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Calcium in PDB 6vu6: Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln

Protein crystallography data

The structure of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln, PDB code: 6vu6 was solved by H.E.Stubbs, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.10 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.213, 269.859, 47.511, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 24.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln (pdb code 6vu6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln, PDB code: 6vu6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6vu6

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Calcium binding site 1 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:39.2
occ:1.00
 OD2 A:ASP253 2.3 39.5 1.0
OD1 A:ASP282 2.3 62.3 1.0
OD2 A:ASP281 2.4 33.4 1.0
O A:THR255 2.5 31.7 1.0
OD1 A:ASP253 2.5 39.6 1.0
OD1 A:ASP281 2.5 33.8 1.0
OD2 A:ASP355 2.7 37.1 1.0
CG A:ASP253 2.7 39.8 1.0
CG A:ASP281 2.8 34.1 1.0
CG A:ASP282 3.4 60.1 1.0
C A:THR255 3.6 34.5 1.0
CG A:ASP355 3.7 38.1 1.0
OD2 A:ASP282 3.7 63.5 1.0
CB A:THR255 4.2 40.5 1.0
N A:THR255 4.2 37.5 1.0
CA A:THR255 4.2 38.1 1.0
ND2 A:ASN359 4.2 37.3 1.0
CB A:ASP253 4.2 38.1 1.0
CB A:ASP355 4.2 37.6 1.0
CB A:ASP281 4.3 32.4 1.0
N A:SER283 4.5 41.0 1.0
N A:ASP282 4.5 28.4 1.0
N A:PRO256 4.6 34.5 1.0
C A:PRO256 4.6 29.3 1.0
CB A:SER283 4.6 40.4 1.0
O A:PRO256 4.7 26.0 1.0
CB A:ASP282 4.7 50.4 1.0
OD1 A:ASP355 4.7 35.8 1.0
CA A:PRO256 4.7 31.4 1.0
O A:HOH894 4.7 35.8 1.0
CG2 A:THR255 4.8 39.4 1.0
OG A:SER283 4.8 41.7 1.0

Calcium binding site 2 out of 8 in 6vu6

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Calcium binding site 2 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:49.4
occ:1.00
 O A:THR379 2.3 46.2 1.0
O A:TYR382 2.4 42.5 1.0
O A:HOH950 2.6 46.5 1.0
OD2 A:ASP441 2.7 44.5 1.0
OG1 A:THR379 2.8 42.5 1.0
C A:THR379 3.2 43.7 1.0
CG A:ASP441 3.3 43.3 1.0
OD1 A:ASP441 3.5 44.5 1.0
C A:TYR382 3.6 42.4 1.0
CA A:THR379 3.7 37.8 1.0
CB A:THR379 3.8 37.7 1.0
CD A:PRO384 4.3 42.7 1.0
N A:GLU380 4.4 39.8 1.0
N A:THR383 4.5 45.1 1.0
CA A:THR383 4.5 46.7 1.0
CA A:TYR382 4.5 42.3 1.0
CB A:ASP441 4.5 38.2 1.0
N A:TYR382 4.6 39.2 1.0
OH A:TYR435 4.6 41.1 1.0
CG2 A:THR379 4.7 31.2 1.0
CA A:GLU380 4.8 40.6 1.0
O A:THR440 4.8 36.0 1.0
CE2 A:TYR435 4.9 39.2 1.0

Calcium binding site 3 out of 8 in 6vu6

Go back to Calcium Binding Sites List in 6vu6
Calcium binding site 3 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:34.9
occ:1.00
 OD2 A:ASP556 2.1 31.6 1.0
OD1 A:ASN482 2.4 35.0 1.0
OD2 A:ASP481 2.5 25.7 1.0
OD1 A:ASP452 2.6 34.4 1.0
O A:VAL454 2.7 30.6 1.0
OD1 A:ASP481 2.8 30.1 1.0
OD2 A:ASP452 2.8 40.3 1.0
CG A:ASP481 3.0 32.1 1.0
CG A:ASP452 3.1 40.4 1.0
CG A:ASP556 3.3 33.8 1.0
CG A:ASN482 3.5 30.4 1.0
C A:VAL454 3.6 32.8 1.0
ND2 A:ASN482 3.9 30.0 1.0
CB A:ASP556 3.9 35.4 1.0
OD1 A:ASP556 4.3 33.5 1.0
O A:HOH818 4.3 36.9 1.0
N A:SER483 4.4 32.9 1.0
N A:ALA455 4.5 31.4 1.0
N A:VAL454 4.5 33.0 1.0
CB A:SER483 4.5 29.3 1.0
OG A:SER483 4.5 32.5 1.0
CA A:ALA455 4.5 33.2 1.0
CB A:ASP481 4.6 30.1 1.0
CB A:ASP452 4.6 32.5 1.0
CA A:VAL454 4.6 35.5 1.0
N A:ASN482 4.6 31.0 1.0
C A:ALA455 4.7 32.1 1.0
CB A:ASN482 4.8 29.2 1.0
CD1 A:LEU560 4.9 43.4 1.0
OG A:SER558 5.0 29.8 1.0
N A:PRO456 5.0 28.1 1.0

