Calcium in PDB 5hlv: Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
Protein crystallography data
The structure of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121, PDB code: 5hlv
was solved by
H.Lin,
G.R.Andersen,
L.Yatime,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.26 /
2.20
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.930,
85.090,
197.200,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.2 /
21.7
|
Other elements in 5hlv:
The structure of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
(pdb code 5hlv). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121, PDB code: 5hlv:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 1 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca101
b:39.1
occ:1.00
|
O
|
A:ASN25
|
2.4
|
27.1
|
1.0
|
|
O
|
A:LYS23
|
2.4
|
20.0
|
1.0
|
|
O
|
A:SER20
|
2.4
|
23.4
|
1.0
|
|
O
|
A:ALA28
|
2.4
|
20.7
|
1.0
|
|
O
|
A:HOH215
|
2.5
|
21.1
|
1.0
|
|
C
|
A:SER20
|
3.3
|
15.7
|
1.0
|
|
C
|
A:ASN25
|
3.4
|
25.6
|
1.0
|
|
C
|
A:ALA28
|
3.6
|
18.9
|
1.0
|
|
C
|
A:LYS23
|
3.6
|
24.1
|
1.0
|
|
CE2
|
A:TYR30
|
3.7
|
19.4
|
1.0
|
|
CA
|
A:SER20
|
3.7
|
20.2
|
1.0
|
|
N
|
A:LYS23
|
3.9
|
22.9
|
1.0
|
|
CA
|
A:PHE26
|
4.0
|
25.7
|
1.0
|
|
N
|
A:ALA28
|
4.0
|
16.9
|
1.0
|
|
N
|
A:PHE26
|
4.1
|
25.3
|
1.0
|
|
CD2
|
A:TYR30
|
4.1
|
20.8
|
1.0
|
|
CA
|
A:ALA28
|
4.2
|
17.3
|
1.0
|
|
N
|
A:ASN25
|
4.3
|
23.3
|
1.0
|
|
C
|
A:GLY24
|
4.3
|
25.5
|
1.0
|
|
CB
|
A:ALA28
|
4.3
|
15.4
|
1.0
|
|
CA
|
A:LYS23
|
4.4
|
24.1
|
1.0
|
|
O
|
A:TYR19
|
4.4
|
24.0
|
1.0
|
|
N
|
A:LEU21
|
4.4
|
19.7
|
1.0
|
|
CA
|
A:ASN25
|
4.5
|
23.8
|
1.0
|
|
OD2
|
A:ASP33
|
4.5
|
24.6
|
1.0
|
|
C
|
A:PHE26
|
4.5
|
25.7
|
1.0
|
|
N
|
A:ILE22
|
4.5
|
22.4
|
1.0
|
|
CB
|
A:SER20
|
4.5
|
21.3
|
1.0
|
|
N
|
A:GLY24
|
4.6
|
25.2
|
1.0
|
|
CZ
|
A:TYR30
|
4.6
|
21.5
|
1.0
|
|
CD1
|
A:PHE26
|
4.6
|
29.9
|
1.0
|
|
O
|
A:GLY24
|
4.6
|
26.6
|
1.0
|
|
N
|
A:VAL29
|
4.7
|
19.2
|
1.0
|
|
CA
|
A:GLY24
|
4.7
|
23.3
|
1.0
|
|
OH
|
A:TYR30
|
4.8
|
21.2
|
1.0
|
|
N
|
A:HIS27
|
4.8
|
24.3
|
1.0
|
|
CA
|
A:LEU21
|
4.8
|
23.2
|
