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Calcium in PDB 5ij3: Srpa Adhesin in Complex with Sialyl T Antigen

Protein crystallography data

The structure of Srpa Adhesin in Complex with Sialyl T Antigen, PDB code: 5ij3 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) 27.82 / 1.70
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 (%) 18.6 / 20.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Srpa Adhesin in Complex with Sialyl T Antigen (pdb code 5ij3). 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 Sialyl T Antigen, PDB code: 5ij3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5ij3

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Calcium binding site 1 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:18.9
occ:1.00
 O B:HOH658 2.3 31.8 1.0
OE1 B:GLU400 2.4 20.4 1.0
OE2 A:GLU400 2.4 20.8 1.0
OE1 A:GLU400 2.4 17.6 1.0
OE2 B:GLU400 2.4 20.8 1.0
O B:HOH717 2.5 28.0 1.0
O A:HOH666 2.5 16.9 1.0
O B:HOH710 2.6 18.0 1.0
CD A:GLU400 2.7 19.7 1.0
CD B:GLU400 2.7 21.6 1.0
O B:HOH826 4.1 36.6 1.0
O B:HOH737 4.3 17.7 1.0
NH1 B:ARG415 4.3 17.2 1.0
CG B:GLU400 4.3 18.9 1.0
CG A:GLU400 4.3 21.5 1.0
NH1 A:ARG415 4.3 17.9 1.0
O B:HOH719 4.4 18.6 1.0
O A:HOH752 4.4 21.3 1.0
NH2 B:ARG415 4.5 17.3 1.0
NH2 A:ARG415 4.5 16.4 1.0
CZ B:ARG415 4.6 16.4 1.0
O A:HOH885 4.6 38.6 1.0
O A:ILE416 4.7 18.8 1.0
O B:ILE416 4.7 17.7 1.0
CZ A:ARG415 4.7 15.6 1.0
O A:HOH661 4.9 25.5 1.0
O B:HOH740 4.9 24.2 1.0
O B:HOH845 4.9 31.1 1.0

Calcium binding site 2 out of 7 in 5ij3

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Calcium binding site 2 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:14.9
occ:1.00
 OD1 A:ASP282 2.4 18.2 1.0
O A:THR255 2.4 14.9 1.0
OD2 A:ASP353 2.4 16.6 1.0
OD2 A:ASP253 2.4 17.0 1.0
OD2 A:ASP281 2.4 14.4 1.0
OD1 A:ASP253 2.4 17.0 1.0
OD1 A:ASP281 2.4 15.6 1.0
CG A:ASP281 2.7 13.0 1.0
CG A:ASP253 2.7 19.3 1.0
CG A:ASP353 3.4 13.1 1.0
CG A:ASP282 3.5 22.9 1.0
C A:THR255 3.5 15.3 1.0
CB A:ASP353 3.8 13.7 1.0
OD2 A:ASP282 4.1 22.4 1.0
ND2 A:ASN357 4.2 17.1 1.0
N A:ASP282 4.2 15.9 1.0
CB A:ASP281 4.3 15.5 1.0
O A:HOH756 4.3 29.3 1.0
CB A:ASP253 4.3 18.8 1.0
N A:SER283 4.3 15.8 1.0
N A:THR255 4.3 14.7 1.0
CA A:THR255 4.3 15.3 1.0
O A:HOH744 4.4 26.1 1.0
OG A:SER283 4.4 16.3 1.0
CB A:SER283 4.5 17.8 1.0
CB A:THR255 4.5 14.5 1.0
OD1 A:ASP353 4.5 14.3 1.0
N A:PRO256 4.5 12.3 1.0
C A:PRO256 4.6 12.3 1.0
CA A:PRO256 4.6 12.8 1.0
CB A:ASP282 4.7 18.5 1.0
O A:PRO256 4.8 13.3 1.0
CA A:ASP282 4.9 19.0 1.0
N A:PRO257 4.9 12.6 1.0
C A:ASP281 4.9 15.3 1.0
O A:HOH797 4.9 35.6 1.0
CA A:ASP281 4.9 14.7 1.0
CB A:ASN357 5.0 13.8 1.0

