Sodium in PDB 4xjk: Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin
Protein crystallography data
The structure of Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin, PDB code: 4xjk
was solved by
C.L.Drennan,
S.E.J.Bowman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.24 /
1.76
|
|
Space group
|
P 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.279,
49.239,
218.067,
90.00,
94.07,
90.00
|
|
R / Rfree (%)
|
18.5 /
22
|
Other elements in 4xjk:
The structure of Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin
(pdb code 4xjk). 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 Mn(II) Ca(II) Na(I) Bound Calprotectin, PDB code: 4xjk:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 1 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na102
b:27.1
occ:1.00
|
O
|
A:SER20
|
2.3
|
25.6
|
1.0
|
|
O
|
A:LYS23
|
2.3
|
25.2
|
1.0
|
|
O
|
A:ALA28
|
2.3
|
27.2
|
1.0
|
|
O
|
A:ASN25
|
2.4
|
25.5
|
1.0
|
|
O
|
A:HOH219
|
2.6
|
26.9
|
1.0
|
|
C
|
A:SER20
|
3.3
|
31.9
|
1.0
|
|
C
|
A:ALA28
|
3.4
|
23.4
|
1.0
|
|
C
|
A:LYS23
|
3.5
|
28.4
|
1.0
|
|
C
|
A:ASN25
|
3.5
|
25.9
|
1.0
|
|
CE2
|
A:TYR30
|
3.6
|
22.6
|
1.0
|
|
CA
|
A:SER20
|
3.8
|
27.2
|
1.0
|
|
N
|
A:ALA28
|
4.0
|
25.5
|
1.0
|
|
N
|
A:ASN25
|
4.0
|
25.7
|
1.0
|
|
CA
|
A:ALA28
|
4.0
|
22.1
|
1.0
|
|
N
|
A:LYS23
|
4.1
|
23.9
|
1.0
|
|
CB
|
A:ALA28
|
4.1
|
22.0
|
1.0
|
|
C
|
A:GLY24
|
4.1
|
29.8
|
1.0
|
|
CD2
|
A:TYR30
|
4.2
|
23.9
|
1.0
|
|
CA
|
A:ASN25
|
4.4
|
25.9
|
1.0
|
|
N
|
A:LEU21
|
4.4
|
28.2
|
1.0
|
|
CA
|
A:LYS23
|
4.4
|
27.6
|
1.0
|
|
CZ
|
A:TYR30
|
4.5
|
21.0
|
1.0
|
|
N
|
A:PHE26
|
4.5
|
28.5
|
1.0
|
|
N
|
A:GLY24
|
4.5
|
27.8
|
1.0
|
|
O
|
A:GLY24
|
4.5
|
26.1
|
1.0
|
|
CB
|
A:SER20
|
4.5
|
27.2
|
1.0
|
|
CA
|
A:PHE26
|
4.5
|
25.7
|
1.0
|
|
O
|
A:TYR19
|
4.6
|
27.7
|
1.0
|
|
CA
|
A:GLY24
|
4.6
|
24.4
|
1.0
|
|
N
|
A:VAL29
|
4.6
|
25.9
|
1.0
|
|
C
|
A:PHE26
|
4.6
|
29.0
|
1.0
|
|
OH
|
A:TYR30
|
4.6
|
25.5
|
1.0
|
|
OD2
|
A:ASP33
|
4.7
|
31.3
|
1.0
|
|
N
|
A:ILE22
|
4.7
|
25.7
|
1.0
|
|
CA
|
A:LEU21
|
4.8
|
28.2
|
1.0
|
|
CA
|
A:VAL29
|
4.9
|
27.6
|
1.0
|
|
