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Calcium in PDB 6vs7: Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin

Protein crystallography data

The structure of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin, PDB code: 6vs7 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) 50.00 / 2.00
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 (%) 21.1 / 24

Other elements in 6vs7:

The structure of Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin (pdb code 6vs7). 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, PDB code: 6vs7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6vs7

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Calcium binding site 1 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:31.4
occ:1.00
 O A:HOH1060 2.0 34.7 1.0
OD2 A:ASP253 2.3 36.2 1.0
O A:THR255 2.3 31.9 1.0
OD2 A:ASP281 2.4 30.8 1.0
OD1 A:ASP253 2.4 33.5 1.0
OD2 A:ASP355 2.5 33.0 1.0
OD1 A:ASP281 2.6 31.0 1.0
CG A:ASP253 2.6 34.2 1.0
CG A:ASP281 2.8 31.4 1.0
CG A:ASP355 3.5 31.4 1.0
C A:THR255 3.5 31.9 1.0
O A:HOH861 3.8 35.0 1.0
CB A:ASP355 3.9 31.4 1.0
CB A:ASP253 4.1 40.1 1.0
O A:HOH1048 4.3 34.6 1.0
CB A:ASP281 4.3 31.3 1.0
CA A:THR255 4.3 35.1 1.0
ND2 A:ASN359 4.3 30.8 1.0
N A:THR255 4.4 35.2 1.0
CB A:THR255 4.4 34.2 1.0
C A:PRO256 4.5 31.0 1.0
N A:PRO256 4.5 30.5 1.0
OD1 A:ASP355 4.6 31.3 1.0
CA A:PRO256 4.6 31.9 1.0
N A:ASP282 4.6 34.4 1.0
O A:PRO256 4.6 30.7 1.0
OG A:SER283 4.8 35.2 1.0
N A:PRO257 4.9 28.7 1.0
N A:SER283 4.9 34.6 1.0
O A:HOH1136 5.0 36.4 1.0

Calcium binding site 2 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 2 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:22.3
occ:1.00
 O A:THR575 2.4 26.8 1.0
O A:TYR578 2.5 28.7 1.0
OD2 A:ASP644 2.5 31.4 1.0
O A:HOH1187 2.6 34.4 1.0
O A:HOH1152 2.6 35.0 1.0
O A:HOH1090 2.7 37.3 1.0
OD1 A:ASP644 2.7 32.3 1.0
CG A:ASP644 3.0 31.3 1.0
C A:THR575 3.4 31.4 1.0
O A:HOH1181 3.4 65.1 1.0
C A:TYR578 3.7 30.3 1.0
CB A:THR575 3.8 31.3 1.0
CA A:THR575 3.8 29.6 1.0
OH A:TYR633 4.4 23.7 1.0
O A:HOH1056 4.5 38.3 1.0
CB A:ASP644 4.5 30.9 1.0
N A:ASP576 4.5 28.2 1.0
N A:THR579 4.6 30.4 1.0
CA A:THR579 4.6 29.6 1.0
N A:TYR578 4.6 28.9 1.0
OG1 A:THR575 4.7 31.4 1.0
CA A:TYR578 4.7 30.6 1.0
CD A:PRO580 4.7 30.3 1.0
CG2 A:THR575 4.8 37.8 1.0
OG1 A:THR579 4.8 35.6 1.0
O A:HOH867 4.8 35.2 1.0
O A:ARG643 4.8 32.0 1.0
CE2 A:TYR633 4.9 26.9 1.0
O A:HOH1177 4.9 49.6 1.0
CA A:ASP576 4.9 31.2 1.0
CZ A:TYR633 5.0 27.4 1.0

Calcium binding site 3 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 3 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:29.3
occ:1.00
 O A:VAL454 2.2 32.1 1.0
OD1 A:ASN482 2.3 30.6 1.0
OD2 A:ASP556 2.3 31.2 1.0
OD1 A:ASP452 2.4 30.7 1.0
OD1 A:ASP481 2.5 30.0 1.0
OD2 A:ASP452 2.5 32.1 1.0
OD2 A:ASP481 2.6 30.0 1.0
CG A:ASP452 2.8 33.7 1.0
CG A:ASP481 2.9 31.6 1.0
CG A:ASP556 3.4 34.8 1.0
CG A:ASN482 3.4 32.6 1.0
C A:VAL454 3.5 35.7 1.0
CB A:ASP556 4.0 32.3 1.0
ND2 A:ASN482 4.0 36.6 1.0
CB A:ASP452 4.2 34.4 1.0
N A:VAL454 4.3 37.8 1.0
CA A:VAL454 4.3 36.5 1.0
OD1 A:ASP556 4.4 30.1 1.0
N A:ALA455 4.4 35.3 1.0
N A:ASN482 4.4 29.4 1.0
CB A:ASP481 4.4 31.0 1.0
N A:SER483 4.4 29.5 1.0
CA A:ALA455 4.4 35.0 1.0
C A:ALA455 4.5 31.5 1.0
OG A:SER483 4.6 29.0 1.0
O A:HOH1027 4.6 33.9 1.0
CB A:VAL454 4.6 38.5 1.0
CB A:ASN482 4.7 33.0 1.0
CD A:PRO456 4.7 33.6 1.0
N A:PRO456 4.7 31.6 1.0
CB A:SER483 4.7 30.8 1.0
CD1 A:LEU560 4.7 37.8 1.0
O A:HOH898 4.8 35.3 1.0
O A:ALA455 4.9 32.0 1.0
CA A:ASN482 4.9 30.9 1.0
CB A:LEU560 5.0 37.0 1.0