Calcium binding site 3 out of 7 in 5ij3

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Calcium binding site 3 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:28.0
occ:1.00
 O A:TYR375 2.3 32.6 1.0
OD2 A:ASP434 2.4 28.2 1.0
O A:ACT509 2.4 72.8 1.0
O A:THR372 2.4 29.6 1.0
OD1 A:ASP434 2.4 40.9 1.0
OXT A:ACT509 2.4 40.1 1.0
OG1 A:THR372 2.4 37.1 1.0
O A:HOH704 2.5 36.6 1.0
O A:HOH779 2.6 37.0 1.0
CG A:ASP434 2.7 24.5 1.0
C A:ACT509 2.8 50.9 1.0
C A:THR372 3.3 31.8 1.0
C A:TYR375 3.5 30.4 1.0
CB A:THR372 3.6 31.8 1.0
CA A:THR372 3.7 29.7 1.0
CB A:ASP434 4.2 24.6 1.0
CA A:ASN376 4.3 36.4 1.0
CH3 A:ACT509 4.3 45.8 1.0
CD A:PRO377 4.3 35.9 1.0
N A:ASN376 4.3 37.2 1.0
O A:HOH701 4.5 35.1 1.0
N A:ASP373 4.5 28.5 1.0
CA A:TYR375 4.5 29.9 1.0
OH A:TYR428 4.6 26.9 1.0
CG2 A:THR372 4.6 25.8 1.0
N A:TYR375 4.6 32.5 1.0
CE2 A:TYR428 4.9 22.6 1.0
OD1 A:ASN376 4.9 45.3 1.0
CA A:ASP373 5.0 29.4 1.0
CB A:ASN376 5.0 40.1 1.0
O A:THR433 5.0 28.4 1.0

Calcium binding site 4 out of 7 in 5ij3

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Calcium binding site 4 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:21.5
occ:1.00
 OD2 B:ASP353 2.4 20.1 1.0
OD2 B:ASP253 2.4 24.2 1.0
O B:THR255 2.4 20.8 1.0
OD1 B:ASP282 2.4 28.4 1.0
OD2 B:ASP281 2.4 27.8 1.0
OD1 B:ASP253 2.4 25.8 1.0
OD1 B:ASP281 2.4 21.1 1.0
CG B:ASP253 2.7 22.5 1.0
CG B:ASP281 2.7 23.4 1.0
CG B:ASP353 3.5 19.6 1.0
CG B:ASP282 3.5 32.5 1.0
C B:THR255 3.5 20.9 1.0
CB B:ASP353 4.0 17.7 1.0
OD2 B:ASP282 4.0 32.2 1.0
ND2 B:ASN357 4.1 22.1 1.0
CB B:ASP253 4.2 28.0 1.0
CB B:ASP281 4.2 21.2 1.0
N B:ASP282 4.3 21.8 1.0
N B:THR255 4.3 23.0 1.0
N B:SER283 4.3 24.5 1.0
CA B:THR255 4.3 24.5 1.0
O B:HOH676 4.4 29.5 1.0
CB B:SER283 4.5 25.6 1.0
CB B:THR255 4.5 28.3 1.0
O B:HOH788 4.5 25.9 1.0
OG B:SER283 4.5 22.3 1.0
OD1 B:ASP353 4.5 19.3 1.0
N B:PRO256 4.6 21.2 1.0
C B:PRO256 4.6 22.1 1.0
CA B:PRO256 4.7 20.8 1.0
CB B:ASP282 4.7 25.6 1.0
O B:PRO256 4.7 23.1 1.0
CB B:ASN357 4.9 22.2 1.0
N B:PRO257 4.9 20.9 1.0
CA B:ASP282 4.9 24.9 1.0
CA B:ASP281 4.9 19.0 1.0
CG B:ASN357 4.9 23.6 1.0
C B:ASP281 5.0 15.6 1.0