Calcium binding site 4 out of 8 in 6vu6

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Calcium binding site 4 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:40.4
occ:1.00
 O A:HOH807 1.9 50.1 1.0
O A:HOH878 2.0 44.5 1.0
O A:HOH915 2.3 41.7 1.0
O A:TYR578 2.5 43.6 1.0
O A:THR575 2.6 41.3 1.0
OD2 A:ASP644 2.7 37.6 1.0
OD1 A:ASP644 2.8 36.4 1.0
OG1 A:THR575 3.1 35.8 1.0
CG A:ASP644 3.1 36.9 1.0
C A:THR575 3.3 33.9 1.0
C A:TYR578 3.7 42.0 1.0
CA A:THR575 3.8 31.3 1.0
CB A:THR575 4.1 30.6 1.0
N A:ASP576 4.4 34.9 1.0
OH A:TYR633 4.5 34.3 1.0
N A:TYR578 4.5 35.3 1.0
N A:THR579 4.5 40.2 1.0
OG1 A:THR579 4.5 45.9 1.0
CA A:THR579 4.5 39.9 1.0
CB A:ASP644 4.6 32.2 1.0
CA A:TYR578 4.6 35.5 1.0
CA A:ASP576 4.8 40.0 1.0
CD A:PRO580 4.9 32.9 1.0
C A:ASP576 4.9 40.1 1.0
CG2 A:THR575 4.9 30.9 1.0

Calcium binding site 5 out of 8 in 6vu6

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Calcium binding site 5 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:33.1
occ:1.00
 OD2 E:ASP355 2.2 36.9 1.0
OD1 E:ASP253 2.4 43.7 1.0
OD2 E:ASP281 2.4 31.1 1.0
O E:THR255 2.5 28.6 1.0
OD1 E:ASP281 2.6 29.6 1.0
OD1 E:ASP282 2.6 50.3 1.0
OD2 E:ASP253 2.7 41.5 1.0
CG E:ASP253 2.8 44.7 1.0
CG E:ASP281 2.8 33.7 1.0
CG E:ASP355 3.4 35.7 1.0
CG E:ASP282 3.6 49.6 1.0
C E:THR255 3.7 30.9 1.0
OD2 E:ASP282 4.0 53.1 1.0
CB E:ASP355 4.1 31.2 1.0
ND2 E:ASN359 4.2 31.7 1.0
CB E:ASP253 4.3 42.7 1.0
CB E:ASP281 4.3 30.6 1.0
N E:ASP282 4.3 26.6 1.0
OD1 E:ASP355 4.4 32.9 1.0
CB E:THR255 4.5 49.1 1.0
N E:PRO256 4.5 32.3 1.0
N E:THR255 4.5 39.1 1.0
CA E:PRO256 4.5 32.6 1.0
C E:PRO256 4.5 27.9 1.0
N E:SER283 4.5 36.7 1.0
CA E:THR255 4.6 40.0 1.0
O E:PRO256 4.6 24.9 1.0
OG E:SER283 4.7 40.1 1.0
CB E:ASP282 4.8 40.9 1.0
O E:HOH853 4.8 38.1 1.0
CB E:SER283 4.8 39.2 1.0
CB E:ASN359 5.0 32.1 1.0
CA E:ASP282 5.0 34.9 1.0