1.0
|
|
C
|
A:LEU21
|
4.9
|
23.9
|
1.0
|
|
N
|
A:SER20
|
4.9
|
21.1
|
1.0
|
|
CA
|
A:VAL29
|
5.0
|
14.6
|
1.0
|
|
O
|
A:PHE26
|
5.0
|
24.9
|
1.0
|
|
C
|
A:ILE22
|
5.0
|
22.5
|
1.0
|
|
Calcium binding site 2 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 2 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca102
b:19.5
occ:1.00
|
OD1
|
A:ASP59
|
2.3
|
22.2
|
1.0
|
|
OD1
|
A:ASN61
|
2.4
|
20.3
|
1.0
|
|
O
|
A:HOH210
|
2.4
|
22.6
|
1.0
|
|
O
|
A:ALA65
|
2.4
|
20.5
|
1.0
|
|
OD1
|
A:ASP63
|
2.4
|
22.9
|
1.0
|
|
OE2
|
A:GLU70
|
2.5
|
16.1
|
1.0
|
|
OE1
|
A:GLU70
|
2.5
|
15.5
|
1.0
|
|
CD
|
A:GLU70
|
2.8
|
14.8
|
1.0
|
|
CG
|
A:ASP63
|
3.2
|
23.4
|
1.0
|
|
CG
|
A:ASP59
|
3.4
|
21.4
|
1.0
|
|
OD2
|
A:ASP63
|
3.4
|
25.7
|
1.0
|
|
CG
|
A:ASN61
|
3.5
|
24.6
|
1.0
|
|
C
|
A:ALA65
|
3.6
|
19.0
|
1.0
|
|
CA
|
A:ASP59
|
4.0
|
18.3
|
1.0
|
|
ND2
|
A:ASN61
|
4.1
|
20.5
|
1.0
|
|
CB
|
A:ASP59
|
4.2
|
17.7
|
1.0
|
|
N
|
A:ASP63
|
4.2
|
24.2
|
1.0
|
|
OD2
|
A:ASP59
|
4.3
|
22.8
|
1.0
|
|
CG
|
A:GLU70
|
4.3
|
17.3
|
1.0
|
|
C
|
A:ASP59
|
4.3
|
21.2
|
1.0
|
|
N
|
A:ILE60
|
4.3
|
23.3
|
1.0
|
|
N
|
A:ASN61
|
4.3
|
21.5
|
1.0
|
|
OXT
|
A:ACT105
|
4.3
|
37.5
|
1.0
|
|
N
|
A:ALA65
|
4.4
|
18.7
|
1.0
|
|
CB
|
A:ASP63
|
4.4
|
22.9
|
1.0
|
|
CA
|
A:VAL66
|
4.5
|
21.8
|
1.0
|
|
N
|
A:VAL66
|
4.5
|
18.4
|
1.0
|
|
O
|
A:ACT105
|
4.5
|
30.7
|
1.0
|
|
N
|
A:ASN67
|
4.6
|
18.3
|
1.0
|
|
N
|
A:THR62
|
4.6
|
24.6
|
1.0
|
|
CA
|
A:ALA65
|
4.6
|
19.2
|
1.0
|
|
CB
|
A:ASN61
|
4.7
|
22.0
|
1.0
|
|
C
|
A:ACT105
|
4.8
|
35.1
|
1.0
|
|
CA
|
A:ASP63
|
4.8
|
24.3
|
1.0
|
|
CA
|
A:ASN61
|
4.9
|
22.9
|
1.0
|
|
C
|
A:ASN61
|
4.9
|
23.5
|
1.0
|
|
CG
|
A:ASN67
|
5.0
|
27.5
|
1.0
|
|
C
|
A:VAL66
|
5.0
|
20.7
|
1.0
|
|
Calcium binding site 3 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 3 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca101
b:49.3
occ:1.00
|
O
|
B:LYS23
|
2.3
|
22.7
|
1.0
|
|
O
|
B:ASN25
|
2.4
|
20.1
|
1.0
|
|
O
|
B:SER20
|
2.4
|
25.2
|
1.0
|
|
O
|
B:HOH209
|
2.4
|
18.2
|
1.0
|
|
O
|
B:ALA28
|
2.4
|
26.3
|
1.0
|
|
C
|
B:SER20
|
3.3
|
22.7