Calcium binding site 4 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 4 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:39.2
occ:1.00
 OD2 A:ASP441 2.2 41.6 1.0
O A:THR379 2.3 32.9 1.0
O A:HOH971 2.5 59.5 1.0
O A:HOH1127 2.7 42.6 1.0
O A:TYR382 2.7 36.8 1.0
O A:HOH1143 2.9 45.9 1.0
OG1 A:THR379 2.9 33.9 1.0
CG A:ASP441 3.1 40.0 1.0
C A:THR379 3.4 34.4 1.0
OD1 A:ASP441 3.5 42.5 1.0
C A:TYR382 3.9 36.4 1.0
CA A:THR379 4.0 32.2 1.0
CB A:THR379 4.0 35.0 1.0
CB A:ASP441 4.4 36.0 1.0
CD A:PRO384 4.4 38.2 1.0
N A:GLU380 4.4 34.5 1.0
OH A:TYR435 4.6 31.6 1.0
CA A:GLU380 4.7 35.1 1.0
CA A:THR383 4.7 38.4 1.0
N A:THR383 4.8 37.2 1.0
CG2 A:THR379 4.8 33.2 1.0
N A:TYR382 4.8 32.4 1.0
CA A:TYR382 4.9 34.2 1.0

Calcium binding site 5 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 5 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:31.9
occ:1.00
 OD2 E:ASP282 2.4 36.7 0.5
OD1 E:ASP281 2.4 32.1 1.0
O E:THR255 2.4 34.4 1.0
OD2 E:ASP355 2.5 34.0 1.0
OD1 E:ASP253 2.5 35.9 1.0
OD2 E:ASP253 2.6 36.8 1.0
OD2 E:ASP281 2.7 37.1 1.0
CG E:ASP281 2.9 35.1 1.0
CG E:ASP253 2.9 39.1 1.0
CG E:ASP282 3.1 36.2 0.5
OD1 E:ASP282 3.3 36.6 0.5
C E:THR255 3.5 34.9 1.0
CG E:ASP355 3.6 34.0 1.0
CB E:ASP355 3.9 33.7 1.0
ND2 E:ASN359 4.2 35.4 1.0
CA E:THR255 4.3 37.6 1.0
CB E:ASP281 4.4 34.4 1.0
CB E:ASP253 4.4 42.4 1.0
N E:THR255 4.4 36.9 1.0
CB E:THR255 4.4 35.7 1.0
C E:PRO256 4.5 31.8 1.0
CB E:ASP282 4.5 36.0 0.5
N E:ASP282 4.6 35.2 0.5
N E:PRO256 4.6 33.5 1.0
N E:ASP282 4.6 35.2 0.5
CA E:PRO256 4.6 29.6 1.0
O E:PRO256 4.7 30.5 1.0
OG E:SER283 4.7 39.0 1.0
N E:SER283 4.7 35.5 1.0
OD1 E:ASP355 4.7 32.6 1.0
CB E:SER283 4.8 37.9 1.0
N E:PRO257 4.8 31.6 1.0
CG2 E:THR255 4.9 39.2 1.0

Calcium binding site 6 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 6 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca702