O
|
A:PHE26
|
4.9
|
26.4
|
1.0
|
|
C
|
A:LEU21
|
4.9
|
32.0
|
1.0
|
|
N
|
A:HIS27
|
5.0
|
27.9
|
1.0
|
|
N
|
A:SER20
|
5.0
|
27.1
|
1.0
|
|
Sodium binding site 2 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 2 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na202
b:32.2
occ:1.00
|
O
|
B:HIS28
|
2.3
|
35.1
|
1.0
|
|
O
|
B:SER23
|
2.4
|
29.6
|
1.0
|
|
O
|
B:THR31
|
2.4
|
32.7
|
1.0
|
|
O
|
B:LEU26
|
2.4
|
37.7
|
1.0
|
|
O
|
B:HOH344
|
2.5
|
44.0
|
1.0
|
|
O
|
B:HOH335
|
2.5
|
42.3
|
1.0
|
|
C
|
B:SER23
|
3.4
|
35.7
|
1.0
|
|
C
|
B:HIS28
|
3.4
|
36.1
|
1.0
|
|
C
|
B:THR31
|
3.6
|
38.6
|
1.0
|
|
C
|
B:LEU26
|
3.6
|
43.6
|
1.0
|
|
CA
|
B:SER23
|
3.8
|
30.6
|
1.0
|
|
OE1
|
B:GLU36
|
3.9
|
40.1
|
1.0
|
|
N
|
B:HIS28
|
4.1
|
38.4
|
1.0
|
|
N
|
B:THR31
|
4.1
|
38.2
|
1.0
|
|
O
|
B:HOH334
|
4.1
|
41.6
|
1.0
|
|
N
|
B:LEU26
|
4.2
|
35.1
|
1.0
|
|
CA
|
B:PRO29
|
4.2
|
34.7
|
1.0
|
|
N
|
B:PRO29
|
4.3
|
38.6
|
1.0
|
|
OG1
|
B:THR31
|
4.3
|
38.0
|
1.0
|
|
C
|
B:GLY27
|
4.3
|
40.9
|
1.0
|
|
CA
|
B:HIS28
|
4.4
|
41.0
|
1.0
|
|
CA
|
B:THR31
|
4.4
|
31.0
|
1.0
|
|
CB
|
B:SER23
|
4.4
|
32.2
|
1.0
|
|
C
|
B:PRO29
|
4.4
|
35.8
|
1.0
|
|
CA
|
B:LEU26
|
4.4
|
40.8
|
1.0
|
|
N
|
B:GLY27
|
4.5
|
45.0
|
1.0
|
|
N
|
B:VAL24
|
4.6
|
32.2
|
1.0
|
|
OE2
|
B:GLU36
|
4.6
|
47.8
|
1.0
|
|
N
|
B:LEU32
|
4.6
|
34.2
|
1.0
|
|
O
|
B:TYR22
|
4.6
|
34.6
|
1.0
|
|
CA
|
B:GLY27
|
4.6
|
42.2
|
1.0
|
|
CD
|
B:GLU36
|
4.7
|
48.6
|
1.0
|
|
CA
|
B:LEU32
|
4.7
|
35.2
|
1.0
|
|
N
|
B:ASP30
|
4.8
|
40.6
|
1.0
|
|
O
|
B:PRO29
|
4.8
|
33.4
|
1.0
|
|
O
|
B:GLY27
|
4.8
|
44.5
|
1.0
|
|
N
|
B:LYS25
|
5.0
|
29.5
|
1.0
|
|
CB
|
B:LEU26
|
5.0
|
43.1
|
1.0
|
|
Sodium binding site 3 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 3 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na102
b:28.9
occ:1.00
|
O
|
C:LYS23
|
2.2
|
30.2
|
1.0
|
|
O
|
C:ALA28
|
2.3
|
28.4
|
1.0
|
|
O
|
C:SER20
|
2.3
|
29.1
|
1.0
|
|
O
|
C:HOH201
|
2.4
|
29.6
|
1.0
|
|
O
|
C:ASN25
|
2.5
|
25.8
|
1.0
|
|
C
|
C:SER20
|
3.3
|
28.6
|
1.0
|
|
C
|
C:ALA28
|
3.4
|
29.9
|
1.0
|
|
C
|
C:LYS23
|
3.5
|
39.4
|
1.0
