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Calcium in PDB 5iiy: Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide

Protein crystallography data

The structure of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide, PDB code: 5iiy 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) 45.10 / 1.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.522, 46.769, 64.761, 90.00, 102.72, 90.00
R / Rfree (%) 17.7 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide (pdb code 5iiy). 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 Adhesin in Complex with the NEU5AC-Galactoside Disaccharide, PDB code: 5iiy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5iiy

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Calcium binding site 1 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:20.4
occ:1.00
 OE1 B:GLU400 2.4 23.1 1.0
OE2 A:GLU400 2.4 21.6 1.0
OE1 A:GLU400 2.4 22.9 1.0
OE2 B:GLU400 2.4 21.2 1.0
O A:HOH689 2.5 30.9 1.0
O B:HOH697 2.5 18.3 1.0
O A:HOH735 2.6 28.1 1.0
O A:HOH700 2.6 19.6 1.0
CD B:GLU400 2.7 22.2 1.0
CD A:GLU400 2.7 19.6 1.0
CG B:GLU400 4.3 19.3 1.0
CG A:GLU400 4.3 23.0 1.0
O B:HOH742 4.3 17.1 1.0
NH1 B:ARG415 4.3 19.1 1.0
O B:HOH755 4.3 20.7 1.0
NH1 A:ARG415 4.4 18.3 1.0
O A:HOH731 4.4 19.1 1.0
NH2 B:ARG415 4.4 17.4 1.0
NH2 A:ARG415 4.5 17.9 1.0
CZ B:ARG415 4.6 19.1 1.0
O B:ILE416 4.7 17.0 1.0
O A:ILE416 4.7 20.7 1.0
CZ A:ARG415 4.7 22.1 1.0
O A:HOH680 4.8 26.4 1.0
O B:HOH737 4.9 22.4 1.0

Calcium binding site 2 out of 7 in 5iiy

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Calcium binding site 2 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:16.6
occ:1.00
 OD2 A:ASP353 2.3 15.7 1.0
OD1 A:ASP282 2.3 20.4 1.0
O A:THR255 2.4 16.5 1.0
OD2 A:ASP281 2.4 16.9 1.0
OD2 A:ASP253 2.4 18.6 1.0
OD1 A:ASP281 2.4 16.2 1.0
OD1 A:ASP253 2.4 18.8 1.0
CG A:ASP281 2.7 14.8 1.0
CG A:ASP253 2.7 18.4 1.0
CG A:ASP353 3.4 16.6 1.0
CG A:ASP282 3.5 23.9 1.0
C A:THR255 3.5 17.0 1.0
CB A:ASP353 3.8 15.7 1.0
OD2 A:ASP282 4.0 25.7 1.0
ND2 A:ASN357 4.1 17.0 1.0
CB A:ASP281 4.2 16.8 1.0
CB A:ASP253 4.2 21.8 1.0
N A:ASP282 4.3 18.5 1.0
O A:HOH740 4.3 25.9 1.0
N A:SER283 4.3 18.4 1.0
CA A:THR255 4.3 18.0 1.0
N A:THR255 4.3 16.9 1.0
O A:HOH713 4.4 27.3 1.0
CB A:SER283 4.4 19.0 1.0
OG A:SER283 4.5 16.7 1.0
CB A:THR255 4.5 18.4 1.0
OD1 A:ASP353 4.5 15.4 1.0
N A:PRO256 4.5 15.9 1.0
C A:PRO256 4.6 15.0 1.0
CA A:PRO256 4.6 13.3 1.0
CB A:ASP282 4.7 20.7 1.0
O A:PRO256 4.8 16.0 1.0
O A:HOH721 4.8 32.8 1.0
C A:ASP281 4.9 19.1 1.0
CA A:ASP282 4.9 21.4 1.0
CA A:ASP281 4.9 15.8 1.0
N A:PRO257 4.9 15.5 1.0
CG A:ASN357 5.0 18.6 1.0
CB A:ASN357 5.0 15.1 1.0

Calcium binding site 3 out of 7 in 5iiy

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Calcium binding site 3 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:31.3
occ:1.00
 O A:HOH619 2.2 33.6 1.0
O A:TYR375 2.3 33.2 1.0
OD2 A:ASP434 2.4 34.0 1.0
O A:THR372 2.4 29.6 1.0
OD1 A:ASP434 2.4 36.8 1.0
OG1 A:THR372 2.4 34.3 1.0
O A:HOH725 2.6 36.5 1.0
CG A:ASP434 2.7 30.0 1.0
O A:HOH707 2.8 40.6 1.0
C A:THR372 3.3 34.4 1.0
C A:TYR375 3.5 34.7 1.0
CB A:THR372 3.6 32.3 1.0
CA A:THR372 3.7 29.9 1.0
CB A:ASP434 4.3 29.2 1.0
CD A:PRO377 4.3 38.2 1.0
OH A:TYR428 4.3 33.8 1.0
CA A:ASN376 4.3 37.4 1.0
N A:ASN376 4.4 38.7 1.0
O A:HOH829 4.4 44.7 1.0
CG2 A:THR372 4.5 30.3 1.0
CA A:TYR375 4.5 34.6 1.0
N A:ASP373 4.5 31.4 1.0
N A:TYR375 4.6 36.0 1.0
O A:HOH633 4.7 36.4 1.0
OD1 A:ASN376 4.7 58.9 1.0
O A:THR433 4.8 30.7 1.0
CE2 A:TYR428 4.8 22.2 1.0
CB A:TYR375 5.0 31.8 1.0
CZ A:TYR428 5.0 29.1 1.0