|
1.0
|
|
C
|
B:ASN25
|
3.5
|
26.1
|
1.0
|
|
C
|
B:LYS23
|
3.6
|
24.8
|
1.0
|
|
C
|
B:ALA28
|
3.6
|
23.9
|
1.0
|
|
CE2
|
B:TYR30
|
3.6
|
17.8
|
1.0
|
|
CA
|
B:SER20
|
3.7
|
22.8
|
1.0
|
|
N
|
B:LYS23
|
4.0
|
28.5
|
1.0
|
|
CD2
|
B:TYR30
|
4.0
|
17.0
|
1.0
|
|
N
|
B:ASN25
|
4.2
|
21.8
|
1.0
|
|
N
|
B:ALA28
|
4.2
|
25.4
|
1.0
|
|
O
|
B:TYR19
|
4.3
|
24.1
|
1.0
|
|
CA
|
B:PHE26
|
4.3
|
32.5
|
1.0
|
|
N
|
B:PHE26
|
4.3
|
27.1
|
1.0
|
|
C
|
B:GLY24
|
4.3
|
24.9
|
1.0
|
|
CA
|
B:ALA28
|
4.3
|
24.3
|
1.0
|
|
N
|
B:LEU21
|
4.4
|
26.9
|
1.0
|
|
CA
|
B:LYS23
|
4.4
|
27.7
|
1.0
|
|
CA
|
B:ASN25
|
4.5
|
27.6
|
1.0
|
|
OD2
|
B:ASP33
|
4.5
|
25.9
|
1.0
|
|
CB
|
B:SER20
|
4.5
|
18.1
|
1.0
|
|
CZ
|
B:TYR30
|
4.5
|
17.9
|
1.0
|
|
N
|
B:ILE22
|
4.5
|
27.3
|
1.0
|
|
N
|
B:GLY24
|
4.5
|
24.1
|
1.0
|
|
CB
|
B:ALA28
|
4.5
|
24.7
|
1.0
|
|
N
|
B:VAL29
|
4.6
|
22.0
|
1.0
|
|
CA
|
B:GLY24
|
4.7
|
23.2
|
1.0
|
|
O
|
B:GLY24
|
4.7
|
26.8
|
1.0
|
|
C
|
B:PHE26
|
4.7
|
35.3
|
1.0
|
|
OH
|
B:TYR30
|
4.7
|
22.0
|
1.0
|
|
CA
|
B:VAL29
|
4.8
|
19.0
|
1.0
|
|
CA
|
B:LEU21
|
4.9
|
30.2
|
1.0
|
|
N
|
B:SER20
|
4.9
|
21.0
|
1.0
|
|
C
|
B:LEU21
|
4.9
|
28.0
|
1.0
|
|
Calcium binding site 4 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 4 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca102
b:20.0
occ:1.00
|
O
|
B:ALA65
|
2.3
|
20.0
|
1.0
|
|
OD1
|
B:ASP59
|
2.4
|
17.9
|
1.0
|
|
OD1
|
B:ASN61
|
2.4
|
16.9
|
1.0
|
|
O
|
B:HOH210
|
2.4
|
19.4
|
1.0
|
|
OD1
|
B:ASP63
|
2.4
|
24.3
|
1.0
|
|
OE1
|
B:GLU70
|
2.5
|
16.2
|
1.0
|
|
OE2
|
B:GLU70
|
2.5
|
20.7
|
1.0
|
|
CD
|
B:GLU70
|
2.8
|
19.2
|
1.0
|
|
CG
|
B:ASP63
|
3.2
|
23.8
|
1.0
|
|
OD2
|
B:ASP63
|
3.4
|
24.1
|
1.0
|
|
CG
|
B:ASP59
|
3.5
|
18.4
|
1.0
|
|
CG
|
B:ASN61
|
3.5
|
17.6
|
1.0
|
|
C
|
B:ALA65
|
3.5
|
19.5
|
1.0
|
|
CA
|
B:ASP59
|
4.0
|
16.5
|
1.0
|
|
OXT
|
B:ACT104
|
4.1
|
40.6
|
1.0
|
|
ND2
|
B:ASN61
|
4.1
|
18.3
|
1.0
|
|
CB
|
B:ASP59
|
4.2
|
14.9
|
1.0
|
|
N
|
B:ASP63
|
4.3
|
21.3
|
1.0
|
|
N
|
B:ALA65
|
4.3
|
19.5
|
1.0
|
|
CG
|
B:GLU70
|
4.3
|
16.6
|
1.0
|
|
N
|
B:VAL66
|
4.4
|
18.0
|
1.0
|