|
|
CE2
|
C:TYR30
|
3.5
|
31.2
|
1.0
|
|
C
|
C:ASN25
|
3.6
|
28.0
|
1.0
|
|
O
|
C:HOH211
|
3.7
|
36.7
|
1.0
|
|
CA
|
C:SER20
|
3.8
|
23.0
|
1.0
|
|
N
|
C:ASN25
|
4.0
|
28.4
|
1.0
|
|
N
|
C:LYS23
|
4.0
|
28.9
|
1.0
|
|
CD2
|
C:TYR30
|
4.0
|
31.4
|
1.0
|
|
N
|
C:ALA28
|
4.0
|
23.7
|
1.0
|
|
CA
|
C:ALA28
|
4.1
|
28.2
|
1.0
|
|
C
|
C:GLY24
|
4.1
|
34.0
|
1.0
|
|
CB
|
C:ALA28
|
4.1
|
26.0
|
1.0
|
|
CA
|
C:LYS23
|
4.4
|
31.6
|
1.0
|
|
CZ
|
C:TYR30
|
4.4
|
29.1
|
1.0
|
|
N
|
C:GLY24
|
4.4
|
33.9
|
1.0
|
|
CA
|
C:ASN25
|
4.4
|
28.1
|
1.0
|
|
CA
|
C:GLY24
|
4.4
|
30.5
|
1.0
|
|
N
|
C:LEU21
|
4.5
|
28.9
|
1.0
|
|
O
|
C:GLY24
|
4.5
|
30.0
|
1.0
|
|
O
|
C:TYR19
|
4.5
|
31.2
|
1.0
|
|
OD2
|
C:ASP33
|
4.5
|
40.2
|
1.0
|
|
CB
|
C:SER20
|
4.5
|
23.6
|
1.0
|
|
N
|
C:VAL29
|
4.5
|
26.6
|
1.0
|
|
OH
|
C:TYR30
|
4.6
|
29.5
|
1.0
|
|
N
|
C:PHE26
|
4.6
|
24.9
|
1.0
|
|
N
|
C:ILE22
|
4.7
|
27.0
|
1.0
|
|
CA
|
C:PHE26
|
4.7
|
26.1
|
1.0
|
|
C
|
C:PHE26
|
4.8
|
24.1
|
1.0
|
|
CA
|
C:VAL29
|
4.8
|
29.9
|
1.0
|
|
CA
|
C:LEU21
|
4.9
|
29.9
|
1.0
|
|
CG
|
C:LYS23
|
4.9
|
35.8
|
1.0
|
|
Sodium binding site 4 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 4 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na202
b:34.7
occ:1.00
|
O
|
D:HOH316
|
1.8
|
30.0
|
1.0
|
|
O
|
D:HIS28
|
2.3
|
40.1
|
1.0
|
|
O
|
D:HOH343
|
2.3
|
45.9
|
1.0
|
|
O
|
D:LEU26
|
2.3
|
46.8
|
1.0
|
|
O
|
D:THR31
|
2.4
|
37.2
|
1.0
|
|
O
|
D:SER23
|
2.5
|
40.8
|
1.0
|
|
OE1
|
D:GLU36
|
3.3
|
47.5
|
1.0
|
|
C
|
D:HIS28
|
3.4
|
39.0
|
1.0
|
|
C
|
D:SER23
|
3.5
|
39.5
|
1.0
|
|
C
|
D:LEU26
|
3.6
|
52.0
|
1.0
|
|
C
|
D:THR31
|
3.6
|
42.7
|
1.0
|
|
N
|
D:HIS28
|
3.8
|
48.0
|
1.0
|
|
CA
|
D:SER23
|
3.9
|
37.9
|
1.0
|
|
OE2
|
D:GLU36
|
3.9
|
49.1
|
1.0
|
|
C
|
D:GLY27
|
4.0
|
47.9
|
1.0
|
|
CD
|
D:GLU36
|
4.0
|
54.5
|
1.0
|
|
CA
|
D:HIS28
|
4.2
|
45.0
|
1.0
|
|
N
|
D:THR31
|
4.2
|
36.6
|
1.0
|
|
OG1
|
D:THR31
|
4.3
|
40.3
|
1.0
|
|
N
|
D:PRO29
|
4.3
|
39.9
|
1.0
|
|
CA
|
D:GLY27
|
4.4
|
46.6
|
1.0
|
|
N
|
D:LEU26
|
4.4
|
46.0
|
1.0
|
|
N
|
D:GLY27
|
4.4
|
48.3
|
1.0
|
|
CA
|
D:PRO29
|
4.4
|
39.0
|
1.0
