Calcium in PDB 5w1f: Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
Protein crystallography data
The structure of Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin, PDB code: 5w1f
was solved by
T.G.Nakashige,
C.L.Drennan,
E.M.Nolan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.24 /
2.60
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.020,
77.611,
222.722,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
22.4 /
26.2
|
Other elements in 5w1f:
The structure of Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
(pdb code 5w1f). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin, PDB code: 5w1f:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 1 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca102
b:26.4
occ:1.00
|
OD1
|
A:ASN61
|
2.4
|
35.5
|
1.0
|
|
O
|
A:ALA65
|
2.4
|
37.8
|
1.0
|
|
OD1
|
A:ASP63
|
2.4
|
31.7
|
1.0
|
|
OE1
|
A:GLU70
|
2.5
|
31.9
|
1.0
|
|
OD1
|
A:ASP59
|
2.5
|
32.2
|
1.0
|
|
O
|
A:HOH212
|
2.6
|
24.9
|
1.0
|
|
OE2
|
A:GLU70
|
2.6
|
31.3
|
1.0
|
|
CD
|
A:GLU70
|
2.8
|
31.5
|
1.0
|
|
CG
|
A:ASP63
|
3.3
|
32.3
|
1.0
|
|
CG
|
A:ASN61
|
3.5
|
34.4
|
1.0
|
|
C
|
A:ALA65
|
3.5
|
36.8
|
1.0
|
|
OD2
|
A:ASP63
|
3.6
|
32.0
|
1.0
|
|
CG
|
A:ASP59
|
3.6
|
33.6
|
1.0
|
|
ND2
|
A:ASN61
|
4.0
|
34.9
|
1.0
|
|
CA
|
A:ASP59
|
4.2
|
36.5
|
1.0
|
|
CA
|
A:VAL66
|
4.3
|
34.4
|
1.0
|
|
N
|
A:VAL66
|
4.3
|
35.8
|
1.0
|
|
CG
|
A:GLU70
|
4.4
|
31.1
|
1.0
|
|
N
|
A:ILE60
|
4.4
|
36.5
|
1.0
|
|
N
|
A:ASN61
|
4.5
|
32.2
|
1.0
|
|
N
|
A:ALA65
|
4.5
|
35.8
|
1.0
|
|
N
|
A:ASP63
|
4.5
|
34.0
|
1.0
|
|
OD2
|
A:ASP59
|
4.5
|
33.7
|
1.0
|
|
ND2
|
A:ASN67
|
4.5
|
35.6
|
1.0
|
|
N
|
A:ASN67
|
4.5
|
32.8
|
1.0
|
|
CB
|
A:ASP59
|
4.5
|
35.1
|
1.0
|
|
C
|
A:ASP59
|
4.5
|
36.9
|
1.0
|
|
CA
|
A:ALA65
|
4.5
|
36.8
|
1.0
|
|
CB
|
A:ASP63
|
4.6
|
33.3
|
1.0
|
|
N
|
A:THR62
|
4.7
|
32.1
|
1.0
|
|
CB
|
A:ASN61
|
4.8
|
32.2
|
1.0
|
|
CG
|
A:ASN67
|
4.8
|
34.4
|
1.0
|
|
C
|
A:VAL66
|
4.9
|
