Calcium in PDB 5ij1: Srpa Adhesin in Complex with Sialyllactose

Protein crystallography data

The structure of Srpa Adhesin in Complex with Sialyllactose, PDB code: 5ij1 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) 42.56 / 1.80
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 (%) 17.6 / 19.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Srpa Adhesin in Complex with Sialyllactose (pdb code 5ij1). 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 Sialyllactose, PDB code: 5ij1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5ij1

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Calcium binding site 1 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:20.5
occ:1.00
 O B:HOH630 2.3 31.6 1.0
OE1 A:GLU400 2.4 19.6 1.0
OE1 B:GLU400 2.4 22.1 1.0
O A:HOH751 2.5 27.4 1.0
OE2 A:GLU400 2.5 21.3 1.0
O A:HOH688 2.5 16.9 1.0
OE2 B:GLU400 2.5 18.2 1.0
O B:HOH711 2.5 17.8 1.0
CD A:GLU400 2.8 18.4 1.0
CD B:GLU400 2.8 20.0 1.0
NH1 B:ARG415 4.2 17.6 1.0
NH1 A:ARG415 4.3 16.7 1.0
O B:HOH734 4.3 16.8 1.0
CG A:GLU400 4.3 23.0 1.0
O B:HOH754 4.3 19.1 1.0
CG B:GLU400 4.3 20.1 1.0
NH2 B:ARG415 4.3 17.0 1.0
NH2 A:ARG415 4.4 16.5 1.0
O A:HOH754 4.5 18.9 1.0
O B:HOH806 4.5 38.6 1.0
CZ B:ARG415 4.5 18.4 1.0
O A:ILE416 4.6 18.9 1.0
O B:ILE416 4.6 15.8 1.0
CZ A:ARG415 4.6 18.8 1.0
O A:HOH894 4.7 40.2 1.0
O A:HOH726 4.9 24.1 1.0
O B:HOH731 4.9 23.6 1.0
O B:HOH840 4.9 29.5 1.0

Calcium binding site 2 out of 7 in 5ij1

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Calcium binding site 2 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:15.4
occ:1.00
 O A:THR255 2.3 15.3 1.0
OD1 A:ASP282 2.3 19.8 1.0
OD2 A:ASP281 2.4 14.9 1.0
OD2 A:ASP253 2.4 17.6 1.0
OD2 A:ASP353 2.4 18.5 1.0
OD1 A:ASP281 2.4 13.5 1.0
OD1 A:ASP253 2.5 16.8 1.0
CG A:ASP281 2.7 13.0 1.0
CG A:ASP253 2.8 17.9 1.0
CG A:ASP353 3.4 14.2 1.0
C A:THR255 3.5 16.0 1.0
CG A:ASP282 3.5 25.3 1.0
CB A:ASP353 3.8 13.8 1.0
OD2 A:ASP282 4.0 25.9 1.0
ND2 A:ASN357 4.2 15.5 1.0
CB A:ASP281 4.2 14.7 1.0
N A:THR255 4.2 15.4 1.0
CA A:THR255 4.3 15.7 1.0
O A:HOH762 4.3 23.7 1.0
N A:ASP282 4.3 15.7 1.0
CB A:ASP253 4.3 19.2 1.0
O A:HOH771 4.3 28.7 1.0
N A:SER283 4.3 17.7 1.0
CB A:THR255 4.4 17.7 1.0
N A:PRO256 4.5 14.2 1.0
OG A:SER283 4.5 16.9 1.0
CB A:SER283 4.5 21.0 1.0
C A:PRO256 4.5 13.6 1.0
OD1 A:ASP353 4.5 15.3 1.0
CA A:PRO256 4.5 10.5 1.0
O A:PRO256 4.7 14.4 1.0
CB A:ASP282 4.7 18.5 1.0
N A:PRO257 4.9 10.8 1.0
O A:HOH705 4.9 32.9 1.0
CA A:ASP282 4.9 20.3 1.0
CA A:ASP281 4.9 15.2 1.0
C A:ASP281 4.9 15.1 1.0
CB A:ASN357 5.0 13.4 1.0
CG A:ASN357 5.0 20.6 1.0