|
|
CA
|
D:THR31
|
4.5
|
33.7
|
1.0
|
|
O
|
D:GLY27
|
4.5
|
48.3
|
1.0
|
|
ND2
|
D:ASN33
|
4.5
|
52.5
|
1.0
|
|
CB
|
D:SER23
|
4.5
|
37.6
|
1.0
|
|
N
|
D:LEU32
|
4.5
|
32.8
|
1.0
|
|
CA
|
D:LEU26
|
4.6
|
50.8
|
1.0
|
|
C
|
D:PRO29
|
4.6
|
39.3
|
1.0
|
|
CA
|
D:LEU32
|
4.6
|
35.3
|
1.0
|
|
N
|
D:VAL24
|
4.6
|
34.3
|
1.0
|
|
O
|
D:TYR22
|
4.7
|
42.4
|
1.0
|
|
N
|
D:ASN33
|
4.8
|
38.8
|
1.0
|
|
CB
|
D:HIS28
|
4.8
|
44.8
|
1.0
|
|
N
|
D:ASP30
|
4.8
|
37.6
|
1.0
|
|
Sodium binding site 5 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 5 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na102
b:20.1
occ:1.00
|
O
|
E:LYS23
|
2.3
|
17.3
|
1.0
|
|
O
|
E:SER20
|
2.3
|
18.9
|
1.0
|
|
O
|
E:ALA28
|
2.3
|
20.2
|
1.0
|
|
O
|
E:HOH206
|
2.4
|
19.2
|
1.0
|
|
O
|
E:ASN25
|
2.5
|
19.6
|
1.0
|
|
C
|
E:SER20
|
3.3
|
18.7
|
1.0
|
|
C
|
E:ALA28
|
3.5
|
22.1
|
1.0
|
|
C
|
E:LYS23
|
3.5
|
21.4
|
1.0
|
|
CE2
|
E:TYR30
|
3.6
|
19.2
|
1.0
|
|
C
|
E:ASN25
|
3.6
|
19.9
|
1.0
|
|
CA
|
E:SER20
|
3.9
|
15.9
|
1.0
|
|
N
|
E:LYS23
|
4.0
|
21.2
|
1.0
|
|
N
|
E:ALA28
|
4.0
|
18.7
|
1.0
|
|
N
|
E:ASN25
|
4.1
|
19.2
|
1.0
|
|
CA
|
E:ALA28
|
4.1
|
17.7
|
1.0
|
|
C
|
E:GLY24
|
4.1
|
22.8
|
1.0
|
|
CD2
|
E:TYR30
|
4.1
|
19.2
|
1.0
|
|
CB
|
E:ALA28
|
4.2
|
16.6
|
1.0
|
|
CA
|
E:LYS23
|
4.4
|
19.8
|
1.0
|
|
CA
|
E:ASN25
|
4.4
|
19.6
|
1.0
|
|
N
|
E:LEU21
|
4.4
|
19.2
|
1.0
|
|
N
|
E:GLY24
|
4.4
|
19.8
|
1.0
|
|
CZ
|
E:TYR30
|
4.4
|
22.4
|
1.0
|
|
O
|
E:GLY24
|
4.5
|
22.5
|
1.0
|
|
N
|
E:PHE26
|
4.5
|
21.1
|
1.0
|
|
O
|
E:TYR19
|
4.5
|
19.8
|
1.0
|
|
CA
|
E:GLY24
|
4.5
|
19.3
|
1.0
|
|
OD2
|
E:ASP33
|
4.6
|
26.0
|
1.0
|
|
CB
|
E:SER20
|
4.6
|
20.2
|
1.0
|
|
N
|
E:VAL29
|
4.6
|
20.6
|
1.0
|
|
OH
|
E:TYR30
|
4.6
|
19.2
|
1.0
|
|
CA
|
E:PHE26
|
4.6
|
19.6
|
1.0
|
|
C
|
E:PHE26
|
4.6
|
20.6
|
1.0
|
|
N
|
E:ILE22
|
4.7
|
20.7
|
1.0
|
|
CA
|
E:LEU21
|
4.8
|
21.5
|
1.0
|
|
O
|
E:PHE26
|
4.9
|
23.5
|
1.0
|
|
C
|
E:LEU21
|
4.9
|
23.7
|
1.0
|
|
CA
|
E:VAL29
|
4.9
|
21.1
|
1.0
|
|
N
|
E:HIS27
|
4.9
|
21.6
|
1.0
|
|
CG
|
E:LYS23
|
5.0
|
23.3
|
1.0
|
|