34.3
|
1.0
|
|
Calcium binding site 2 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 2 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:46.0
occ:1.00
|
OD1
|
B:ASN69
|
2.4
|
49.9
|
1.0
|
|
OD1
|
B:ASP71
|
2.4
|
48.1
|
1.0
|
|
O
|
B:GLN73
|
2.5
|
44.3
|
1.0
|
|
OE1
|
B:GLU78
|
2.5
|
36.0
|
1.0
|
|
OD1
|
B:ASP67
|
2.6
|
38.3
|
1.0
|
|
O
|
B:HOH316
|
2.7
|
40.6
|
1.0
|
|
OE2
|
B:GLU78
|
2.9
|
34.5
|
1.0
|
|
CD
|
B:GLU78
|
3.0
|
35.4
|
1.0
|
|
C
|
B:GLN73
|
3.2
|
45.3
|
1.0
|
|
CG
|
B:ASN69
|
3.3
|
49.0
|
1.0
|
|
CG
|
B:ASP71
|
3.4
|
47.1
|
1.0
|
|
ND2
|
B:ASN69
|
3.6
|
49.9
|
1.0
|
|
OD2
|
B:ASP71
|
3.6
|
47.6
|
1.0
|
|
CG
|
B:ASP67
|
3.7
|
38.7
|
1.0
|
|
N
|
B:LEU74
|
3.9
|
45.9
|
1.0
|
|
CA
|
B:GLN73
|
4.0
|
46.0
|
1.0
|
|
N
|
B:GLN73
|
4.1
|
45.3
|
1.0
|
|
CA
|
B:LEU74
|
4.1
|
45.9
|
1.0
|
|
CB
|
B:GLN73
|
4.1
|
46.5
|
1.0
|
|
N
|
B:SER75
|
4.2
|
44.9
|
1.0
|
|
OD2
|
B:ASP67
|
4.4
|
39.2
|
1.0
|
|
CG
|
B:GLU78
|
4.5
|
35.6
|
1.0
|
|
N
|
B:ASP71
|
4.6
|
46.1
|
1.0
|
|
CA
|
B:ASP67
|
4.6
|
36.2
|
1.0
|
|
C
|
B:LEU74
|
4.7
|
45.9
|
1.0
|
|
O
|
C:HOH202
|
4.7
|
24.1
|
1.0
|
|
N
|
B:ASN69
|
4.7
|
45.2
|
1.0
|
|
CB
|
B:ASP71
|
4.7
|
46.2
|
1.0
|
|
CB
|
B:ASP67
|
4.7
|
38.4
|
1.0
|
|
CB
|
B:ASN69
|
4.7
|
47.4
|
1.0
|
|
N
|
B:THR68
|
4.8
|
38.8
|
1.0
|
|
OG
|
B:SER75
|
4.8
|
42.2
|
1.0
|
|
N
|
B:ALA70
|
4.9
|
47.9
|
1.0
|
|
C
|
B:ASP67
|
4.9
|
37.4
|
1.0
|
|
CD2
|
B:LEU74
|
4.9
|
45.7
|
1.0
|
|
Calcium binding site 3 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 3 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca103
b:31.1
occ:1.00
|
OD1
|
C:ASN61
|
2.4
|
28.4
|
1.0
|
|
OD1
|
C:ASP63
|
2.4
|
37.9
|
1.0
|
|
OE1
|
C:GLU70
|
2.5
|
30.5
|
1.0
|
|
OD1
|
C:ASP59
|
2.5
|
35.8
|
1.0
|
|
O
|
C:ALA65
|
2.5
|
34.4
|
1.0
|
|
O
|
C:HOH204
|
2.6
|
35.0
|
1.0
|
|
OE2
|
C:GLU70
|
2.7
|
31.0
|
1.0
|
|
CD
|
C:GLU70
|
2.9
|
30.6
|
1.0
|
|
CG
|
C:ASP63
|
3.2
|
37.4
|
1.0
|
|
OD2
|
C:ASP63
|
3.3
|
38.2
|