Calcium binding site 4 out of 7 in 5iiy

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Calcium binding site 4 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:22.9
occ:1.00
 OD1 B:ASP282 2.4 28.0 1.0
OD2 B:ASP353 2.4 24.6 1.0
OD2 B:ASP281 2.4 27.6 1.0
OD2 B:ASP253 2.4 25.1 1.0
O B:THR255 2.4 23.2 1.0
OD1 B:ASP253 2.4 27.1 1.0
OD1 B:ASP281 2.4 23.4 1.0
CG B:ASP253 2.7 27.5 1.0
CG B:ASP281 2.7 26.2 1.0
CG B:ASP353 3.5 20.8 1.0
CG B:ASP282 3.5 31.0 1.0
C B:THR255 3.6 25.5 1.0
OD2 B:ASP282 3.9 35.0 1.0
CB B:ASP353 3.9 20.1 1.0
ND2 B:ASN357 4.1 25.9 1.0
CB B:ASP253 4.2 30.8 1.0
CB B:ASP281 4.2 21.7 1.0
N B:ASP282 4.2 22.2 1.0
N B:THR255 4.3 27.7 1.0
N B:SER283 4.3 25.9 1.0
CA B:THR255 4.3 29.9 1.0
O B:HOH662 4.4 31.7 1.0
O B:HOH747 4.4 25.5 1.0
CB B:SER283 4.5 27.4 1.0
OD1 B:ASP353 4.5 23.7 1.0
OG B:SER283 4.5 25.5 1.0
N B:PRO256 4.6 24.5 1.0
CB B:THR255 4.6 31.4 1.0
C B:PRO256 4.6 23.3 1.0
CA B:PRO256 4.7 22.3 1.0
CB B:ASP282 4.7 26.4 1.0
O B:PRO256 4.7 23.8 1.0
CB B:ASN357 4.8 24.4 1.0
N B:PRO257 4.9 20.9 1.0
CA B:ASP282 4.9 27.5 1.0
CG B:ASN357 4.9 26.7 1.0
CA B:ASP281 4.9 24.4 1.0
C B:ASP281 4.9 22.5 1.0

Calcium binding site 5 out of 7 in 5iiy

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Calcium binding site 5 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:38.3
occ:1.00
 O B:HOH689 2.3 25.8 1.0
O B:HOH854 2.4 39.7 1.0
O B:HOH705 2.6 35.0 1.0
O B:HOH869 2.6 43.4 1.0
O B:HOH820 2.6 33.2 1.0
O B:HOH612 2.7 21.3 1.0
O B:HOH872 2.7 52.2 1.0
ND2 B:ASN309 4.1 26.2 1.0
CB B:ASN320 4.3 33.9 1.0
O B:ASN315 4.4 23.6 1.0
O B:ASN320 4.5 24.1 1.0
O B:GLY314 4.5 25.0 1.0
O B:HOH764 4.6 26.1 1.0
CA B:ASN315 4.6 20.2 1.0
O B:HOH853 4.7 47.3 1.0
O B:HOH911 4.7 38.4 1.0
C B:ASN315 4.7 21.4 1.0
O B:HOH798 4.8 33.0 1.0
O B:PRO321 4.8 22.5 1.0
O B:HOH603 4.9 50.0 1.0

Calcium binding site 6 out of 7 in 5iiy

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Calcium binding site 6 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:19.0
occ:1.00
 O B:TYR375 2.3 22.9 1.0
O B:HOH708 2.3 24.3 1.0
O B:THR372 2.4 21.2 1.0
OD2 B:ASP434 2.4 20.1 1.0
OD1 B:ASP434 2.4 21.6 1.0
OG1 B:THR372 2.4 23.3 1.0
O B:HOH794 2.6 24.9 1.0
O B:HOH707 2.6 22.5 1.0
CG B:ASP434 2.7 19.3 1.0
C B:THR372 3.3 21.5 1.0
C B:TYR375 3.5 20.3 1.0
CB B:THR372 3.6 19.2 1.0
CA B:THR372 3.7 18.8 1.0
CB B:ASP434 4.2 23.6 1.0
N B:ASN376 4.4 23.7 1.0
CA B:ASN376 4.4 24.5 1.0
O B:HOH664 4.5 31.4 1.0
N B:ASP373 4.5 20.0 1.0
CG2 B:THR372 4.5 21.4 1.0
CA B:TYR375 4.6 19.6 1.0
O B:HOH765 4.6 34.3 1.0
N B:TYR375 4.7 21.5 1.0
CD B:PRO377 4.7 25.1 1.0
OH B:TYR428 4.7 22.8 1.0
CA B:ASP373 4.9 26.5 1.0
O B:THR433 4.9 23.8 1.0
CE2 B:TYR428 5.0 20.8 1.0
O B:HOH827 5.0 38.2 1.0

Calcium binding site 7 out of 7 in 5iiy

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Calcium binding site 7 out of 7 in the Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Srpa Adhesin in Complex with the NEU5AC-Galactoside Disaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:32.8
occ:1.00
 O B:HOH826 2.3 38.5 1.0
O B:HOH723 2.4 31.2 1.0
O B:ASP373 2.4 23.4 1.0
O B:HOH827 2.5 38.2 1.0
O B:HOH918 2.5 41.0 1.0
O B:HOH743 2.5 27.3 1.0
C B:ASP373 3.5 23.7 1.0
CA B:ASP373 4.3 26.5 1.0
O B:HOH794 4.3 24.9 1.0
O B:HOH953 4.4 51.3 1.0
N B:LYS374 4.6 20.9 1.0
O B:LYS374 4.7 23.4 1.0
CB B:ASP373 4.7 22.8 1.0
CA B:LYS374 4.8 22.5 1.0
OH B:TYR268 4.8 25.9 1.0
C B:LYS374 5.0 23.6 1.0

Reference:

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
Page generated: Wed Jul 9 06:48:39 2025

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