Sodium binding site 6 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 6 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na202
b:27.7
occ:1.00
|
O
|
F:HIS28
|
2.3
|
28.4
|
1.0
|
|
O
|
F:SER23
|
2.4
|
29.8
|
1.0
|
|
O
|
F:THR31
|
2.4
|
25.5
|
1.0
|
|
O
|
F:HOH321
|
2.4
|
29.9
|
1.0
|
|
O
|
F:LEU26
|
2.5
|
31.4
|
1.0
|
|
OE1
|
F:GLU36
|
2.6
|
30.0
|
1.0
|
|
C
|
F:HIS28
|
3.4
|
29.8
|
1.0
|
|
C
|
F:SER23
|
3.4
|
31.1
|
1.0
|
|
CD
|
F:GLU36
|
3.4
|
36.6
|
1.0
|
|
OE2
|
F:GLU36
|
3.4
|
34.0
|
1.0
|
|
C
|
F:THR31
|
3.6
|
28.8
|
1.0
|
|
C
|
F:LEU26
|
3.7
|
38.6
|
1.0
|
|
CA
|
F:SER23
|
3.8
|
28.7
|
1.0
|
|
N
|
F:HIS28
|
3.8
|
31.2
|
1.0
|
|
C
|
F:GLY27
|
3.9
|
37.9
|
1.0
|
|
OG1
|
F:THR31
|
4.2
|
29.6
|
1.0
|
|
CA
|
F:HIS28
|
4.2
|
31.4
|
1.0
|
|
CA
|
F:GLY27
|
4.3
|
32.4
|
1.0
|
|
N
|
F:THR31
|
4.3
|
24.4
|
1.0
|
|
O
|
F:GLY27
|
4.3
|
36.3
|
1.0
|
|
CB
|
F:SER23
|
4.3
|
32.3
|
1.0
|
|
N
|
F:ASN33
|
4.3
|
28.3
|
1.0
|
|
N
|
F:PRO29
|
4.4
|
30.2
|
1.0
|
|
N
|
F:GLY27
|
4.4
|
33.7
|
1.0
|
|
N
|
F:LEU32
|
4.5
|
21.8
|
1.0
|
|
CA
|
F:LEU32
|
4.5
|
25.1
|
1.0
|
|
CA
|
F:THR31
|
4.5
|
27.5
|
1.0
|
|
CA
|
F:PRO29
|
4.5
|
29.5
|
1.0
|
|
N
|
F:LEU26
|
4.5
|
31.6
|
1.0
|
|
N
|
F:VAL24
|
4.6
|
29.3
|
1.0
|
|
ND2
|
F:ASN33
|
4.7
|
38.5
|
1.0
|
|
C
|
F:PRO29
|
4.7
|
32.6
|
1.0
|
|
CA
|
F:LEU26
|
4.8
|
33.8
|
1.0
|
|
C
|
F:LEU32
|
4.8
|
34.0
|
1.0
|
|
O
|
F:TYR22
|
4.8
|
31.4
|
1.0
|
|
CB
|
F:HIS28
|
4.8
|
34.9
|
1.0
|
|
CG
|
F:GLU36
|
4.9
|
31.5
|
1.0
|
|
N
|
F:ASP30
|
4.9
|
30.3
|
1.0
|
|
O
|
F:HOH331
|
4.9
|
37.8
|
1.0
|
|
CB
|
F:THR31
|
5.0
|
32.2
|
1.0
|
|
CG
|
F:ASN33
|
5.0
|
29.5
|
1.0
|
|
Sodium binding site 7 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 7 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na102
b:26.6
occ:1.00
|
O
|
G:LYS23
|
2.3
|
24.1
|
1.0
|
|
O
|
G:SER20
|
2.3
|
28.6
|
1.0
|
|
O
|
G:ALA28
|
2.3
|
27.3
|
1.0
|
|
O
|
G:ASN25
|
2.4
|
25.7
|
1.0
|
|
O
|
G:HOH203
|
2.5
|
25.1
|
1.0
|
|
C
|
G:SER20
|
3.3
|
31.5
|
1.0
|
|
C
|
G:ALA28
|
3.4
|
29.8
|
1.0
|
|
C
|
G:LYS23
|
3.5
|
24.9
|
1.0
|
|
C
|
G:ASN25
|
3.5
|
25.3
|
1.0
|
|
CE2
|
G:TYR30
|
3.5
|
24.2
|
