Sodium in PDB 6ds2: Crystal Structure of Ni(II)-Bound Human Calprotectin
Protein crystallography data
The structure of Crystal Structure of Ni(II)-Bound Human Calprotectin, PDB code: 6ds2
was solved by
E.M.Nolan,
C.L.Drennan,
T.G.Nakashige,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.48 /
2.10
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.145,
78.082,
223.787,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.6 /
22.2
|
Other elements in 6ds2:
The structure of Crystal Structure of Ni(II)-Bound Human Calprotectin also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Ni(II)-Bound Human Calprotectin
(pdb code 6ds2). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the
Crystal Structure of Ni(II)-Bound Human Calprotectin, PDB code: 6ds2:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 1 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na101
b:21.4
occ:1.00
|
O
|
A:SER20
|
2.3
|
22.5
|
1.0
|
|
O
|
A:ALA28
|
2.3
|
22.9
|
1.0
|
|
O
|
A:LYS23
|
2.3
|
19.3
|
1.0
|
|
O
|
A:ASN25
|
2.4
|
18.5
|
1.0
|
|
O
|
A:HOH230
|
2.6
|
16.9
|
1.0
|
|
C
|
A:SER20
|
3.3
|
22.4
|
1.0
|
|
C
|
A:ALA28
|
3.4
|
21.4
|
1.0
|
|
O
|
A:HOH237
|
3.5
|
44.9
|
1.0
|
|
C
|
A:ASN25
|
3.5
|
20.6
|
1.0
|
|
C
|
A:LYS23
|
3.6
|
22.2
|
1.0
|
|
CE2
|
A:TYR30
|
3.7
|
16.2
|
1.0
|
|
CA
|
A:SER20
|
3.7
|
21.1
|
1.0
|
|
N
|
A:ALA28
|
3.9
|
20.9
|
1.0
|
|
N
|
A:ASN25
|
4.0
|
19.7
|
1.0
|
|
CA
|
A:ALA28
|
4.0
|
16.8
|
1.0
|
|
N
|
A:LYS23
|
4.1
|
22.1
|
1.0
|
|
C
|
A:GLY24
|
4.1
|
22.2
|
1.0
|
|
CB
|
A:ALA28
|
4.2
|
16.7
|
1.0
|
|
CD2
|
A:TYR30
|
4.2
|
15.9
|
1.0
|
|
CA
|
A:ASN25
|
4.4
|
20.4
|
1.0
|
|
O
|
A:GLY24
|
4.4
|
23.3
|
1.0
|
|
CB
|
A:SER20
|
4.4
|
19.9
|
1.0
|
|
N
|
A:LEU21
|
4.4
|
20.1
|
1.0
|
|
CA
|
A:LYS23
|
4.5
|
21.9
|
1.0
|
|
N
|
A:PHE26
|
4.5
|
22.8
|
1.0
|
|
N
|
A:GLY24
|
4.5
|
19.9
|
1.0
|
|
O
|
A:TYR19
|
4.5
|
24.1
|
1.0
|
|
N
|
A:VAL29
|
4.5
|
18.1
|
1.0
|
|
CA
|
A:GLY24
|
4.5
|
19.4
|
1.0
|
|
CZ
|
A:TYR30
|
4.6
|
16.1
|
1.0
|
|
C
|
A:PHE26
|
4.6
|
26.1
|
1.0
|
|
CA
|
A:PHE26
|
4.6
|