1.0
|
|
CG
|
C:ASN61
|
3.5
|
29.9
|
1.0
|
|
C
|
C:ALA65
|
3.7
|
33.9
|
1.0
|
|
CG
|
C:ASP59
|
3.7
|
35.6
|
1.0
|
|
ND2
|
C:ASN61
|
4.1
|
29.2
|
1.0
|
|
CA
|
C:ASP59
|
4.1
|
32.3
|
1.0
|
|
N
|
C:ILE60
|
4.3
|
33.4
|
1.0
|
|
N
|
C:ASP63
|
4.3
|
34.2
|
1.0
|
|
N
|
C:ALA65
|
4.4
|
32.4
|
1.0
|
|
N
|
C:ASN61
|
4.4
|
34.6
|
1.0
|
|
CG
|
C:GLU70
|
4.4
|
30.7
|
1.0
|
|
CA
|
C:VAL66
|
4.4
|
29.5
|
1.0
|
|
N
|
C:VAL66
|
4.5
|
32.2
|
1.0
|
|
CB
|
C:ASP59
|
4.5
|
34.0
|
1.0
|
|
CB
|
C:ASP63
|
4.5
|
35.4
|
1.0
|
|
C
|
C:ASP59
|
4.5
|
32.7
|
1.0
|
|
OD2
|
C:ASP59
|
4.5
|
36.3
|
1.0
|
|
N
|
C:ASN67
|
4.6
|
28.3
|
1.0
|
|
N
|
C:THR62
|
4.6
|
36.8
|
1.0
|
|
CA
|
C:ALA65
|
4.6
|
33.6
|
1.0
|
|
ND2
|
C:ASN67
|
4.7
|
34.3
|
1.0
|
|
CB
|
C:ASN61
|
4.8
|
32.2
|
1.0
|
|
CG
|
C:ASN67
|
4.9
|
33.5
|
1.0
|
|
CA
|
C:ASP63
|
4.9
|
33.5
|
1.0
|
|
N
|
C:GLY64
|
4.9
|
31.4
|
1.0
|
|
CA
|
C:ASN61
|
5.0
|
35.0
|
1.0
|
|
Calcium binding site 4 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 4 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:34.8
occ:1.00
|
O
|
D:LEU26
|
2.4
|
34.5
|
1.0
|
|
O
|
D:THR31
|
2.4
|
38.7
|
1.0
|
|
O
|
D:SER23
|
2.4
|
32.9
|
1.0
|
|
OE1
|
D:GLU36
|
2.5
|
36.6
|
1.0
|
|
O
|
D:HIS28
|
2.5
|
41.3
|
1.0
|
|
O
|
D:HOH317
|
2.6
|
37.0
|
1.0
|
|
OE2
|
D:GLU36
|
2.7
|
37.6
|
1.0
|
|
CD
|
D:GLU36
|
2.9
|
36.6
|
1.0
|
|
C
|
D:SER23
|
3.4
|
33.4
|
1.0
|
|
C
|
D:THR31
|
3.6
|
38.0
|
1.0
|
|
C
|
D:HIS28
|
3.6
|
42.0
|
1.0
|
|
C
|
D:LEU26
|
3.6
|
35.4
|
1.0
|
|
CA
|
D:SER23
|
3.8
|
34.0
|
1.0
|
|
N
|
D:HIS28
|
4.1
|
41.2
|
1.0
|
|
N
|
D:LEU26
|
4.2
|
36.3
|
1.0
|
|
C
|
D:GLY27
|
4.3
|
39.8
|
1.0
|
|
N
|
D:THR31
|
4.4
|
34.5
|
1.0
|
|
CA
|
D:HIS28
|
4.4
|
41.4
|
1.0
|
|
CG
|
D:GLU36
|
4.5
|
36.8
|
1.0
|
|
ND2
|
D:ASN33
|
4.5
|
44.8
|
1.0
|
|
N
|
D:LEU32
|
4.5
|
39.8
|
1.0
|
|
CA
|
D:LEU32
|
4.5
|
41.4
|
1.0
|
|
CB
|
D:SER23
|
4.5
|
33.3
|
1.0
|
|
N
|
D:ASN33
|
4.5
|
42.0
|
1.0
|
|
O
|
D:TYR22
|
4.5
|
38.1
|
1.0