1.0
|
|
CA
|
G:SER20
|
3.8
|
25.3
|
1.0
|
|
N
|
G:LYS23
|
4.0
|
24.5
|
1.0
|
|
N
|
G:ALA28
|
4.0
|
25.5
|
1.0
|
|
CA
|
G:ALA28
|
4.0
|
22.1
|
1.0
|
|
CB
|
G:ALA28
|
4.0
|
20.8
|
1.0
|
|
N
|
G:ASN25
|
4.0
|
23.4
|
1.0
|
|
C
|
G:GLY24
|
4.1
|
24.3
|
1.0
|
|
CD2
|
G:TYR30
|
4.1
|
20.8
|
1.0
|
|
CA
|
G:LYS23
|
4.3
|
21.2
|
1.0
|
|
CA
|
G:ASN25
|
4.4
|
22.6
|
1.0
|
|
N
|
G:LEU21
|
4.4
|
31.6
|
1.0
|
|
CZ
|
G:TYR30
|
4.4
|
24.5
|
1.0
|
|
N
|
G:PHE26
|
4.4
|
22.4
|
1.0
|
|
O
|
G:GLY24
|
4.4
|
28.1
|
1.0
|
|
N
|
G:GLY24
|
4.4
|
27.3
|
1.0
|
|
CA
|
G:PHE26
|
4.5
|
24.6
|
1.0
|
|
CA
|
G:GLY24
|
4.5
|
24.5
|
1.0
|
|
CB
|
G:SER20
|
4.5
|
24.7
|
1.0
|
|
OH
|
G:TYR30
|
4.5
|
25.0
|
1.0
|
|
OD2
|
G:ASP33
|
4.5
|
31.0
|
1.0
|
|
C
|
G:PHE26
|
4.5
|
25.4
|
1.0
|
|
N
|
G:VAL29
|
4.6
|
25.0
|
1.0
|
|
O
|
G:TYR19
|
4.6
|
26.6
|
1.0
|
|
N
|
G:ILE22
|
4.7
|
26.4
|
1.0
|
|
CA
|
G:LEU21
|
4.7
|
33.1
|
1.0
|
|
O
|
G:PHE26
|
4.8
|
26.7
|
1.0
|
|
C
|
G:LEU21
|
4.9
|
32.3
|
1.0
|
|
CA
|
G:VAL29
|
4.9
|
27.1
|
1.0
|
|
N
|
G:HIS27
|
5.0
|
29.6
|
1.0
|
|
Sodium binding site 8 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 8 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na202
b:24.2
occ:1.00
|
O
|
H:HIS28
|
2.4
|
26.3
|
1.0
|
|
O
|
H:HOH310
|
2.4
|
28.8
|
1.0
|
|
O
|
H:THR31
|
2.4
|
25.6
|
1.0
|
|
O
|
H:SER23
|
2.4
|
25.4
|
1.0
|
|
OE1
|
H:GLU36
|
2.4
|
23.6
|
1.0
|
|
O
|
H:LEU26
|
2.5
|
31.7
|
1.0
|
|
CD
|
H:GLU36
|
3.2
|
32.5
|
1.0
|
|
OE2
|
H:GLU36
|
3.3
|
30.0
|
1.0
|
|
C
|
H:SER23
|
3.4
|
26.7
|
1.0
|
|
C
|
H:HIS28
|
3.5
|
28.1
|
1.0
|
|
C
|
H:THR31
|
3.6
|
25.8
|
1.0
|
|
CA
|
H:SER23
|
3.7
|
26.0
|
1.0
|
|
C
|
H:LEU26
|
3.7
|
34.3
|
1.0
|
|
N
|
H:HIS28
|
3.9
|
27.8
|
1.0
|
|
C
|
H:GLY27
|
4.0
|
32.4
|
1.0
|
|
CB
|
H:SER23
|
4.2
|
30.8
|
1.0
|
|
N
|
H:ASN33
|
4.3
|
22.5
|
1.0
|
|
OG1
|
H:THR31
|
4.3
|
30.1
|
1.0
|
|
CA
|
H:GLY27
|
4.3
|
29.0
|
1.0
|
|
CA
|
H:HIS28
|
4.3
|
27.7
|
1.0
|
|
N
|
H:THR31
|
4.4
|
25.2
|
1.0
|
|
CA
|
H:LEU32
|
4.4
|
23.3
|
1.0
|
|
N
|
H:PRO29
|
4.4
|
29.3
|
1.0
|
|
N
|
H:LEU32
|
4.4
|
20.2
|
1.0
|
|
O
|
H:GLY27
|
4.5
|
33.0
|
1.0