25.6
|
1.0
|
|
N
|
A:ILE22
|
4.7
|
22.6
|
1.0
|
|
OH
|
A:TYR30
|
4.7
|
18.7
|
1.0
|
|
OD2
|
A:ASP33
|
4.7
|
23.8
|
1.0
|
|
O
|
A:PHE26
|
4.7
|
25.4
|
1.0
|
|
CA
|
A:LEU21
|
4.8
|
22.9
|
1.0
|
|
CA
|
A:VAL29
|
4.9
|
17.8
|
1.0
|
|
N
|
A:HIS27
|
4.9
|
25.4
|
1.0
|
|
C
|
A:LEU21
|
4.9
|
22.2
|
1.0
|
|
N
|
A:SER20
|
5.0
|
21.8
|
1.0
|
|
Sodium binding site 2 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 2 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na102
b:22.1
occ:1.00
|
OD1
|
A:ASN61
|
2.3
|
27.1
|
1.0
|
|
O
|
A:ALA65
|
2.4
|
20.4
|
1.0
|
|
OD1
|
A:ASP59
|
2.5
|
19.9
|
1.0
|
|
OD1
|
A:ASP63
|
2.5
|
23.6
|
1.0
|
|
O
|
A:HOH214
|
2.6
|
32.5
|
1.0
|
|
OE1
|
A:GLU70
|
2.7
|
34.8
|
1.0
|
|
OE2
|
A:GLU70
|
2.8
|
36.7
|
1.0
|
|
CD
|
A:GLU70
|
3.2
|
35.2
|
1.0
|
|
CG
|
A:ASP63
|
3.3
|
24.9
|
1.0
|
|
CG
|
A:ASN61
|
3.4
|
28.3
|
1.0
|
|
C
|
A:ALA65
|
3.5
|
25.5
|
1.0
|
|
CG
|
A:ASP59
|
3.6
|
22.8
|
1.0
|
|
OD2
|
A:ASP63
|
3.6
|
25.0
|
1.0
|
|
CA
|
A:ASP59
|
3.9
|
21.1
|
1.0
|
|
ND2
|
A:ASN61
|
4.0
|
25.0
|
1.0
|
|
N
|
A:ILE60
|
4.2
|
19.4
|
1.0
|
|
CB
|
A:ASP59
|
4.2
|
19.9
|
1.0
|
|
N
|
A:ALA65
|
4.3
|
19.6
|
1.0
|
|
C
|
A:ASP59
|
4.3
|
23.0
|
1.0
|
|
N
|
A:ASN61
|
4.3
|
20.4
|
1.0
|
|
N
|
A:VAL66
|
4.3
|
22.1
|
1.0
|
|
CA
|
A:ALA65
|
4.4
|
21.8
|
1.0
|
|
CA
|
A:VAL66
|
4.4
|
24.0
|
1.0
|
|
N
|
A:ASP63
|
4.4
|
22.2
|
1.0
|
|
OD2
|
A:ASP59
|
4.4
|
22.4
|
1.0
|
|
CB
|
A:ASP63
|
4.5
|
21.5
|
1.0
|
|
N
|
A:ASN67
|
4.7
|
22.0
|
1.0
|
|
CB
|
A:ASN61
|
4.7
|
17.6
|
1.0
|
|
CG
|
A:GLU70
|
4.7
|
31.7
|
1.0
|
|
N
|
A:THR62
|
4.8
|
20.3
|
1.0
|
|
CB
|
A:ALA65
|
4.8
|
20.4
|
1.0
|
|
CA
|
A:ASN61
|
4.9
|
19.5
|
1.0
|
|
O
|
A:LEU58
|
4.9
|
21.2
|
1.0
|
|
CA
|
A:ASP63
|
4.9
|
22.5
|
1.0
|
|
C
|
A:ASN61
|
5.0
|
21.6
|
1.0
|
|
C
|
A:VAL66
|
5.0
|
23.2
|
1.0
|
|
Sodium binding site 3 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 3 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na102
b:33.1
occ:1.00
|
O
|
C:LYS23
|
2.3
|
35.0
|
1.0
|
|
O
|
C:ALA28
|
2.3
|
30.8
|
1.0
|
|
O
|
C:SER20
|
2.3