Calcium binding site 5 out of 7 in 5ij3

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Calcium binding site 5 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:44.6
occ:1.00
 O B:HOH825 2.2 39.3 1.0
O B:HOH682 2.2 30.3 1.0
O B:ACT506 2.4 41.7 1.0
O B:HOH628 2.7 23.9 1.0
C B:ACT506 3.5 52.0 1.0
OXT B:ACT506 3.9 76.2 1.0
ND2 B:ASN309 4.1 26.2 1.0
O B:ASN315 4.4 22.0 1.0
CB B:ASN320 4.4 35.5 1.0
CH3 B:ACT507 4.5 18.5 1.0
O B:ASN320 4.5 23.8 1.0
O B:GLY314 4.6 25.0 1.0
CA B:ASN315 4.6 18.9 1.0
O B:ACT507 4.8 65.0 1.0
C B:ASN315 4.8 21.2 1.0
CH3 B:ACT506 4.8 28.1 1.0
O B:PRO321 4.8 21.5 1.0

Calcium binding site 6 out of 7 in 5ij3

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Calcium binding site 6 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:20.5
occ:1.00
 O B:TYR375 2.3 20.3 1.0
O B:HOH696 2.3 28.7 1.0
O B:THR372 2.4 19.2 1.0
OD2 B:ASP434 2.4 21.6 1.0
OD1 B:ASP434 2.4 20.9 1.0
OG1 B:THR372 2.4 24.0 1.0
O B:HOH777 2.6 25.7 1.0
O B:HOH703 2.6 23.5 1.0
CG B:ASP434 2.7 21.1 1.0
C B:THR372 3.3 20.8 1.0
C B:TYR375 3.5 19.6 1.0
CB B:THR372 3.6 19.6 1.0
CA B:THR372 3.8 20.4 1.0
CB B:ASP434 4.2 19.6 1.0
N B:ASN376 4.4 24.4 1.0
CA B:ASN376 4.4 24.6 1.0
O B:HOH692 4.4 33.0 1.0
N B:ASP373 4.5 19.4 1.0
CG2 B:THR372 4.5 22.2 1.0
CA B:TYR375 4.5 17.1 1.0
O B:HOH927 4.6 40.3 1.0
N B:TYR375 4.6 19.2 1.0
O B:HOH857 4.6 42.2 1.0
OH B:TYR428 4.7 20.9 1.0
CD B:PRO377 4.7 26.1 1.0
O B:HOH754 4.8 36.5 1.0
O B:HOH818 4.9 38.4 1.0
O B:HOH702 4.9 26.4 1.0
CA B:ASP373 4.9 25.0 1.0
O B:THR433 5.0 18.9 1.0
CE2 B:TYR428 5.0 17.3 1.0
CB B:TYR375 5.0 17.3 1.0

Calcium binding site 7 out of 7 in 5ij3

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Calcium binding site 7 out of 7 in the Srpa Adhesin in Complex with Sialyl T Antigen


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 Sialyl T Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:31.8
occ:1.00
 O B:HOH816 2.2 37.3 1.0
O B:HOH699 2.3 27.0 1.0
O B:ASP373 2.4 22.1 1.0
O B:HOH742 2.5 29.1 1.0
O B:HOH936 2.6 38.4 1.0
O B:HOH818 2.7 38.4 1.0
C B:ASP373 3.6 24.5 1.0
O B:HOH777 4.3 25.7 1.0
CA B:ASP373 4.3 25.0 1.0
O B:HOH973 4.5 41.8 1.0
N B:LYS374 4.6 17.2 1.0
O B:LYS374 4.7 22.1 1.0
CA B:LYS374 4.7 18.5 1.0
CB B:ASP373 4.8 20.8 1.0
OH B:TYR268 4.8 22.8 1.0
C B:LYS374 5.0 22.4 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: Sun Jul 14 20:33:59 2024

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