|
|
CA
|
D:LEU26
|
4.5
|
35.4
|
1.0
|
|
CA
|
D:PRO29
|
4.5
|
39.5
|
1.0
|
|
OG1
|
D:THR31
|
4.5
|
37.4
|
1.0
|
|
N
|
D:PRO29
|
4.5
|
41.8
|
1.0
|
|
N
|
D:VAL24
|
4.6
|
33.3
|
1.0
|
|
CA
|
D:THR31
|
4.6
|
36.0
|
1.0
|
|
OE1
|
D:GLN73
|
4.6
|
44.9
|
1.0
|
|
N
|
D:GLY27
|
4.6
|
37.0
|
1.0
|
|
CA
|
D:GLY27
|
4.7
|
37.9
|
1.0
|
|
C
|
D:PRO29
|
4.7
|
36.7
|
1.0
|
|
O
|
D:GLY27
|
4.8
|
41.0
|
1.0
|
|
N
|
D:LYS25
|
4.8
|
33.7
|
1.0
|
|
C
|
D:LEU32
|
4.9
|
42.6
|
1.0
|
|
CG
|
D:ASN33
|
4.9
|
44.0
|
1.0
|
|
N
|
D:SER23
|
5.0
|
34.4
|
1.0
|
|
CB
|
D:HIS28
|
5.0
|
40.1
|
1.0
|
|
Calcium binding site 5 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 5 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca203
b:33.9
occ:1.00
|
OD1
|
D:ASN69
|
2.4
|
42.8
|
1.0
|
|
O
|
D:GLN73
|
2.4
|
44.2
|
1.0
|
|
OE1
|
D:GLU78
|
2.4
|
39.8
|
1.0
|
|
O
|
D:HOH303
|
2.5
|
49.9
|
1.0
|
|
OD1
|
D:ASP67
|
2.6
|
36.4
|
1.0
|
|
OD1
|
D:ASP71
|
2.6
|
45.3
|
1.0
|
|
OE2
|
D:GLU78
|
2.7
|
39.9
|
1.0
|
|
CD
|
D:GLU78
|
2.9
|
39.0
|
1.0
|
|
CG
|
D:ASP71
|
3.3
|
45.5
|
1.0
|
|
CG
|
D:ASN69
|
3.3
|
42.7
|
1.0
|
|
OD2
|
D:ASP71
|
3.3
|
44.9
|
1.0
|
|
C
|
D:GLN73
|
3.5
|
43.1
|
1.0
|
|
ND2
|
D:ASN69
|
3.7
|
43.0
|
1.0
|
|
CG
|
D:ASP67
|
3.8
|
37.6
|
1.0
|
|
N
|
D:SER75
|
4.2
|
37.4
|
1.0
|
|
N
|
D:LEU74
|
4.3
|
41.2
|
1.0
|
|
CG
|
D:GLU78
|
4.3
|
37.1
|
1.0
|
|
CA
|
D:LEU74
|
4.4
|
39.2
|
1.0
|
|
CA
|
D:GLN73
|
4.4
|
43.8
|
1.0
|
|
N
|
D:GLN73
|
4.4
|
44.9
|
1.0
|
|
OD2
|
D:ASP67
|
4.5
|
38.2
|
1.0
|
|
CB
|
D:GLN73
|
4.5
|
43.6
|
1.0
|
|
CB
|
D:ASN69
|
4.6
|
43.0
|
1.0
|
|
CA
|
D:ASP67
|
4.6
|
38.2
|
1.0
|
|
N
|
D:ASN69
|
4.7
|
43.4
|
1.0
|
|
OG
|
D:SER75
|
4.7
|
34.9
|
1.0
|
|
O
|
A:HOH205
|
4.7
|
26.4
|
1.0
|
|
CB
|
D:ASP71
|
4.7
|
46.4
|
1.0
|
|
CB
|
D:ASP67
|
4.7
|
38.4
|
1.0
|
|
N
|
D:ASP71
|
4.7
|
47.8
|
1.0
|
|
C
|
D:LEU74
|
4.8
|
38.7
|
1.0
|
|
N
|
D:THR68
|
4.9
|
41.9
|
1.0
|
|
C
|
D:ASP67
|
5.0
|
40.2
|
1.0
|
|
CB
|
D:SER75
|
5.0