|
33.8
|
1.0
|
|
O
|
C:ASN25
|
2.4
|
34.2
|
1.0
|
|
O
|
C:HOH220
|
2.5
|
34.0
|
1.0
|
|
C
|
C:SER20
|
3.3
|
41.5
|
1.0
|
|
C
|
C:ALA28
|
3.5
|
30.1
|
1.0
|
|
C
|
C:LYS23
|
3.5
|
38.6
|
1.0
|
|
CE2
|
C:TYR30
|
3.6
|
35.7
|
1.0
|
|
C
|
C:ASN25
|
3.6
|
34.5
|
1.0
|
|
CA
|
C:SER20
|
3.8
|
38.5
|
1.0
|
|
N
|
C:ALA28
|
4.0
|
36.4
|
1.0
|
|
N
|
C:LYS23
|
4.0
|
41.5
|
1.0
|
|
N
|
C:ASN25
|
4.1
|
34.2
|
1.0
|
|
CA
|
C:ALA28
|
4.1
|
29.4
|
1.0
|
|
C
|
C:GLY24
|
4.1
|
35.5
|
1.0
|
|
CD2
|
C:TYR30
|
4.1
|
31.9
|
1.0
|
|
CB
|
C:ALA28
|
4.2
|
29.8
|
1.0
|
|
CA
|
C:LYS23
|
4.4
|
41.6
|
1.0
|
|
CA
|
C:ASN25
|
4.4
|
34.1
|
1.0
|
|
N
|
C:LEU21
|
4.4
|
40.0
|
1.0
|
|
O
|
C:GLY24
|
4.4
|
43.1
|
1.0
|
|
N
|
C:GLY24
|
4.4
|
36.8
|
1.0
|
|
CB
|
C:SER20
|
4.5
|
37.1
|
1.0
|
|
CZ
|
C:TYR30
|
4.5
|
33.1
|
1.0
|
|
O
|
C:TYR19
|
4.5
|
38.7
|
1.0
|
|
CA
|
C:GLY24
|
4.5
|
35.9
|
1.0
|
|
N
|
C:VAL29
|
4.6
|
29.6
|
1.0
|
|
N
|
C:PHE26
|
4.6
|
34.5
|
1.0
|
|
OD2
|
C:ASP33
|
4.6
|
38.4
|
1.0
|
|
N
|
C:ILE22
|
4.7
|
36.4
|
1.0
|
|
OH
|
C:TYR30
|
4.7
|
32.2
|
1.0
|
|
C
|
C:PHE26
|
4.7
|
35.9
|
1.0
|
|
CA
|
C:PHE26
|
4.7
|
36.4
|
1.0
|
|
CA
|
C:LEU21
|
4.8
|
38.3
|
1.0
|
|
O
|
C:PHE26
|
4.8
|
33.0
|
1.0
|
|
CA
|
C:VAL29
|
4.9
|
29.0
|
1.0
|
|
C
|
C:LEU21
|
5.0
|
39.1
|
1.0
|
|
N
|
C:SER20
|
5.0
|
35.5
|
1.0
|
|
CG
|
C:LYS23
|
5.0
|
41.0
|
1.0
|
|
Sodium binding site 4 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 4 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na103
b:28.9
occ:1.00
|
O
|
C:ALA65
|
2.4
|
28.8
|
1.0
|
|
OD1
|
C:ASN61
|
2.4
|
27.0
|
1.0
|
|
OD1
|
C:ASP63
|
2.5
|
29.4
|
1.0
|
|
OD1
|
C:ASP59
|
2.5
|
23.7
|
1.0
|
|
O
|
C:HOH205
|
2.6
|
31.5
|
1.0
|
|
OE1
|
C:GLU70
|
2.7
|
40.1
|
1.0
|
|
OE2
|
C:GLU70
|
2.7
|
39.2
|
1.0
|
|
CD
|
C:GLU70
|
3.0
|
37.2
|
1.0
|
|
CG
|
C:ASP63
|
3.3
|
31.9
|
1.0
|
|
C
|
C:ALA65
|
3.5
|
29.3
|
1.0
|
|
CG
|
C:ASN61
|
3.5
|
29.2
|
1.0
|
|
OD2
|
C:ASP63
|
3.6
|
33.3
|
1.0
|
|
CG
|
C:ASP59
|
3.6
|
32.0
|
1.0
|
|
CA
|
C:ASP59
|
3.9
|
24.8
|
1.0
|
|
ND2
|
C:ASN61
|
4.1
|
27.7