|
CA
|
B:VAL66
|
4.4
|
18.8
|
1.0
|
|
C
|
B:ASP59
|
4.4
|
19.0
|
1.0
|
|
OD2
|
B:ASP59
|
4.4
|
17.8
|
1.0
|
|
N
|
B:ASN61
|
4.5
|
20.6
|
1.0
|
|
CB
|
B:ASP63
|
4.5
|
20.1
|
1.0
|
|
CA
|
B:ALA65
|
4.5
|
22.3
|
1.0
|
|
N
|
B:ASN67
|
4.5
|
17.1
|
1.0
|
|
N
|
B:ILE60
|
4.5
|
17.0
|
1.0
|
|
N
|
B:THR62
|
4.6
|
20.0
|
1.0
|
|
O
|
B:ACT104
|
4.7
|
36.7
|
1.0
|
|
CB
|
B:ASN61
|
4.7
|
22.8
|
1.0
|
|
ND2
|
B:ASN67
|
4.8
|
34.0
|
1.0
|
|
C
|
B:ACT104
|
4.8
|
38.8
|
1.0
|
|
CA
|
B:ASP63
|
4.8
|
18.6
|
1.0
|
|
CG
|
B:ASN67
|
4.9
|
29.7
|
1.0
|
|
CA
|
B:ASN61
|
4.9
|
22.0
|
1.0
|
|
C
|
B:VAL66
|
4.9
|
19.4
|
1.0
|
|
C
|
B:ASN61
|
4.9
|
23.4
|
1.0
|
|
N
|
B:GLY64
|
5.0
|
20.1
|
1.0
|
|
Calcium binding site 5 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 5 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca101
b:50.3
occ:1.00
|
O
|
C:LYS23
|
2.3
|
28.6
|
1.0
|
|
O
|
C:SER20
|
2.4
|
28.1
|
1.0
|
|
O
|
C:ASN25
|
2.4
|
27.5
|
1.0
|
|
O
|
C:HOH215
|
2.4
|
17.1
|
1.0
|
|
O
|
C:ALA28
|
2.4
|
27.1
|
1.0
|
|
C
|
C:SER20
|
3.3
|
30.8
|
1.0
|
|
C
|
C:ALA28
|
3.5
|
27.2
|
1.0
|
|
C
|
C:LYS23
|
3.6
|
30.8
|
1.0
|
|
C
|
C:ASN25
|
3.6
|
30.9
|
1.0
|
|
CE2
|
C:TYR30
|
3.6
|
24.4
|
1.0
|
|
CA
|
C:SER20
|
3.8
|
28.8
|
1.0
|
|
N
|
C:ASN25
|
3.9
|
35.9
|
1.0
|
|
N
|
C:LYS23
|
4.0
|
31.6
|
1.0
|
|
N
|
C:ALA28
|
4.0
|
25.1
|
1.0
|
|
CA
|
C:ALA28
|
4.1
|
24.6
|
1.0
|
|
C
|
C:GLY24
|
4.1
|
39.8
|
1.0
|
|
CD2
|
C:TYR30
|
4.2
|
23.6
|
1.0
|
|
CB
|
C:ALA28
|
4.2
|
21.4
|
1.0
|
|
N
|
C:LEU21
|
4.3
|
33.7
|
1.0
|
|
CA
|
C:ASN25
|
4.3
|
32.8
|
1.0
|
|
CA
|
C:LYS23
|
4.4
|
35.9
|
1.0
|
|
N
|
C:GLY24
|
4.5
|
31.8
|
1.0
|
|
CZ
|
C:TYR30
|
4.5
|
25.1
|
1.0
|
|
O
|
C:TYR19
|
4.5
|
29.4
|
1.0
|
|
CB
|
C:SER20
|
4.5
|
24.8
|
1.0
|
|
N
|
C:ILE22
|
4.5
|
31.1
|
1.0
|
|
CA
|
C:GLY24
|
4.5
|
32.5
|
1.0
|
|
N
|
C:PHE26
|
4.6
|
33.8
|
1.0
|
|
O
|
C:GLY24
|
4.6
|
44.3
|
1.0
|
|
N
|
C:VAL29
|
4.6
|
25.4
|
1.0
|
|
OD2
|
C:ASP33
|
4.6
|
31.4
|
1.0
|
|
OH
|
C:TYR30
|
4.7
|
26.7
|
1.0
|
|
CA
|
C:LEU21
|
4.7
|
38.7
|
1.0
|
|
CA
|
C:PHE26
|
4.7
|
33.8
|
1.0
|
|
C
|
C:PHE26
|
4.8