|
35.8
|
1.0
|
|
Calcium binding site 6 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 6 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca102
b:34.2
occ:1.00
|
OD1
|
G:ASN61
|
2.4
|
30.7
|
1.0
|
|
OD1
|
G:ASP63
|
2.4
|
28.6
|
1.0
|
|
OD1
|
G:ASP59
|
2.5
|
29.1
|
1.0
|
|
OE1
|
G:GLU70
|
2.5
|
30.9
|
1.0
|
|
O
|
G:ALA65
|
2.5
|
31.3
|
1.0
|
|
OE2
|
G:GLU70
|
2.5
|
31.4
|
1.0
|
|
O
|
G:HOH202
|
2.5
|
34.0
|
1.0
|
|
CD
|
G:GLU70
|
2.9
|
30.9
|
1.0
|
|
CG
|
G:ASP63
|
3.2
|
28.3
|
1.0
|
|
OD2
|
G:ASP63
|
3.3
|
29.3
|
1.0
|
|
CG
|
G:ASN61
|
3.6
|
29.3
|
1.0
|
|
CG
|
G:ASP59
|
3.6
|
28.4
|
1.0
|
|
C
|
G:ALA65
|
3.7
|
31.5
|
1.0
|
|
CA
|
G:ASP59
|
4.0
|
29.2
|
1.0
|
|
ND2
|
G:ASN61
|
4.1
|
28.3
|
1.0
|
|
N
|
G:ILE60
|
4.3
|
28.2
|
1.0
|
|
N
|
G:ASP63
|
4.4
|
24.6
|
1.0
|
|
CB
|
G:ASP59
|
4.4
|
28.1
|
1.0
|
|
CA
|
G:VAL66
|
4.4
|
34.4
|
1.0
|
|
N
|
G:ASN61
|
4.4
|
28.1
|
1.0
|
|
CG
|
G:GLU70
|
4.4
|
30.9
|
1.0
|
|
C
|
G:ASP59
|
4.4
|
29.1
|
1.0
|
|
OD2
|
G:ASP59
|
4.4
|
28.4
|
1.0
|
|
N
|
G:VAL66
|
4.4
|
33.1
|
1.0
|
|
N
|
G:ASN67
|
4.4
|
35.7
|
1.0
|
|
N
|
G:ALA65
|
4.5
|
28.5
|
1.0
|
|
CB
|
G:ASP63
|
4.5
|
25.6
|
1.0
|
|
N
|
G:THR62
|
4.6
|
28.1
|
1.0
|
|
CA
|
G:ALA65
|
4.7
|
29.9
|
1.0
|
|
ND2
|
G:ASN67
|
4.7
|
36.4
|
1.0
|
|
CB
|
G:ASN61
|
4.8
|
28.5
|
1.0
|
|
CG
|
G:ASN67
|
4.8
|
37.0
|
1.0
|
|
OD1
|
G:ASN67
|
4.9
|
38.6
|
1.0
|
|
CA
|
G:ASP63
|
4.9
|
24.4
|
1.0
|
|
C
|
G:VAL66
|
4.9
|
36.0
|
1.0
|
|
CA
|
G:ASN61
|
5.0
|
28.5
|
1.0
|
|
Calcium binding site 7 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 7 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca203
b:54.0
occ:1.00
|
OD1
|
H:ASN69
|
2.4
|
51.4
|
1.0
|
|
OE1
|
H:GLU78
|
2.4
|
43.0
|
1.0
|
|
O
|
H:GLN73
|
2.4
|
49.4
|
1.0
|
|
OD1
|
H:ASP71
|
2.5
|
47.0
|
1.0
|
|
O
|
H:HOH313
|
2.6
|
40.2
|
1.0
|
|
OD1
|
H:ASP67
|
2.7
|
46.0
|
1.0
|
|
OE2
|
H:GLU78
|
2.7
|
42.6
|
1.0
|
|
CD
|
H:GLU78
|
2.9
|
42.8
|
1.0
|
|
CG
|
H:ASN69
|
3.3