|
1.0
|
|
N
|
C:ILE60
|
4.2
|
24.9
|
1.0
|
|
CB
|
C:ASP59
|
4.3
|
23.2
|
1.0
|
|
N
|
C:ALA65
|
4.3
|
26.5
|
1.0
|
|
C
|
C:ASP59
|
4.3
|
27.2
|
1.0
|
|
N
|
C:ASN61
|
4.3
|
21.9
|
1.0
|
|
N
|
C:VAL66
|
4.4
|
28.3
|
1.0
|
|
CA
|
C:ALA65
|
4.4
|
28.2
|
1.0
|
|
N
|
C:ASP63
|
4.4
|
28.2
|
1.0
|
|
CA
|
C:VAL66
|
4.4
|
27.2
|
1.0
|
|
CB
|
C:ASP63
|
4.5
|
28.3
|
1.0
|
|
OD2
|
C:ASP59
|
4.5
|
24.2
|
1.0
|
|
CG
|
C:GLU70
|
4.6
|
33.2
|
1.0
|
|
N
|
C:ASN67
|
4.7
|
27.6
|
1.0
|
|
CB
|
C:ASN61
|
4.7
|
22.9
|
1.0
|
|
N
|
C:THR62
|
4.8
|
25.3
|
1.0
|
|
CB
|
C:ALA65
|
4.9
|
29.9
|
1.0
|
|
CA
|
C:ASN61
|
4.9
|
22.4
|
1.0
|
|
O
|
C:LEU58
|
4.9
|
22.1
|
1.0
|
|
CA
|
C:ASP63
|
4.9
|
29.1
|
1.0
|
|
C
|
C:ASN61
|
5.0
|
26.5
|
1.0
|
|
Sodium binding site 5 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 5 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na202
b:38.1
occ:1.00
|
O
|
D:THR31
|
2.3
|
30.7
|
1.0
|
|
O
|
D:LEU26
|
2.4
|
43.0
|
1.0
|
|
O
|
D:HIS28
|
2.4
|
30.0
|
1.0
|
|
O
|
D:HOH325
|
2.4
|
36.5
|
1.0
|
|
O
|
D:SER23
|
2.4
|
25.1
|
1.0
|
|
O
|
D:HOH313
|
2.7
|
37.4
|
1.0
|
|
C
|
D:SER23
|
3.3
|
30.5
|
1.0
|
|
C
|
D:HIS28
|
3.5
|
33.9
|
1.0
|
|
C
|
D:THR31
|
3.5
|
29.4
|
1.0
|
|
C
|
D:LEU26
|
3.6
|
42.4
|
1.0
|
|
CA
|
D:SER23
|
3.7
|
28.7
|
1.0
|
|
N
|
D:HIS28
|
3.8
|
35.2
|
1.0
|
|
OG1
|
D:THR31
|
4.1
|
28.3
|
1.0
|
|
N
|
D:LEU26
|
4.2
|
37.3
|
1.0
|
|
N
|
D:THR31
|
4.2
|
27.2
|
1.0
|
|
C
|
D:GLY27
|
4.3
|
40.4
|
1.0
|
|
CA
|
D:HIS28
|
4.3
|
36.6
|
1.0
|
|
CB
|
D:SER23
|
4.3
|
29.7
|
1.0
|
|
OE1
|
D:GLU36
|
4.3
|
49.0
|
1.0
|
|
OD1
|
D:ASN33
|
4.3
|
50.7
|
1.0
|
|
CA
|
D:THR31
|
4.4
|
27.2
|
1.0
|
|
N
|
D:PRO29
|
4.5
|
36.7
|
1.0
|
|
CA
|
D:LEU26
|
4.5
|
39.2
|
1.0
|
|
N
|
D:GLY27
|
4.5
|
42.0
|
1.0
|
|
N
|
D:VAL24
|
4.5
|
29.3
|
1.0
|
|
N
|
D:LEU32
|
4.5
|
28.0
|
1.0
|
|
CA
|
D:PRO29
|
4.5
|
40.3
|
1.0
|
|
CA
|
D:GLY27
|
4.5
|
40.6
|
1.0
|
|
O
|
D:TYR22
|
4.6
|
29.0
|
1.0
|
|
C
|
D:PRO29
|
4.6
|
40.4
|
1.0
|
|
CA
|
D:LEU32
|
4.6
|
27.6
|
1.0
|
|
N
|
D:LYS25
|
4.8
|
29.7
|
1.0
|
|
N
|
D:ASN33