Calcium binding site 6 out of 8 in 6vu6

Go back to Calcium Binding Sites List in 6vu6
Calcium binding site 6 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca702

b:47.8
occ:1.00
 O E:TYR382 2.4 36.6 1.0
O E:THR379 2.5 38.5 1.0
OG1 E:THR379 2.7 32.6 1.0
OD2 E:ASP441 2.9 44.0 1.0
OD1 E:ASP441 2.9 45.8 1.0
O E:HOH934 2.9 41.0 1.0
O E:HOH913 3.3 42.3 1.0
CG E:ASP441 3.3 46.0 1.0
C E:THR379 3.5 38.4 1.0
C E:TYR382 3.6 37.6 1.0
CB E:THR379 3.9 27.4 1.0
CA E:THR379 4.0 30.8 1.0
OH E:TYR435 4.3 35.7 1.0
CD E:PRO384 4.4 42.1 1.0
N E:THR383 4.4 38.6 1.0
CA E:THR383 4.4 41.8 1.0
CA E:TYR382 4.6 36.6 1.0
N E:GLU380 4.6 33.2 1.0
CE2 E:TYR435 4.7 28.5 1.0
N E:TYR382 4.7 36.1 1.0
CB E:ASP441 4.7 42.1 1.0
CG2 E:THR379 4.8 26.6 1.0
O E:THR440 4.9 32.9 1.0
CZ E:TYR435 4.9 30.7 1.0

Calcium binding site 7 out of 8 in 6vu6

Go back to Calcium Binding Sites List in 6vu6
Calcium binding site 7 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca703

b:38.5
occ:1.00
 O E:VAL454 2.0 38.0 1.0
OD2 E:ASP556 2.2 38.2 1.0
OD1 E:ASP452 2.4 36.7 1.0
OD1 E:ASN482 2.6 40.4 1.0
OD2 E:ASP452 2.7 42.7 1.0
OD1 E:ASP481 2.7 35.9 1.0
OD2 E:ASP481 2.9 38.5 1.0
CG E:ASP452 2.9 39.8 1.0
CG E:ASP481 3.2 37.9 1.0
C E:VAL454 3.2 39.2 1.0
CG E:ASP556 3.4 39.4 1.0
CG E:ASN482 3.7 45.1 1.0
CB E:ASP556 4.0 38.9 1.0
N E:ALA455 4.1 43.2 1.0
CA E:ALA455 4.2 41.6 1.0
N E:ASN482 4.3 39.7 1.0
CA E:VAL454 4.3 42.6 1.0
N E:VAL454 4.3 40.8 1.0
C E:ALA455 4.3 34.9 1.0
ND2 E:ASN482 4.3 48.0 1.0
N E:SER483 4.4 39.3 1.0
OD1 E:ASP556 4.4 35.1 1.0
O E:HOH837 4.4 39.8 1.0
CB E:ASP452 4.4 39.1 1.0
CG2 E:VAL454 4.6 46.7 1.0
CB E:ASP481 4.6 31.6 1.0
CD1 E:LEU560 4.6 45.9 1.0
O E:ALA455 4.6 29.1 1.0
N E:PRO456 4.6 37.0 1.0
OG E:SER483 4.7 39.6 1.0
CB E:VAL454 4.8 46.7 1.0
CB E:SER483 4.8 37.6 1.0
CG1 E:VAL454 4.8 47.1 1.0
CD E:PRO456 4.9 35.5 1.0
CB E:ASN482 4.9 43.5 1.0
CA E:ASN482 4.9 41.9 1.0
OG E:SER558 5.0 51.3 1.0
O E:HOH829 5.0 39.7 1.0

Calcium binding site 8 out of 8 in 6vu6

Go back to Calcium Binding Sites List in 6vu6
Calcium binding site 8 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin Bound to 3'Sln within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca704

b:37.0
occ:1.00
 OD2 E:ASP644 2.3 33.0 1.0
O E:TYR578 2.5 35.1 1.0
O E:THR575 2.5 42.6 1.0
OD1 E:ASP644 2.8 33.0 1.0
O E:HOH927 2.8 38.5 1.0
CG E:ASP644 2.9 32.2 1.0
O E:HOH928 2.9 40.2 1.0
O E:HOH828 2.9 42.1 1.0
OG1 E:THR575 2.9 34.5 1.0
C E:THR575 3.5 38.3 1.0
C E:TYR578 3.7 35.1 1.0
CA E:THR575 4.0 32.5 1.0
CB E:THR575 4.1 31.4 1.0
CB E:ASP644 4.3 26.2 1.0
OH E:TYR633 4.5 27.8 1.0
N E:THR579 4.5 33.6 1.0
CA E:THR579 4.6 33.3 1.0
OG1 E:THR579 4.6 39.1 1.0
N E:ASP576 4.6 37.0 1.0
N E:TYR578 4.6 33.5 1.0
CA E:TYR578 4.7 33.1 1.0
CD E:PRO580 4.8 28.0 1.0
O E:ARG643 5.0 33.1 1.0

Reference:

H.E.Stubbs, T.M.Iverson. Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin To Be Published.
Page generated: Tue Jul 16 17:14:06 2024

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