|
|
N
|
H:GLY27
|
4.5
|
31.8
|
1.0
|
|
N
|
H:LEU26
|
4.5
|
27.8
|
1.0
|
|
CA
|
H:PRO29
|
4.5
|
30.0
|
1.0
|
|
CA
|
H:THR31
|
4.5
|
23.9
|
1.0
|
|
N
|
H:VAL24
|
4.6
|
28.9
|
1.0
|
|
O
|
H:TYR22
|
4.7
|
28.9
|
1.0
|
|
CA
|
H:LEU26
|
4.7
|
29.5
|
1.0
|
|
CG
|
H:GLU36
|
4.7
|
29.4
|
1.0
|
|
C
|
H:LEU32
|
4.7
|
26.3
|
1.0
|
|
C
|
H:PRO29
|
4.8
|
27.2
|
1.0
|
|
ND2
|
H:ASN33
|
4.8
|
36.1
|
1.0
|
|
N
|
H:SER23
|
5.0
|
31.4
|
1.0
|
|
O
|
H:HOH336
|
5.0
|
41.8
|
1.0
|
|
CG
|
H:ASN33
|
5.0
|
32.1
|
1.0
|
|
Sodium binding site 9 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 9 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na102
b:22.4
occ:1.00
|
O
|
I:LYS23
|
2.3
|
19.9
|
1.0
|
|
O
|
I:ALA28
|
2.3
|
23.1
|
1.0
|
|
O
|
I:SER20
|
2.3
|
18.2
|
1.0
|
|
O
|
I:ASN25
|
2.4
|
20.3
|
1.0
|
|
O
|
I:HOH279
|
2.6
|
30.0
|
1.0
|
|
C
|
I:SER20
|
3.3
|
22.0
|
1.0
|
|
C
|
I:ALA28
|
3.5
|
24.1
|
1.0
|
|
C
|
I:LYS23
|
3.5
|
21.1
|
1.0
|
|
C
|
I:ASN25
|
3.6
|
17.9
|
1.0
|
|
CE2
|
I:TYR30
|
3.6
|
22.6
|
1.0
|
|
O
|
I:HOH223
|
3.8
|
26.6
|
1.0
|
|
CA
|
I:SER20
|
3.8
|
16.4
|
1.0
|
|
N
|
I:ASN25
|
4.0
|
18.4
|
1.0
|
|
N
|
I:LYS23
|
4.0
|
21.3
|
1.0
|
|
N
|
I:ALA28
|
4.0
|
19.3
|
1.0
|
|
C
|
I:GLY24
|
4.1
|
23.9
|
1.0
|
|
CA
|
I:ALA28
|
4.1
|
19.3
|
1.0
|
|
CB
|
I:ALA28
|
4.1
|
18.9
|
1.0
|
|
CD2
|
I:TYR30
|
4.2
|
21.2
|
1.0
|
|
CA
|
I:LYS23
|
4.4
|
20.6
|
1.0
|
|
CA
|
I:ASN25
|
4.4
|
18.6
|
1.0
|
|
O
|
I:GLY24
|
4.4
|
23.5
|
1.0
|
|
N
|
I:GLY24
|
4.4
|
24.0
|
1.0
|
|
CZ
|
I:TYR30
|
4.4
|
22.2
|
1.0
|
|
N
|
I:LEU21
|
4.4
|
20.2
|
1.0
|
|
CA
|
I:GLY24
|
4.4
|
24.5
|
1.0
|
|
CB
|
I:SER20
|
4.5
|
19.2
|
1.0
|
|
O
|
I:TYR19
|
4.5
|
19.5
|
1.0
|
|
N
|
I:PHE26
|
4.5
|
18.4
|
1.0
|
|
N
|
I:VAL29
|
4.6
|
21.2
|
1.0
|
|
OD2
|
I:ASP33
|
4.6
|
28.8
|
1.0
|
|
CA
|
I:PHE26
|
4.6
|
19.2
|
1.0
|
|
OH
|
I:TYR30
|
4.6
|
21.2
|
1.0
|
|
N
|
I:ILE22
|
4.7
|
19.5
|
1.0
|
|
C
|
I:PHE26
|
4.7
|
18.9
|
1.0
|
|
CA
|
I:LEU21
|
4.8
|
21.7
|
1.0
|
|
CA
|
I:VAL29
|
4.9
|
22.4
|
1.0
|
|
CG
|
I:LYS23
|
4.9
|
28.4
|
1.0
|
|
Sodium binding site 10 out
of 10 in 4xjk
Go back to