|
4.8
|
28.6
|
1.0
|
|
O
|
D:GLY27
|
4.9
|
40.9
|
1.0
|
|
CB
|
D:THR31
|
4.9
|
27.6
|
1.0
|
|
N
|
D:ASP30
|
4.9
|
36.6
|
1.0
|
|
O
|
D:PRO29
|
4.9
|
44.5
|
1.0
|
|
C
|
D:VAL24
|
4.9
|
31.6
|
1.0
|
|
N
|
D:SER23
|
4.9
|
29.2
|
1.0
|
|
CA
|
D:VAL24
|
5.0
|
30.4
|
1.0
|
|
CB
|
D:HIS28
|
5.0
|
43.0
|
1.0
|
|
Sodium binding site 6 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 6 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na102
b:17.0
occ:1.00
|
O
|
E:ALA28
|
2.3
|
16.9
|
1.0
|
|
O
|
E:SER20
|
2.3
|
19.1
|
1.0
|
|
O
|
E:LYS23
|
2.3
|
17.1
|
1.0
|
|
O
|
E:ASN25
|
2.4
|
17.8
|
1.0
|
|
O
|
E:HOH224
|
2.5
|
17.5
|
1.0
|
|
C
|
E:SER20
|
3.3
|
20.5
|
1.0
|
|
C
|
E:ALA28
|
3.4
|
18.4
|
1.0
|
|
C
|
E:LYS23
|
3.5
|
20.8
|
1.0
|
|
C
|
E:ASN25
|
3.6
|
21.6
|
1.0
|
|
CE2
|
E:TYR30
|
3.7
|
20.5
|
1.0
|
|
CA
|
E:SER20
|
3.7
|
18.1
|
1.0
|
|
N
|
E:ALA28
|
3.9
|
18.6
|
1.0
|
|
CA
|
E:ALA28
|
4.0
|
17.5
|
1.0
|
|
N
|
E:LYS23
|
4.1
|
17.0
|
1.0
|
|
N
|
E:ASN25
|
4.1
|
17.9
|
1.0
|
|
C
|
E:GLY24
|
4.1
|
20.6
|
1.0
|
|
CB
|
E:ALA28
|
4.2
|
17.4
|
1.0
|
|
CD2
|
E:TYR30
|
4.2
|
17.3
|
1.0
|
|
O
|
E:GLY24
|
4.4
|
18.3
|
1.0
|
|
CB
|
E:SER20
|
4.4
|
19.9
|
1.0
|
|
CA
|
E:ASN25
|
4.4
|
18.3
|
1.0
|
|
N
|
E:LEU21
|
4.4
|
20.0
|
1.0
|
|
CA
|
E:LYS23
|
4.4
|
22.5
|
1.0
|
|
N
|
E:GLY24
|
4.5
|
18.8
|
1.0
|
|
O
|
E:TYR19
|
4.5
|
20.6
|
1.0
|
|
N
|
E:VAL29
|
4.5
|
16.8
|
1.0
|
|
N
|
E:PHE26
|
4.5
|
20.5
|
1.0
|
|
CA
|
E:GLY24
|
4.5
|
20.1
|
1.0
|
|
C
|
E:PHE26
|
4.6
|
22.4
|
1.0
|
|
OD2
|
E:ASP33
|
4.6
|
23.7
|
1.0
|
|
CZ
|
E:TYR30
|
4.6
|
18.4
|
1.0
|
|
CA
|
E:PHE26
|
4.6
|
23.0
|
1.0
|
|
N
|
E:ILE22
|
4.7
|
17.2
|
1.0
|
|
O
|
E:PHE26
|
4.7
|
23.8
|
1.0
|
|
OH
|
E:TYR30
|
4.8
|
18.7
|
1.0
|
|
CA
|
E:VAL29
|
4.8
|
19.6
|
1.0
|
|
CA
|
E:LEU21
|
4.9
|
22.8
|
1.0
|
|
N
|
E:SER20
|
5.0
|
18.1
|
1.0
|
|
N
|
E:HIS27
|
5.0
|
22.0
|
1.0
|
|
CG
|
E:LYS23
|
5.0
|
21.8
|
1.0
|
|
Sodium binding site 7 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 7 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na103