|
50.3
|
1.0
|
|
CG
|
H:ASP71
|
3.4
|
47.7
|
1.0
|
|
C
|
H:GLN73
|
3.4
|
50.3
|
1.0
|
|
ND2
|
H:ASN69
|
3.6
|
50.9
|
1.0
|
|
OD2
|
H:ASP71
|
3.6
|
48.0
|
1.0
|
|
CG
|
H:ASP67
|
3.8
|
46.5
|
1.0
|
|
N
|
H:LEU74
|
4.1
|
50.1
|
1.0
|
|
CA
|
H:LEU74
|
4.2
|
49.7
|
1.0
|
|
CA
|
H:GLN73
|
4.3
|
53.1
|
1.0
|
|
N
|
H:SER75
|
4.3
|
51.3
|
1.0
|
|
CG
|
H:GLU78
|
4.3
|
42.1
|
1.0
|
|
N
|
H:GLN73
|
4.4
|
53.1
|
1.0
|
|
CB
|
H:GLN73
|
4.5
|
55.6
|
1.0
|
|
CA
|
H:ASP67
|
4.5
|
47.4
|
1.0
|
|
OD2
|
H:ASP67
|
4.6
|
47.4
|
1.0
|
|
CB
|
H:ASN69
|
4.7
|
48.1
|
1.0
|
|
CB
|
H:ASP67
|
4.7
|
46.6
|
1.0
|
|
CB
|
H:ASP71
|
4.7
|
49.7
|
1.0
|
|
N
|
H:ASN69
|
4.7
|
45.4
|
1.0
|
|
N
|
H:ASP71
|
4.7
|
51.9
|
1.0
|
|
C
|
H:LEU74
|
4.8
|
52.3
|
1.0
|
|
CD2
|
H:LEU74
|
4.8
|
44.2
|
1.0
|
|
OG
|
H:SER75
|
4.8
|
48.0
|
1.0
|
|
N
|
H:THR68
|
4.9
|
45.4
|
1.0
|
|
C
|
H:ASP67
|
5.0
|
47.2
|
1.0
|
|
Calcium binding site 8 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 8 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca103
b:42.9
occ:1.00
|
O
|
E:ALA65
|
2.4
|
36.4
|
1.0
|
|
OD1
|
E:ASP63
|
2.4
|
42.8
|
1.0
|
|
OE1
|
E:GLU70
|
2.4
|
30.2
|
1.0
|
|
OD1
|
E:ASN61
|
2.5
|
36.7
|
1.0
|
|
O
|
E:HOH205
|
2.5
|
31.6
|
1.0
|
|
OD1
|
E:ASP59
|
2.5
|
40.8
|
1.0
|
|
OE2
|
E:GLU70
|
2.7
|
30.2
|
1.0
|
|
CD
|
E:GLU70
|
2.9
|
30.3
|
1.0
|
|
CG
|
E:ASP63
|
3.4
|
43.0
|
1.0
|
|
C
|
E:ALA65
|
3.5
|
36.4
|
1.0
|
|
CG
|
E:ASN61
|
3.6
|
36.8
|
1.0
|
|
CG
|
E:ASP59
|
3.7
|
40.5
|
1.0
|
|
OD2
|
E:ASP63
|
3.7
|
43.5
|
1.0
|
|
ND2
|
E:ASN61
|
4.1
|
36.0
|
1.0
|
|
CA
|
E:ASP59
|
4.2
|
37.1
|
1.0
|
|
N
|
E:VAL66
|
4.3
|
36.4
|
1.0
|
|
CA
|
E:VAL66
|
4.3
|
35.6
|
1.0
|
|
CG
|
E:GLU70
|
4.4
|
30.8
|
1.0
|
|
N
|
E:ILE60
|
4.4
|
35.0
|
1.0
|
|
N
|
E:ALA65
|
4.4
|
37.2
|
1.0
|
|
N
|
E:ASN67
|
4.5
|
37.4
|
1.0
|
|
OD2
|
E:ASP59
|
4.5
|
42.2
|
1.0
|
|
CB
|
E:ASP59
|
4.5
|
38.2
|
1.0
|
|
CA
|
E:ALA65
|
4.5
|
37.0
|
1.0
|
|
N
|
E:ASN61
|
4.5
|
39.3
|
1.0
|
|