|
33.4
|
1.0
|
|
C
|
C:LEU21
|
4.9
|
32.7
|
1.0
|
|
CA
|
C:VAL29
|
4.9
|
24.6
|
1.0
|
|
N
|
C:SER20
|
5.0
|
26.6
|
1.0
|
|
Calcium binding site 6 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 6 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca102
b:21.3
occ:1.00
|
OD1
|
C:ASN61
|
2.3
|
19.0
|
1.0
|
|
OD1
|
C:ASP59
|
2.4
|
25.0
|
1.0
|
|
O
|
C:ALA65
|
2.4
|
20.5
|
1.0
|
|
O
|
C:HOH214
|
2.4
|
23.2
|
1.0
|
|
OD1
|
C:ASP63
|
2.4
|
28.9
|
1.0
|
|
OE1
|
C:GLU70
|
2.5
|
21.1
|
1.0
|
|
OE2
|
C:GLU70
|
2.5
|
21.2
|
1.0
|
|
CD
|
C:GLU70
|
2.9
|
19.6
|
1.0
|
|
CG
|
C:ASP63
|
3.1
|
27.1
|
1.0
|
|
OD2
|
C:ASP63
|
3.3
|
28.9
|
1.0
|
|
CG
|
C:ASN61
|
3.5
|
21.6
|
1.0
|
|
CG
|
C:ASP59
|
3.5
|
24.3
|
1.0
|
|
C
|
C:ALA65
|
3.6
|
21.8
|
1.0
|
|
CA
|
C:ASP59
|
4.0
|
19.7
|
1.0
|
|
ND2
|
C:ASN61
|
4.1
|
20.4
|
1.0
|
|
N
|
C:ASP63
|
4.1
|
23.8
|
1.0
|
|
O
|
C:ACT105
|
4.3
|
37.5
|
1.0
|
|
CB
|
C:ASP59
|
4.3
|
19.6
|
1.0
|
|
CB
|
C:ASP63
|
4.3
|
25.9
|
1.0
|
|
N
|
C:ALA65
|
4.3
|
20.4
|
1.0
|
|
N
|
C:ASN61
|
4.3
|
20.8
|
1.0
|
|
N
|
C:ILE60
|
4.3
|
19.0
|
1.0
|
|
C
|
C:ASP59
|
4.3
|
20.6
|
1.0
|
|
CG
|
C:GLU70
|
4.4
|
19.9
|
1.0
|
|
OD2
|
C:ASP59
|
4.4
|
23.9
|
1.0
|
|
N
|
C:VAL66
|
4.5
|
17.4
|
1.0
|
|
CA
|
C:VAL66
|
4.5
|
20.4
|
1.0
|
|
OXT
|
C:ACT105
|
4.5
|
30.3
|
1.0
|
|
N
|
C:THR62
|
4.5
|
25.0
|
1.0
|
|
N
|
C:ASN67
|
4.6
|
21.2
|
1.0
|
|
CA
|
C:ALA65
|
4.6
|
17.7
|
1.0
|
|
CB
|
C:ASN61
|
4.7
|
22.6
|
1.0
|
|
CA
|
C:ASP63
|
4.7
|
24.4
|
1.0
|
|
C
|
C:ACT105
|
4.8
|
34.2
|
1.0
|
|
CA
|
C:ASN61
|
4.8
|
21.7
|
1.0
|
|
C
|
C:ASN61
|
4.9
|
25.7
|
1.0
|
|
OD1
|
C:ASN67
|
5.0
|
30.0
|
1.0
|
|
N
|
C:GLY64
|
5.0
|
25.0
|
1.0
|
|
Calcium binding site 7 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 7 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca101
b:37.9
occ:1.00
|
O
|
D:LYS23
|
2.3
|
26.9
|
1.0
|
|
O
|
D:SER20
|
2.3
|
24.0
|
1.0
|
|
O
|
D:ALA28
|
2.4
|
22.9
|
1.0
|
|
O
|
D:ASN25
|
2.4
|
25.5
|
1.0
|
|
O
|
D:HOH215
|
2.5
|
25.1
|
1.0
|
|
C
|
D:SER20
|
3.2
|
22.5
|
1.0
|
|
C
|
D:LYS23
|
3.5
|
28.7
|
1.0
|
|
C
|
D:ALA28
|