b:24.0
occ:1.00
|
O
|
E:ALA65
|
2.3
|
24.6
|
1.0
|
|
OD1
|
E:ASN61
|
2.4
|
32.8
|
1.0
|
|
O
|
E:HOH220
|
2.5
|
26.6
|
1.0
|
|
OD1
|
E:ASP63
|
2.7
|
24.6
|
1.0
|
|
OD1
|
E:ASP59
|
2.7
|
23.5
|
1.0
|
|
OE1
|
E:GLU70
|
2.7
|
36.6
|
1.0
|
|
OE2
|
E:GLU70
|
2.8
|
41.3
|
1.0
|
|
CD
|
E:GLU70
|
3.1
|
36.2
|
1.0
|
|
C
|
E:ALA65
|
3.4
|
25.4
|
1.0
|
|
CG
|
E:ASP63
|
3.5
|
30.0
|
1.0
|
|
CG
|
E:ASN61
|
3.5
|
31.2
|
1.0
|
|
OD2
|
E:ASP63
|
3.7
|
28.1
|
1.0
|
|
CG
|
E:ASP59
|
3.7
|
26.9
|
1.0
|
|
CA
|
E:ASP59
|
4.0
|
24.8
|
1.0
|
|
ND2
|
E:ASN61
|
4.1
|
30.4
|
1.0
|
|
N
|
E:ILE60
|
4.2
|
22.2
|
1.0
|
|
N
|
E:VAL66
|
4.2
|
23.9
|
1.0
|
|
CA
|
E:VAL66
|
4.2
|
23.8
|
1.0
|
|
N
|
E:ASN61
|
4.3
|
22.1
|
1.0
|
|
C
|
E:ASP59
|
4.3
|
23.1
|
1.0
|
|
CB
|
E:ASP59
|
4.3
|
25.6
|
1.0
|
|
N
|
E:ALA65
|
4.4
|
22.3
|
1.0
|
|
CA
|
E:ALA65
|
4.4
|
25.6
|
1.0
|
|
N
|
E:ASN67
|
4.5
|
22.2
|
1.0
|
|
CG
|
E:GLU70
|
4.6
|
33.4
|
1.0
|
|
N
|
E:ASP63
|
4.6
|
26.5
|
1.0
|
|
OD2
|
E:ASP59
|
4.6
|
24.7
|
1.0
|
|
CB
|
E:ASP63
|
4.7
|
24.9
|
1.0
|
|
CB
|
E:ASN61
|
4.7
|
26.4
|
1.0
|
|
CB
|
E:ALA65
|
4.8
|
23.5
|
1.0
|
|
C
|
E:VAL66
|
4.8
|
22.6
|
1.0
|
|
O
|
E:LEU58
|
4.9
|
22.1
|
1.0
|
|
N
|
E:THR62
|
4.9
|
25.3
|
1.0
|
|
CA
|
E:ASN61
|
4.9
|
23.8
|
1.0
|
|
Sodium binding site 8 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 8 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na202
b:44.8
occ:1.00
|
O
|
F:LEU26
|
2.3
|
43.2
|
1.0
|
|
O
|
F:HIS28
|
2.4
|
42.7
|
1.0
|
|
O
|
F:THR31
|
2.4
|
40.9
|
1.0
|
|
O
|
F:HOH312
|
2.4
|
43.9
|
1.0
|
|
O
|
F:SER23
|
2.5
|
37.9
|
1.0
|
|
O
|
F:HOH313
|
2.7
|
51.8
|
1.0
|
|
C
|
F:HIS28
|
3.4
|
44.9
|
1.0
|
|
C
|
F:SER23
|
3.4
|
42.6
|
1.0
|
|
C
|
F:LEU26
|
3.5
|
44.8
|
1.0
|
|
C
|
F:THR31
|
3.6
|
43.8
|
1.0
|
|
N
|
F:HIS28
|
3.7
|
47.8
|
1.0
|
|
ND2
|
F:ASN33
|
3.8
|
58.3
|
1.0
|
|
CA
|
F:SER23
|
3.8
|
37.1
|
1.0
|
|
N
|
F:LEU26
|
4.1
|
44.1
|
1.0
|
|
CA
|
F:HIS28
|
4.2
|
47.6
|
1.0
|
|
OG1
|
F:THR31
|
4.2
|
47.0
|
1.0
|
|
N
|
F:THR31
|
4.2
|
45.5
|
1.0
|
|
OE1
|
F:GLU36
|
4.3
|
60.4
|
