / 21.8

The binding sites of Calcium atom in the Srpa with Sialyl Lewisx (pdb code 5kiq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Srpa with Sialyl Lewisx, PDB code: 5kiq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:24.7 occ:1.00 OE1 B:GLU400 2.4 26.4 1.0 OE1 A:GLU400 2.4 25.8 1.0 O B:HOH711 2.4 22.7 1.0 OE2 A:GLU400 2.4 28.9 1.0 OE2 B:GLU400 2.4 25.6 1.0 O A:HOH673 2.4 31.4 1.0 O A:HOH687 2.5 25.2 1.0 O B:HOH636 2.6 41.9 1.0 CD A:GLU400 2.8 28.9 1.0 CD B:GLU400 2.8 38.3 1.0 O B:HOH703 4.1 25.8 1.0 O A:HOH678 4.2 25.8 1.0 NH1 A:ARG415 4.3 23.1 1.0 NH1 B:ARG415 4.3 20.4 1.0 O B:HOH699 4.3 22.8 1.0 CG A:GLU400 4.4 30.6 1.0 CG B:GLU400 4.4 27.8 1.0 NH2 A:ARG415 4.5 22.7 1.0 NH2 B:ARG415 4.5 23.4 1.0 O B:ILE416 4.6 24.6 1.0 O A:HOH860 4.7 44.8 1.0 CZ B:ARG415 4.7 20.8 1.0 CZ A:ARG415 4.7 29.0 1.0 O A:ILE416 4.8 24.8 1.0 O A:HOH747 4.9 33.8 1.0 O B:HOH707 5.0 30.7 1.0

Calcium binding site 2 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:21.3 occ:1.00 OD1 A:ASP282 2.4 27.0 1.0 O A:THR255 2.4 19.2 1.0 OD2 A:ASP353 2.4 21.0 1.0 OD2 A:ASP253 2.4 26.1 1.0 OD2 A:ASP281 2.4 21.6 1.0 OD1 A:ASP253 2.4 22.4 1.0 OD1 A:ASP281 2.4 21.3 1.0 CG A:ASP253 2.7 27.3 1.0 CG A:ASP281 2.8 21.9 1.0 CG A:ASP353 3.4 17.8 1.0 CG A:ASP282 3.5 30.8 1.0 C A:THR255 3.5 20.7 1.0 CB A:ASP353 3.8 19.2 1.0 OD2 A:ASP282 4.0 31.2 1.0 ND2 A:ASN357 4.2 23.1 1.0 N A:THR255 4.2 22.2 1.0 CB A:ASP253 4.3 29.0 1.0 CA A:THR255 4.3 21.9 1.0 N A:ASP282 4.3 23.4 1.0 CB A:ASP281 4.3 21.4 1.0 N A:SER283 4.3 23.7 1.0 CB A:THR255 4.5 21.6 1.0 O A:HOH729 4.5 30.7 1.0 OG A:SER283 4.5 25.1 1.0 CB A:SER283 4.5 20.9 1.0 CA A:PRO256 4.5 17.5 1.0 OD1 A:ASP353 4.5 21.0 1.0 N A:PRO256 4.5 17.4 1.0 C A:PRO256 4.6 17.8 1.0 CB A:ASP282 4.8 23.9 1.0 O A:PRO256 4.8 18.1 1.0 N A:PRO257 4.9 17.2 1.0 CA A:ASP282 4.9 23.7 1.0

Calcium binding site 3 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:33.7 occ:1.00 O A:TYR375 2.3 39.1 1.0 OD2 A:ASP434 2.4 34.9 1.0 O A:ACT510 2.4 75.7 1.0 O A:THR372 2.4 33.9 1.0 OXT A:ACT510 2.4 45.3 1.0 OD1 A:ASP434 2.4 53.1 1.0 OG1 A:THR372 2.4 34.1 1.0 O A:HOH753 2.6 43.8 1.0 O A:HOH725 2.7 46.0 1.0 CG A:ASP434 2.7 23.6 1.0 C A:ACT510 2.8 64.4 1.0 C A:THR372 3.4 38.0 1.0 C A:TYR375 3.5 37.7 1.0 CB A:THR372 3.6 41.7 1.0 CA A:THR372 3.8 35.1 1.0 CA A:ASN376 4.3 43.5 1.0 CH3 A:ACT510 4.3 47.7 1.0 CB A:ASP434 4.3 26.9 1.0 N A:ASN376 4.3 45.3 1.0 O A:HOH760 4.5 57.3 1.0 CD A:PRO377 4.5 45.3 1.0 O A:HOH669 4.5 38.8 1.0 CG2 A:THR372 4.5 34.8 1.0 N A:ASP373 4.5 35.0 1.0 CA A:TYR375 4.5 39.6 1.0 OD1 A:ASN376 4.6 71.1 1.0 N A:TYR375 4.6 40.0 1.0 OH A:TYR428 4.6 31.2 1.0 CB A:ASN376 4.9 46.2 1.0 CA A:ASP373 4.9 39.8 1.0 O A:THR433 5.0 30.9 1.0