3.5
|
23.7
|
1.0
|
|
C
|
D:ASN25
|
3.5
|
29.5
|
1.0
|
|
CA
|
D:SER20
|
3.6
|
21.1
|
1.0
|
|
CE2
|
D:TYR30
|
3.9
|
30.0
|
1.0
|
|
N
|
D:LYS23
|
4.0
|
29.0
|
1.0
|
|
N
|
D:ALA28
|
4.0
|
24.1
|
1.0
|
|
N
|
D:ASN25
|
4.1
|
26.1
|
1.0
|
|
C
|
D:GLY24
|
4.1
|
33.7
|
1.0
|
|
CA
|
D:ALA28
|
4.1
|
24.4
|
1.0
|
|
CB
|
D:ALA28
|
4.2
|
21.8
|
1.0
|
|
CD2
|
D:TYR30
|
4.2
|
31.3
|
1.0
|
|
N
|
D:LEU21
|
4.3
|
23.4
|
1.0
|
|
CB
|
D:SER20
|
4.3
|
25.2
|
1.0
|
|
O
|
D:GLY24
|
4.4
|
27.6
|
1.0
|
|
O
|
D:TYR19
|
4.4
|
31.0
|
1.0
|
|
N
|
D:PHE26
|
4.4
|
28.6
|
1.0
|
|
CA
|
D:LYS23
|
4.4
|
34.1
|
1.0
|
|
CA
|
D:ASN25
|
4.4
|
32.9
|
1.0
|
|
CA
|
D:PHE26
|
4.4
|
28.4
|
1.0
|
|
N
|
D:GLY24
|
4.4
|
29.7
|
1.0
|
|
CA
|
D:GLY24
|
4.5
|
28.9
|
1.0
|
|
N
|
D:ILE22
|
4.5
|
30.2
|
1.0
|
|
C
|
D:PHE26
|
4.6
|
31.5
|
1.0
|
|
OD2
|
D:ASP33
|
4.6
|
36.1
|
1.0
|
|
N
|
D:VAL29
|
4.6
|
24.4
|
1.0
|
|
CA
|
D:LEU21
|
4.8
|
29.4
|
1.0
|
|
N
|
D:SER20
|
4.8
|
25.4
|
1.0
|
|
CZ
|
D:TYR30
|
4.9
|
30.7
|
1.0
|
|
O
|
D:PHE26
|
4.9
|
30.5
|
1.0
|
|
C
|
D:LEU21
|
4.9
|
31.5
|
1.0
|
|
N
|
D:HIS27
|
4.9
|
31.0
|
1.0
|
|
CA
|
D:VAL29
|
5.0
|
26.4
|
1.0
|
|
Calcium binding site 8 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 8 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca102
b:25.7
occ:1.00
|
OD1
|
D:ASN61
|
2.3
|
36.0
|
1.0
|
|
O
|
D:ALA65
|
2.3
|
26.4
|
1.0
|
|
OD1
|
D:ASP63
|
2.4
|
37.0
|
1.0
|
|
O
|
D:HOH216
|
2.4
|
31.3
|
1.0
|
|
OD1
|
D:ASP59
|
2.4
|
27.5
|
1.0
|
|
OE1
|
D:GLU70
|
2.5
|
21.8
|
1.0
|
|
OE2
|
D:GLU70
|
2.5
|
21.9
|
1.0
|
|
CD
|
D:GLU70
|
2.8
|
21.6
|
1.0
|
|
CG
|
D:ASP63
|
3.3
|
36.5
|
1.0
|
|
CG
|
D:ASN61
|
3.4
|
36.8
|
1.0
|
|
C
|
D:ALA65
|
3.5
|
26.6
|
1.0
|
|
OD2
|
D:ASP63
|
3.6
|
36.9
|
1.0
|
|
CG
|
D:ASP59
|
3.6
|
28.5
|
1.0
|
|
ND2
|
D:ASN61
|
4.0
|
37.1
|
1.0
|
|
CA
|
D:ASP59
|
4.1
|
26.8
|
1.0
|
|
ND2
|
D:ASN67
|
4.1
|
29.1
|
1.0
|
|
N
|
D:ASN61
|
4.3
|
26.2
|
1.0
|
|
N
|
D:ILE60
|
4.3
|
26.3
|
1.0
|
|
N
|
D:ASP63
|
4.3
|
36.9
|
1.0
|
|
N
|
D:VAL66
|
4.3
|
22.8
|
1.0
|
|
N
|
D:ALA65
|
4.3
|
31.0
|
1.0
|
|
CG
|
D:GLU70
|
4.3
|
21.7