1.0
|
|
C
|
F:GLY27
|
4.3
|
48.8
|
1.0
|
|
CB
|
F:SER23
|
4.3
|
35.0
|
1.0
|
|
N
|
F:PRO29
|
4.4
|
47.1
|
1.0
|
|
CA
|
F:LEU26
|
4.4
|
43.8
|
1.0
|
|
N
|
F:GLY27
|
4.4
|
47.8
|
1.0
|
|
CA
|
F:THR31
|
4.5
|
44.7
|
1.0
|
|
CA
|
F:PRO29
|
4.5
|
49.5
|
1.0
|
|
CA
|
F:GLY27
|
4.5
|
48.6
|
1.0
|
|
N
|
F:LEU32
|
4.6
|
42.9
|
1.0
|
|
C
|
F:PRO29
|
4.6
|
51.0
|
1.0
|
|
N
|
F:VAL24
|
4.6
|
42.0
|
1.0
|
|
CA
|
F:LEU32
|
4.7
|
41.5
|
1.0
|
|
O
|
F:TYR22
|
4.7
|
37.3
|
1.0
|
|
N
|
F:LYS25
|
4.7
|
39.3
|
1.0
|
|
N
|
F:ASN33
|
4.8
|
42.9
|
1.0
|
|
N
|
F:ASP30
|
4.9
|
49.5
|
1.0
|
|
CG
|
F:ASN33
|
4.9
|
56.0
|
1.0
|
|
C
|
F:VAL24
|
5.0
|
39.1
|
1.0
|
|
CB
|
F:HIS28
|
5.0
|
54.2
|
1.0
|
|
CB
|
F:THR31
|
5.0
|
47.0
|
1.0
|
|
O
|
F:PRO29
|
5.0
|
54.1
|
1.0
|
|
Sodium binding site 9 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 9 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na101
b:54.0
occ:1.00
|
O
|
G:ALA28
|
2.3
|
49.1
|
1.0
|
|
O
|
G:LYS23
|
2.3
|
50.4
|
1.0
|
|
O
|
G:SER20
|
2.4
|
51.2
|
1.0
|
|
O
|
G:HOH201
|
2.5
|
42.9
|
1.0
|
|
O
|
G:ASN25
|
2.6
|
46.1
|
1.0
|
|
C
|
G:SER20
|
3.4
|
53.2
|
1.0
|
|
C
|
G:ALA28
|
3.4
|
45.1
|
1.0
|
|
CE2
|
G:TYR30
|
3.5
|
41.5
|
1.0
|
|
C
|
G:LYS23
|
3.6
|
52.6
|
1.0
|
|
C
|
G:ASN25
|
3.7
|
47.9
|
1.0
|
|
CA
|
G:SER20
|
3.8
|
52.0
|
1.0
|
|
CD2
|
G:TYR30
|
4.0
|
41.2
|
1.0
|
|
N
|
G:ALA28
|
4.0
|
45.5
|
1.0
|
|
CA
|
G:ALA28
|
4.1
|
44.6
|
1.0
|
|
N
|
G:LYS23
|
4.1
|
55.1
|
1.0
|
|
N
|
G:ASN25
|
4.1
|
47.8
|
1.0
|
|
CB
|
G:ALA28
|
4.1
|
45.4
|
1.0
|
|
C
|
G:GLY24
|
4.2
|
47.8
|
1.0
|
|
CZ
|
G:TYR30
|
4.4
|
43.4
|
1.0
|
|
OD2
|
G:ASP33
|
4.4
|
56.4
|
1.0
|
|
CA
|
G:LYS23
|
4.5
|
53.8
|
1.0
|
|
CA
|
G:ASN25
|
4.5
|
49.0
|
1.0
|
|
O
|
G:GLY24
|
4.5
|
48.0
|
1.0
|
|
N
|
G:GLY24
|
4.5
|
52.7
|
1.0
|
|
N
|
G:LEU21
|
4.5
|
53.8
|
1.0
|
|
O
|
G:TYR19
|
4.5
|
48.8
|
1.0
|
|
N
|
G:VAL29
|
4.5
|
42.3
|
1.0
|
|
CB
|
G:SER20
|
4.5
|
50.0
|
1.0
|
|
CA
|
G:GLY24
|
4.5
|
48.8
|
1.0
|
|
OH
|
G:TYR30
|
4.6
|
43.0
|
1.0
|
|
N
|
G:ILE22
|
4.7
|
53.4
|
1.0
|
|
N
|
G:PHE26
|