Calcium binding site 3 out of 7 in 5ij1

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Calcium binding site 3 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:27.1
occ:1.00
 O A:HOH698 2.3 35.1 1.0
O A:THR372 2.3 24.8 1.0
O A:TYR375 2.3 28.8 1.0
OD2 A:ASP434 2.4 26.1 1.0
O A:HOH623 2.5 34.8 1.0
OG1 A:THR372 2.6 27.9 1.0
OD1 A:ASP434 2.6 30.2 1.0
O A:HOH649 2.7 38.8 1.0
CG A:ASP434 2.8 24.0 1.0
C A:THR372 3.3 27.5 1.0
C A:TYR375 3.5 28.0 1.0
CB A:THR372 3.7 27.1 1.0
CA A:THR372 3.7 25.6 1.0
CA A:ASN376 4.3 34.6 1.0
N A:ASN376 4.3 30.0 1.0
CB A:ASP434 4.4 22.2 1.0
CD A:PRO377 4.4 33.7 1.0
OH A:TYR428 4.5 26.8 1.0
N A:ASP373 4.5 27.9 1.0
CG2 A:THR372 4.5 28.1 1.0
OD1 A:ASN376 4.5 51.8 1.0
O A:HOH630 4.5 33.1 1.0
CA A:TYR375 4.6 27.7 1.0
CG A:ASN376 4.6 49.8 1.0
N A:TYR375 4.6 30.9 1.0
ND2 A:ASN376 4.8 52.1 1.0
CE2 A:TYR428 4.9 20.7 1.0
CA A:ASP373 4.9 25.6 1.0
O A:THR433 5.0 24.7 1.0

Calcium binding site 4 out of 7 in 5ij1

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Calcium binding site 4 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:20.9
occ:1.00
 O B:THR255 2.2 21.9 1.0
OD2 B:ASP353 2.3 18.3 1.0
OD1 B:ASP282 2.4 27.4 1.0
OD2 B:ASP281 2.4 23.1 1.0
OD2 B:ASP253 2.4 22.3 1.0
OD1 B:ASP253 2.4 23.4 1.0
OD1 B:ASP281 2.4 18.7 1.0
CG B:ASP253 2.7 19.7 1.0
CG B:ASP281 2.7 21.2 1.0
CG B:ASP353 3.4 20.0 1.0
C B:THR255 3.4 18.1 1.0
CG B:ASP282 3.5 29.2 1.0
CB B:ASP353 3.9 17.2 1.0
OD2 B:ASP282 4.0 30.5 1.0
ND2 B:ASN357 4.2 22.5 1.0
N B:THR255 4.2 22.4 1.0
CA B:THR255 4.2 21.4 1.0
CB B:ASP253 4.2 25.5 1.0
CB B:ASP281 4.2 19.4 1.0
N B:ASP282 4.3 20.3 1.0
N B:SER283 4.3 24.9 1.0
O B:HOH684 4.4 29.6 1.0
O B:HOH738 4.4 26.6 1.0
CB B:THR255 4.4 30.5 1.0
N B:PRO256 4.4 22.6 1.0
OD1 B:ASP353 4.5 18.3 1.0
C B:PRO256 4.5 21.8 1.0
CA B:PRO256 4.5 19.7 1.0
OG B:SER283 4.6 22.7 1.0
CB B:SER283 4.6 27.0 1.0
O B:PRO256 4.7 19.9 1.0
CB B:ASP282 4.8 22.3 1.0
N B:PRO257 4.9 18.2 1.0
CB B:ASN357 4.9 22.8 1.0
CA B:ASP282 4.9 23.8 1.0
CA B:ASP281 4.9 21.0 1.0
CG2 B:THR255 4.9 28.3 1.0
C B:ASP281 5.0 15.9 1.0
CG B:ASN357 5.0 23.7 1.0