|
1.0
|
|
CA
|
D:VAL66
|
4.3
|
21.1
|
1.0
|
|
CB
|
D:ASP59
|
4.4
|
25.5
|
1.0
|
|
C
|
D:ASP59
|
4.4
|
27.2
|
1.0
|
|
N
|
D:ASN67
|
4.4
|
22.7
|
1.0
|
|
CA
|
D:ALA65
|
4.5
|
29.4
|
1.0
|
|
OD2
|
D:ASP59
|
4.5
|
29.0
|
1.0
|
|
CB
|
D:ASP63
|
4.5
|
39.0
|
1.0
|
|
O
|
C:HOH219
|
4.5
|
24.2
|
1.0
|
|
N
|
D:THR62
|
4.6
|
34.0
|
1.0
|
|
CB
|
D:ASN61
|
4.6
|
35.3
|
1.0
|
|
O
|
D:HOH223
|
4.6
|
34.6
|
1.0
|
|
CG
|
D:ASN67
|
4.8
|
26.9
|
1.0
|
|
CA
|
D:ASN61
|
4.8
|
31.5
|
1.0
|
|
CA
|
D:ASP63
|
4.8
|
38.5
|
1.0
|
|
C
|
D:VAL66
|
4.9
|
22.5
|
1.0
|
|
C
|
D:ASN61
|
4.9
|
32.5
|
1.0
|
|
Calcium binding site 9 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 9 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca101
b:38.5
occ:1.00
|
O
|
E:SER20
|
2.3
|
20.6
|
1.0
|
|
O
|
E:ALA28
|
2.4
|
26.4
|
1.0
|
|
O
|
E:LYS23
|
2.4
|
20.2
|
1.0
|
|
O
|
E:HOH205
|
2.5
|
19.2
|
1.0
|
|
O
|
E:ASN25
|
2.5
|
21.4
|
1.0
|
|
C
|
E:SER20
|
3.1
|
20.5
|
1.0
|
|
C
|
E:ALA28
|
3.5
|
25.9
|
1.0
|
|
CA
|
E:SER20
|
3.5
|
22.6
|
1.0
|
|
C
|
E:LYS23
|
3.6
|
23.6
|
1.0
|
|
C
|
E:ASN25
|
3.6
|
22.5
|
1.0
|
|
CE2
|
E:TYR30
|
3.8
|
25.2
|
1.0
|
|
N
|
E:LYS23
|
4.0
|
23.7
|
1.0
|
|
N
|
E:ALA28
|
4.0
|
24.5
|
1.0
|
|
CA
|
E:ALA28
|
4.2
|
25.6
|
1.0
|
|
N
|
E:LEU21
|
4.2
|
19.5
|
1.0
|
|
CD2
|
E:TYR30
|
4.3
|
24.2
|
1.0
|
|
N
|
E:ASN25
|
4.3
|
22.5
|
1.0
|
|
O
|
E:TYR19
|
4.3
|
21.6
|
1.0
|
|
CB
|
E:SER20
|
4.3
|
25.0
|
1.0
|
|
CB
|
E:ALA28
|
4.3
|
25.1
|
1.0
|
|
C
|
E:GLY24
|
4.4
|
26.2
|
1.0
|
|
CA
|
E:PHE26
|
4.4
|
21.8
|
1.0
|
|
N
|
E:PHE26
|
4.4
|
22.3
|
1.0
|
|
CA
|
E:LYS23
|
4.4
|
24.8
|
1.0
|
|
N
|
E:ILE22
|
4.5
|
25.1
|
1.0
|
|
OD2
|
E:ASP33
|
4.5
|
31.9
|
1.0
|
|
N
|
E:VAL29
|
4.6
|
21.1
|
1.0
|
|
CA
|
E:ASN25
|
4.6
|
22.2
|
1.0
|
|
C
|
E:PHE26
|
4.6
|
24.3
|
1.0
|
|
N
|
E:GLY24
|
4.6
|
25.4
|
1.0
|
|
O
|
E:GLY24
|
4.7
|
28.9
|
1.0
|
|
CA
|
E:LEU21
|
4.7
|
22.9
|
1.0
|
|
CA
|
E:GLY24
|
4.7
|
26.8
|
1.0
|
|
CZ
|
E:TYR30
|
4.7
|
25.9
|
1.0
|
|
N
|
E:SER20
|
4.7
|
23.7
|
1.0
|
|
C
|
E:LEU21
|
4.8
|
26.9
|
1.0
|
|
N
|
E:HIS27
|
4.8
|
23.0
|
1.0
|
|
CA
|
E:VAL29