4.7
|
50.8
|
1.0
|
|
CA
|
G:VAL29
|
4.8
|
43.2
|
1.0
|
|
C
|
G:PHE26
|
4.8
|
51.6
|
1.0
|
|
CA
|
G:PHE26
|
4.9
|
53.2
|
1.0
|
|
CG
|
G:LYS23
|
4.9
|
50.3
|
1.0
|
|
CA
|
G:LEU21
|
4.9
|
54.0
|
1.0
|
|
Sodium binding site 10 out
of 10 in 6ds2
Go back to
Sodium Binding Sites List in 6ds2
Sodium binding site 10 out
of 10 in the Crystal Structure of Ni(II)-Bound Human Calprotectin
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na102
b:41.0
occ:1.00
|
O
|
G:ALA65
|
2.4
|
35.6
|
1.0
|
|
OD1
|
G:ASN61
|
2.4
|
44.0
|
1.0
|
|
O
|
G:HOH204
|
2.5
|
44.0
|
1.0
|
|
OD1
|
G:ASP63
|
2.5
|
45.6
|
1.0
|
|
OE1
|
G:GLU70
|
2.6
|
49.8
|
1.0
|
|
OD1
|
G:ASP59
|
2.6
|
40.1
|
1.0
|
|
OE2
|
G:GLU70
|
2.7
|
46.3
|
1.0
|
|
CD
|
G:GLU70
|
3.0
|
46.2
|
1.0
|
|
CG
|
G:ASP63
|
3.4
|
46.0
|
1.0
|
|
C
|
G:ALA65
|
3.5
|
39.5
|
1.0
|
|
O
|
G:HOH202
|
3.5
|
51.8
|
1.0
|
|
CG
|
G:ASN61
|
3.5
|
37.8
|
1.0
|
|
OD2
|
G:ASP63
|
3.7
|
45.9
|
1.0
|
|
CG
|
G:ASP59
|
3.7
|
41.5
|
1.0
|
|
CA
|
G:ASP59
|
3.9
|
38.0
|
1.0
|
|
N
|
G:ILE60
|
4.1
|
32.9
|
1.0
|
|
ND2
|
G:ASN61
|
4.1
|
38.1
|
1.0
|
|
C
|
G:ASP59
|
4.2
|
36.7
|
1.0
|
|
N
|
G:ASN61
|
4.2
|
27.2
|
1.0
|
|
CB
|
G:ASP59
|
4.3
|
40.0
|
1.0
|
|
N
|
G:ALA65
|
4.3
|
41.0
|
1.0
|
|
N
|
G:VAL66
|
4.4
|
39.6
|
1.0
|
|
CA
|
G:VAL66
|
4.4
|
39.1
|
1.0
|
|
CA
|
G:ALA65
|
4.4
|
41.6
|
1.0
|
|
N
|
G:ASP63
|
4.4
|
42.3
|
1.0
|
|
CG
|
G:GLU70
|
4.5
|
41.4
|
1.0
|
|
CB
|
G:ASP63
|
4.6
|
43.9
|
1.0
|
|
OD2
|
G:ASP59
|
4.7
|
40.6
|
1.0
|
|
N
|
G:ASN67
|
4.7
|
36.6
|
1.0
|
|
CB
|
G:ASN61
|
4.7
|
31.0
|
1.0
|
|
N
|
G:THR62
|
4.7
|
36.5
|
1.0
|
|
O
|
G:LEU58
|
4.8
|
33.9
|
1.0
|
|
CA
|
G:ASN61
|
4.9
|
31.9
|
1.0
|
|
CB
|
G:ALA65
|
4.9
|
43.0
|
1.0
|
|
CA
|
G:ASP63
|
5.0
|
42.1
|
1.0
|
|
Reference:
T.G.Nakashige,
S.E.J.Bowman,
E.M.Zygiel,
C.L.Drennan,
E.M.Nolan.
Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the Ef-Hand Domains and HIS3ASP Site. Biochemistry V. 57 4155 2018.
ISSN: ISSN 1520-4995
PubMed: 29890074
DOI: 10.1021/ACS.BIOCHEM.8B00415
Page generated: Tue Oct 8 08:11:09 2024
|