Calcium binding site 5 out of 7 in 5ij1

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Calcium binding site 5 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:42.2
occ:1.00
 O B:HOH805 2.3 37.9 1.0
O B:HOH686 2.3 30.3 1.0
O B:HOH851 2.4 44.9 1.0
OXT B:ACT506 2.4 43.4 1.0
O B:HOH836 2.4 43.7 1.0
O B:HOH659 2.6 23.3 1.0
C B:ACT506 3.4 45.1 1.0
O B:ACT506 3.6 60.6 1.0
ND2 B:ASN309 3.9 25.9 1.0
O B:ASN315 4.3 19.9 1.0
O B:HOH794 4.4 23.2 1.0
CB B:ASN320 4.4 34.8 1.0
O B:HOH899 4.4 33.0 1.0
CA B:ASN315 4.5 20.8 1.0
O B:ASN320 4.5 20.8 1.0
O B:GLY314 4.5 23.1 1.0
C B:ASN315 4.7 20.1 1.0
O B:PRO321 4.8 19.2 1.0
CH3 B:ACT506 4.8 29.8 1.0

Calcium binding site 6 out of 7 in 5ij1

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Calcium binding site 6 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:21.5
occ:1.00
 O B:TYR375 1.5 30.7 1.0
O B:THR372 2.3 17.6 1.0
OD2 B:ASP434 2.4 18.5 1.0
O B:HOH730 2.5 21.6 1.0
O B:HOH605 2.5 21.5 1.0
C B:TYR375 2.6 11.9 1.0
OD1 B:ASP434 2.6 20.4 1.0
OG1 B:THR372 2.8 23.1 1.0
O B:HOH817 2.8 22.9 1.0
CG B:ASP434 2.8 19.9 1.0
C B:THR372 3.3 19.0 1.0
N B:ASN376 3.5 26.9 1.0
CA B:TYR375 3.7 22.4 1.0
CA B:THR372 3.8 19.0 1.0
CA B:ASN376 3.8 23.1 1.0
CB B:THR372 3.9 17.1 1.0
N B:TYR375 4.0 21.7 1.0
CB B:TYR375 4.3 19.3 1.0
CB B:ASP434 4.4 21.4 1.0
CB B:ASN376 4.5 25.9 1.0
OH B:TYR428 4.5 18.3 1.0
O B:HOH847 4.5 42.0 1.0
N B:ASP373 4.5 18.8 1.0
CD B:PRO377 4.6 25.9 1.0
O B:HOH697 4.7 27.2 1.0
CG2 B:THR372 4.8 17.8 1.0
O B:HOH929 4.8 40.8 1.0
O B:HOH666 4.8 29.7 1.0
CE2 B:TYR428 4.8 17.8 1.0
CA B:ASP373 4.9 22.8 1.0
O B:HOH764 4.9 37.3 1.0
C B:LYS374 4.9 23.2 1.0
O B:HOH808 4.9 34.7 1.0
ND2 B:ASN376 5.0 26.0 1.0

Calcium binding site 7 out of 7 in 5ij1

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Calcium binding site 7 out of 7 in the Srpa Adhesin in Complex with Sialyllactose


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 Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:32.8
occ:1.00
 O B:ASP373 2.3 20.5 1.0
O B:HOH908 2.4 37.4 1.0
O B:HOH839 2.5 38.6 1.0
O B:HOH808 2.5 34.7 1.0
O B:HOH697 2.6 27.2 1.0
C B:ASP373 3.5 22.2 1.0
CA B:ASP373 4.2 22.8 1.0
O B:HOH605 4.2 21.5 1.0
O B:HOH849 4.4 31.2 1.0
N B:LYS374 4.6 19.0 1.0
CB B:ASP373 4.6 17.7 1.0
CA B:LYS374 4.8 19.2 1.0
OH B:TYR268 4.8 22.6 1.0
O B:LYS374 4.9 22.3 1.0
C B:LYS374 5.0 23.2 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: Sat Dec 12 05:30:30 2020

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