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
Go back to
Calcium Binding Sites List in 6vu6
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 Sites List in 6vu6
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 Sites List in 6vu6
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
Go back to
Calcium Binding Sites List in 6vu6
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
|