N
|
E:ASP63
|
4.5
|
40.0
|
1.0
|
|
C
|
E:ASP59
|
4.5
|
35.4
|
1.0
|
|
CB
|
E:ASP63
|
4.7
|
41.7
|
1.0
|
|
N
|
E:THR62
|
4.8
|
40.7
|
1.0
|
|
CB
|
E:ASN61
|
4.9
|
37.9
|
1.0
|
|
C
|
E:VAL66
|
4.9
|
36.8
|
1.0
|
|
CB
|
E:ALA65
|
4.9
|
37.6
|
1.0
|
|
Calcium binding site 9 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 9 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca202
b:33.1
occ:1.00
|
O
|
F:LEU26
|
2.4
|
35.4
|
1.0
|
|
O
|
F:THR31
|
2.4
|
31.7
|
1.0
|
|
O
|
F:SER23
|
2.5
|
30.3
|
1.0
|
|
O
|
F:HIS28
|
2.5
|
32.5
|
1.0
|
|
OE1
|
F:GLU36
|
2.5
|
33.5
|
1.0
|
|
OE2
|
F:GLU36
|
2.7
|
33.9
|
1.0
|
|
O
|
F:HOH321
|
2.9
|
19.3
|
1.0
|
|
CD
|
F:GLU36
|
2.9
|
33.1
|
1.0
|
|
C
|
F:SER23
|
3.4
|
30.4
|
1.0
|
|
C
|
F:LEU26
|
3.6
|
33.8
|
1.0
|
|
C
|
F:HIS28
|
3.6
|
31.0
|
1.0
|
|
C
|
F:THR31
|
3.6
|
30.0
|
1.0
|
|
CA
|
F:SER23
|
3.8
|
29.4
|
1.0
|
|
N
|
F:HIS28
|
4.0
|
29.9
|
1.0
|
|
N
|
F:LEU26
|
4.2
|
32.4
|
1.0
|
|
ND2
|
F:ASN33
|
4.2
|
33.2
|
1.0
|
|
C
|
F:GLY27
|
4.3
|
30.2
|
1.0
|
|
N
|
F:ASN33
|
4.4
|
30.4
|
1.0
|
|
CA
|
F:HIS28
|
4.4
|
29.7
|
1.0
|
|
OG1
|
F:THR31
|
4.4
|
25.0
|
1.0
|
|
CG
|
F:GLU36
|
4.4
|
31.2
|
1.0
|
|
CA
|
F:LEU32
|
4.5
|
29.9
|
1.0
|
|
N
|
F:THR31
|
4.5
|
27.2
|
1.0
|
|
CA
|
F:LEU26
|
4.5
|
32.9
|
1.0
|
|
CB
|
F:SER23
|
4.5
|
27.5
|
1.0
|
|
OE1
|
F:GLN73
|
4.5
|
36.8
|
1.0
|
|
N
|
F:LEU32
|
4.5
|
29.5
|
1.0
|
|
O
|
F:TYR22
|
4.5
|
30.4
|
1.0
|
|
N
|
F:GLY27
|
4.5
|
32.8
|
1.0
|
|
N
|
F:VAL24
|
4.6
|
31.1
|
1.0
|
|
CA
|
F:GLY27
|
4.6
|
30.9
|
1.0
|
|
N
|
F:PRO29
|
4.6
|
30.4
|
1.0
|
|
CA
|
F:THR31
|
4.6
|
27.1
|
1.0
|
|
CA
|
F:PRO29
|
4.6
|
30.2
|
1.0
|
|
CG
|
F:ASN33
|
4.7
|
32.3
|
1.0
|
|
C
|
F:LEU32
|
4.7
|
30.1
|
1.0
|
|
O
|
F:GLY27
|
4.8
|
31.4
|
1.0
|
|
C
|
F:PRO29
|
4.8
|
30.1
|
1.0
|
|
N
|
F:LYS25
|
4.8
|
31.2
|
1.0
|
|
CB
|
F:HIS28
|
4.9
|
27.6
|
1.0
|
|
N
|
F:SER23
|
5.0
|
29.5
|
1.0
|
|
Calcium binding site 10 out
of 10 in 5w1f
Go back to
Calcium Binding Sites List in 5w1f