Calcium binding site 4 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:31.0 occ:1.00 O B:THR255 2.3 31.2 1.0 OD1 B:ASP282 2.4 46.2 1.0 OD2 B:ASP253 2.4 31.6 1.0 OD2 B:ASP353 2.4 31.7 1.0 OD2 B:ASP281 2.4 30.3 1.0 OD1 B:ASP253 2.4 32.7 1.0 OD1 B:ASP281 2.4 26.4 1.0 CG B:ASP253 2.7 32.5 1.0 CG B:ASP281 2.8 27.1 1.0 CG B:ASP282 3.5 45.0 1.0 CG B:ASP353 3.5 27.4 1.0 C B:THR255 3.5 32.1 1.0 OD2 B:ASP282 3.9 56.8 1.0 CB B:ASP353 4.0 24.7 1.0 ND2 B:ASN357 4.0 30.2 1.0 CB B:ASP253 4.2 32.4 1.0 CA B:THR255 4.3 31.9 1.0 CB B:ASP281 4.3 26.3 1.0 N B:THR255 4.3 35.0 1.0 N B:SER283 4.3 36.7 1.0 CB B:THR255 4.4 32.0 1.0 N B:ASP282 4.4 31.0 1.0 OG B:SER283 4.4 31.5 1.0 O B:HOH733 4.4 34.8 1.0 O B:HOH719 4.4 39.3 1.0 CB B:SER283 4.5 44.8 1.0 C B:PRO256 4.5 32.1 1.0 N B:PRO256 4.5 32.2 1.0 CA B:PRO256 4.5 24.4 1.0 OD1 B:ASP353 4.6 25.2 1.0 O B:PRO256 4.7 31.4 1.0 CB B:ASP282 4.8 34.5 1.0 N B:PRO257 4.9 25.8 1.0 CB B:ASN357 4.9 23.7 1.0 CG B:ASN357 5.0 27.9 1.0

Calcium binding site 5 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:52.9 occ:1.00 O B:HOH716 2.2 46.1 1.0 O B:HOH660 2.3 40.0 1.0 O B:ACT506 2.4 62.4 1.0 O B:HOH654 2.8 35.8 1.0 O B:HOH734 2.9 45.1 1.0 C B:ACT506 3.5 65.0 1.0 OXT B:ACT506 3.8 92.9 1.0 ND2 B:ASN309 4.2 43.0 1.0 O B:ACT507 4.4 63.7 1.0 CB B:ASN320 4.5 47.4 1.0 O B:GLY314 4.5 36.6 1.0 O B:ASN315 4.5 30.9 1.0 O B:ASN320 4.6 35.7 1.0 CH3 B:ACT507 4.6 27.8 1.0 CA B:ASN315 4.7 31.4 1.0 CH3 B:ACT506 4.7 45.7 1.0 C B:ASN315 4.8 28.9 1.0 O B:PRO321 5.0 36.2 1.0

Calcium binding site 6 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:30.0 occ:1.00 O B:TYR375 2.3 75.0 1.0 OD2 B:ASP434 2.4 29.7 1.0 O B:THR372 2.4 29.1 1.0 N B:ASN376 2.4 57.8 1.0 OD1 B:ASP434 2.4 32.9 1.0 O B:HOH680 2.4 44.7 1.0 OG1 B:THR372 2.4 31.5 1.0 O B:HOH750 2.5 41.0 1.0 C B:TYR375 2.6 29.1 1.0 O B:HOH603 2.6 36.2 1.0 CG B:ASP434 2.7 33.5 1.0 CA B:ASN376 3.4 52.7 1.0 C B:THR372 3.4 34.0 1.0 CB B:THR372 3.7 32.9 1.0 CA B:THR372 3.9 26.7 1.0 CA B:TYR375 3.9 32.7 1.0 CB B:ASN376 4.0 61.7 1.0 CB B:ASP434 4.3 28.1 1.0 N B:TYR375 4.3 35.4 1.0 CB B:TYR375 4.5 30.6 1.0 N B:ASP373 4.5 27.8 1.0 O B:HOH720 4.6 42.0 1.0 CG2 B:THR372 4.6 35.3 1.0 CD B:PRO377 4.7 48.2 1.0 O B:HOH737 4.7 48.0 1.0 OH B:TYR428 4.7 26.0 1.0 O B:HOH816 4.8 51.7 1.0 C B:ASN376 4.8 60.0 1.0 O B:HOH695 4.9 36.0 1.0 CA B:ASP373 4.9 30.2 1.0

Calcium binding site 7 out of 7 in the Srpa with Sialyl Lewisx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Srpa with Sialyl Lewisx within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:76.8 occ:1.00 O B:ASP373 2.4 42.3 1.0 C B:ASP373 3.5 31.1 1.0 OH B:TYR268 4.1 30.2 1.0 CA B:ASP373 4.4 30.2 1.0 N B:LYS374 4.4 25.8 1.0 CA B:LYS374 4.5 27.5 1.0 CB B:ASP373 4.6 30.6 1.0 O B:LYS374 5.0 30.2 1.0 C B:LYS374 5.0 39.0 1.0

L.V.Loukachevitch, B.A.Bensing, H.Yu, J.Zeng, X.Chen, P.M.Sullam, T.M.Iverson. Structures of the Streptococcus Sanguinis Srpa Binding Region with Human Sialoglycans Suggest Features of the Physiological Ligand. Biochemistry 2016.
ISSN: ISSN 1520-4995
PubMed: 27685666
DOI: 10.1021/ACS.BIOCHEM.6B00704