Sodium Binding Sites List in 4xjk
Sodium binding site 10 out
of 10 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound 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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na202
b:23.8
occ:1.00
|
O
|
J:HIS28
|
2.3
|
26.3
|
1.0
|
|
O
|
J:LEU26
|
2.3
|
25.6
|
1.0
|
|
O
|
J:THR31
|
2.4
|
24.0
|
1.0
|
|
O
|
J:SER23
|
2.4
|
21.3
|
1.0
|
|
O
|
J:HOH365
|
2.5
|
28.5
|
1.0
|
|
O
|
J:HOH368
|
2.6
|
30.5
|
1.0
|
|
C
|
J:SER23
|
3.4
|
25.2
|
1.0
|
|
C
|
J:HIS28
|
3.4
|
29.1
|
1.0
|
|
C
|
J:LEU26
|
3.5
|
30.0
|
1.0
|
|
C
|
J:THR31
|
3.6
|
26.7
|
1.0
|
|
CA
|
J:SER23
|
3.8
|
20.6
|
1.0
|
|
O
|
J:HOH377
|
3.9
|
32.1
|
1.0
|
|
OE1
|
J:GLU36
|
3.9
|
31.9
|
1.0
|
|
N
|
J:HIS28
|
4.1
|
27.7
|
1.0
|
|
N
|
J:LEU26
|
4.1
|
24.6
|
1.0
|
|
CA
|
J:PRO29
|
4.2
|
22.2
|
1.0
|
|
N
|
J:THR31
|
4.2
|
28.1
|
1.0
|
|
N
|
J:PRO29
|
4.3
|
28.7
|
1.0
|
|
C
|
J:GLY27
|
4.3
|
33.7
|
1.0
|
|
CA
|
J:LEU26
|
4.3
|
31.4
|
1.0
|
|
OG1
|
J:THR31
|
4.4
|
27.8
|
1.0
|
|
CA
|
J:HIS28
|
4.4
|
28.3
|
1.0
|
|
CA
|
J:THR31
|
4.4
|
29.7
|
1.0
|
|
N
|
J:GLY27
|
4.5
|
29.7
|
1.0
|
|
CB
|
J:SER23
|
4.5
|
23.4
|
1.0
|
|
OE2
|
J:GLU36
|
4.5
|
32.1
|
1.0
|
|
C
|
J:PRO29
|
4.5
|
27.3
|
1.0
|
|
CA
|
J:GLY27
|
4.6
|
34.3
|
1.0
|
|
N
|
J:LEU32
|
4.6
|
21.8
|
1.0
|
|
CD
|
J:GLU36
|
4.6
|
35.1
|
1.0
|
|
N
|
J:VAL24
|
4.6
|
20.9
|
1.0
|
|
O
|
J:TYR22
|
4.7
|
21.8
|
1.0
|
|
CA
|
J:LEU32
|
4.7
|
21.5
|
1.0
|
|
O
|
J:HOH328
|
4.7
|
40.1
|
1.0
|
|
O
|
J:HOH383
|
4.8
|
34.4
|
1.0
|
|
O
|
J:GLY27
|
4.8
|
28.7
|
1.0
|
|
CB
|
J:LEU26
|
4.8
|
32.2
|
1.0
|
|
N
|
J:ASP30
|
4.8
|
27.2
|
1.0
|
|
N
|
J:LYS25
|
4.9
|
21.9
|
1.0
|
|
O
|
J:PRO29
|
4.9
|
29.2
|
1.0
|
|
C
|
J:VAL24
|
5.0
|
24.4
|
1.0
|
|
Reference:
D.M.Gagnon,
M.B.Brophy,
S.E.Bowman,
T.A.Stich,
C.L.Drennan,
R.D.Britt,
E.M.Nolan.
Manganese Binding Properties of Human Calprotectin Under Conditions of High and Low Calcium: X-Ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis. J.Am.Chem.Soc. V. 137 3004 2015.
ISSN: ESSN 1520-5126
PubMed: 25597447
DOI: 10.1021/JA512204S
Page generated: Mon Oct 7 19:07:47 2024
|