|
4.9
|
16.9
|
1.0
|
|
OH
|
E:TYR30
|
4.9
|
22.8
|
1.0
|
|
C
|
E:TYR19
|
5.0
|
24.0
|
1.0
|
|
O
|
E:PHE26
|
5.0
|
24.3
|
1.0
|
|
Calcium binding site 10 out
of 16 in 5hlv
Go back to
Calcium Binding Sites List in 5hlv
Calcium binding site 10 out
of 16 in the Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Calcium and Zinc-Bound Human S100A8 in Space Group P212121 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca102
b:23.8
occ:1.00
|
OD1
|
E:ASN61
|
2.3
|
27.6
|
1.0
|
|
O
|
E:ALA65
|
2.4
|
21.8
|
1.0
|
|
OD1
|
E:ASP63
|
2.4
|
34.5
|
1.0
|
|
OD1
|
E:ASP59
|
2.4
|
26.4
|
1.0
|
|
O
|
E:HOH209
|
2.4
|
18.1
|
1.0
|
|
OE1
|
E:GLU70
|
2.5
|
17.0
|
1.0
|
|
OE2
|
E:GLU70
|
2.6
|
20.2
|
1.0
|
|
CD
|
E:GLU70
|
2.9
|
21.1
|
1.0
|
|
CG
|
E:ASP63
|
3.2
|
32.3
|
1.0
|
|
CG
|
E:ASN61
|
3.4
|
28.1
|
1.0
|
|
C
|
E:ALA65
|
3.5
|
17.2
|
1.0
|
|
CG
|
E:ASP59
|
3.6
|
25.3
|
1.0
|
|
OD2
|
E:ASP63
|
3.6
|
29.0
|
1.0
|
|
ND2
|
E:ASN61
|
4.0
|
30.1
|
1.0
|
|
CA
|
E:ASP59
|
4.1
|
23.2
|
1.0
|
|
ND2
|
E:ASN67
|
4.2
|
24.8
|
1.0
|
|
N
|
E:ASP63
|
4.3
|
28.6
|
1.0
|
|
N
|
E:VAL66
|
4.3
|
19.6
|
1.0
|
|
CA
|
E:VAL66
|
4.3
|
17.9
|
1.0
|
|
N
|
E:ASN61
|
4.3
|
24.1
|
1.0
|
|
N
|
E:ILE60
|
4.3
|
22.8
|
1.0
|
|
N
|
E:ALA65
|
4.3
|
21.4
|
1.0
|
|
CB
|
E:ASP59
|
4.3
|
25.0
|
1.0
|
|
C
|
E:ASP59
|
4.4
|
23.1
|
1.0
|
|
N
|
E:ASN67
|
4.4
|
18.1
|
1.0
|
|
CG
|
E:GLU70
|
4.4
|
22.4
|
1.0
|
|
OD2
|
E:ASP59
|
4.4
|
23.6
|
1.0
|
|
CA
|
E:ALA65
|
4.5
|
18.4
|
1.0
|
|
CB
|
E:ASP63
|
4.5
|
33.2
|
1.0
|
|
N
|
E:THR62
|
4.6
|
26.4
|
1.0
|
|
O
|
A:HOH218
|
4.6
|
22.1
|
1.0
|
|
O
|
E:HOH217
|
4.6
|
29.6
|
1.0
|
|
CB
|
E:ASN61
|
4.6
|
26.5
|
1.0
|
|
CA
|
E:ASN61
|
4.8
|
26.6
|
1.0
|
|
CG
|
E:ASN67
|
4.8
|
23.8
|
1.0
|
|
C
|
E:VAL66
|
4.8
|
18.3
|
1.0
|
|
CA
|
E:ASP63
|
4.8
|
31.2
|
1.0
|
|
C
|
E:ASN61
|
4.8
|
28.1
|
1.0
|
|
Reference:
H.Lin,
G.R.Andersen,
L.Yatime.
Crystal Structure of Human S100A8 in Complex with Zinc and Calcium. Bmc Struct.Biol. V. 16 8 2016.
ISSN: ESSN 1472-6807
PubMed: 27251136
DOI: 10.1186/S12900-016-0058-4
Page generated: Wed Jul 9 06:30:03 2025
|