b:31.4
occ:1.00
 O E:THR379 2.4 29.8 1.0
OD2 E:ASP441 2.4 34.9 1.0
OD1 E:ASP441 2.6 35.8 1.0
O E:HOH1147 2.6 38.4 1.0
O E:TYR382 2.6 33.2 1.0
O E:HOH1068 2.6 38.5 1.0
OG1 E:THR379 2.7 33.9 1.0
CG E:ASP441 2.9 34.5 1.0
O E:HOH1132 2.9 40.2 1.0
C E:THR379 3.4 31.0 1.0
CB E:THR379 3.8 28.9 1.0
CA E:THR379 3.9 29.5 1.0
C E:TYR382 3.9 33.0 1.0
CB E:ASP441 4.4 30.8 1.0
CD E:PRO384 4.4 35.1 1.0
N E:GLU380 4.5 29.2 1.0
OH E:TYR435 4.5 29.4 1.0
CG2 E:THR379 4.7 27.8 1.0
CA E:THR383 4.7 36.3 1.0
N E:THR383 4.7 34.5 1.0
CA E:GLU380 4.8 31.7 1.0
N E:TYR382 4.8 32.3 1.0
CA E:TYR382 4.8 33.0 1.0
CE2 E:TYR435 4.9 27.1 1.0
O E:HOH891 4.9 36.0 1.0
O E:HOH1163 5.0 43.2 1.0
O E:THR440 5.0 31.4 1.0

Calcium binding site 7 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 7 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca703

b:33.8
occ:1.00
 OD1 E:ASN482 2.2 41.0 1.0
O E:VAL454 2.4 43.5 1.0
OD2 E:ASP556 2.4 40.2 1.0
OD1 E:ASP481 2.4 38.1 1.0
OD2 E:ASP481 2.5 38.2 1.0
OD2 E:ASP452 2.6 38.7 1.0
OD1 E:ASP452 2.6 40.3 1.0
CG E:ASP481 2.8 38.6 1.0
CG E:ASP452 2.9 40.1 1.0
CG E:ASN482 3.3 40.1 1.0
CG E:ASP556 3.5 39.7 1.0
C E:VAL454 3.6 45.1 1.0
ND2 E:ASN482 3.8 42.8 1.0
CB E:ASP556 4.0 39.0 1.0
N E:SER483 4.3 39.5 1.0
N E:ASN482 4.3 38.9 1.0
CB E:ASP481 4.3 38.1 1.0
CA E:ALA455 4.4 41.3 1.0
CB E:ASP452 4.4 38.7 1.0
N E:ALA455 4.4 43.1 1.0
C E:ALA455 4.4 38.7 1.0
CD1 E:LEU560 4.5 43.2 1.0
OD1 E:ASP556 4.5 40.5 1.0
CA E:VAL454 4.5 48.1 1.0
N E:VAL454 4.6 45.0 1.0
CB E:SER483 4.6 38.4 1.0
CB E:ASN482 4.6 39.1 1.0
OG E:SER483 4.6 36.1 1.0
O E:ALA455 4.7 39.0 1.0
O E:HOH954 4.7 40.5 1.0
N E:PRO456 4.8 38.3 1.0
CA E:ASN482 4.9 40.1 1.0
CG1 E:VAL454 4.9 47.8 1.0
CG2 E:VAL454 4.9 45.4 1.0
CA E:ASP481 5.0 38.3 1.0
OG E:SER558 5.0 40.9 1.0
C E:ASP481 5.0 42.4 1.0

Calcium binding site 8 out of 8 in 6vs7

Go back to Calcium Binding Sites List in 6vs7
Calcium binding site 8 out of 8 in the Sialic Acid Binding Region of Streptococcus Sanguinis SK1 Adhesin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca704

b:30.4
occ:1.00
 O E:TYR578 2.4 34.7 1.0
O E:THR575 2.4 35.6 1.0
OD2 E:ASP644 2.4 34.8 1.0
O E:HOH991 2.5 38.3 1.0
O E:HOH1075 2.5 36.8 1.0
OG1 E:THR575 2.6 36.0 1.0
OD1 E:ASP644 2.8 35.1 1.0
O E:HOH1099 2.8 37.7 1.0
CG E:ASP644 3.0 36.7 1.0
C E:THR575 3.3 35.1 1.0
C E:TYR578 3.6 33.9 1.0
CB E:THR575 3.8 37.0 1.0
CA E:THR575 3.8 35.5 1.0
OH E:TYR633 4.4 33.1 1.0
N E:TYR578 4.5 32.9 1.0
CB E:ASP644 4.5 35.9 1.0
N E:ASP576 4.5 36.4 1.0
N E:THR579 4.5 34.4 1.0
O E:HOH917 4.5 37.7 1.0
CA E:TYR578 4.5 34.7 1.0
CA E:THR579 4.6 33.2 1.0
O E:HOH944 4.7 47.6 1.0
CG2 E:THR575 4.7 35.0 1.0
CD E:PRO580 4.8 32.5 1.0
CE2 E:TYR633 4.8 34.1 1.0
O E:HOH1146 4.9 35.8 1.0
CA E:ASP576 4.9 38.0 1.0
O E:HOH1203 4.9 56.6 1.0
CZ E:TYR633 5.0 33.3 1.0
OG1 E:THR579 5.0 39.7 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 17:13:37 2024

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