Calcium binding site 10 out
of 10 in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin
 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 Ni(II)- and Ca(II)-Bound Human Calprotectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca203
b:37.9
occ:1.00
|
O
|
F:GLN73
|
2.4
|
30.7
|
1.0
|
|
OE1
|
F:GLU78
|
2.4
|
30.8
|
1.0
|
|
OD1
|
F:ASP71
|
2.4
|
36.0
|
1.0
|
|
OD1
|
F:ASN69
|
2.4
|
38.8
|
1.0
|
|
O
|
F:HOH320
|
2.4
|
24.2
|
1.0
|
|
OD1
|
F:ASP67
|
2.6
|
31.3
|
1.0
|
|
OE2
|
F:GLU78
|
2.7
|
30.5
|
1.0
|
|
CD
|
F:GLU78
|
2.9
|
30.3
|
1.0
|
|
CG
|
F:ASP71
|
3.3
|
35.1
|
1.0
|
|
C
|
F:GLN73
|
3.3
|
29.9
|
1.0
|
|
CG
|
F:ASN69
|
3.5
|
37.1
|
1.0
|
|
OD2
|
F:ASP71
|
3.6
|
35.7
|
1.0
|
|
CG
|
F:ASP67
|
3.7
|
30.7
|
1.0
|
|
ND2
|
F:ASN69
|
4.1
|
35.8
|
1.0
|
|
N
|
F:LEU74
|
4.1
|
29.6
|
1.0
|
|
CA
|
F:GLN73
|
4.2
|
30.8
|
1.0
|
|
CA
|
F:LEU74
|
4.2
|
30.2
|
1.0
|
|
N
|
F:GLN73
|
4.3
|
31.4
|
1.0
|
|
N
|
F:SER75
|
4.3
|
34.9
|
1.0
|
|
CG
|
F:GLU78
|
4.3
|
30.4
|
1.0
|
|
CA
|
F:ASP67
|
4.4
|
26.2
|
1.0
|
|
N
|
F:ASN69
|
4.4
|
33.8
|
1.0
|
|
N
|
F:THR68
|
4.4
|
27.8
|
1.0
|
|
CB
|
F:GLN73
|
4.5
|
32.0
|
1.0
|
|
N
|
F:ASP71
|
4.5
|
33.7
|
1.0
|
|
O
|
F:HOH303
|
4.5
|
21.3
|
1.0
|
|
OD2
|
F:ASP67
|
4.5
|
31.9
|
1.0
|
|
C
|
F:ASP67
|
4.6
|
27.2
|
1.0
|
|
CB
|
F:ASP71
|
4.6
|
33.9
|
1.0
|
|
CB
|
F:ASP67
|
4.6
|
28.2
|
1.0
|
|
CB
|
F:ASN69
|
4.7
|
36.2
|
1.0
|
|
N
|
F:ALA70
|
4.8
|
34.0
|
1.0
|
|
C
|
F:LEU74
|
4.8
|
33.6
|
1.0
|
|
CD2
|
F:LEU74
|
4.9
|
29.9
|
1.0
|
|
OG
|
F:SER75
|
4.9
|
34.3
|
1.0
|
|
CA
|
F:ASP71
|
5.0
|
33.7
|
1.0
|
|
CA
|
F:ASN69
|
5.0
|
34.5
|
1.0
|
|
Reference:
T.G.Nakashige,
E.M.Zygiel,
C.L.Drennan,
E.M.Nolan.
Nickel Sequestration By the Host-Defense Protein Human Calprotectin. J. Am. Chem. Soc. V. 139 8828 2017.
ISSN: ESSN 1520-5126
PubMed: 28573847
DOI: 10.1021/JACS.7B01212
Page generated: Mon Jul 15 12:42:29 2024
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