Calcium in PDB 5th6: Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
Enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
All present enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9):
3.4.24.35;
Protein crystallography data
The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9), PDB code: 5th6
was solved by
T.C.Appleby,
A.E.Greenstein,
H.J.Kwon,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.22 /
1.70
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.546,
69.233,
84.093,
90.00,
101.77,
90.00
|
|
R / Rfree (%)
|
20.8 /
23.5
|
Other elements in 5th6:
The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
(pdb code 5th6). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9), PDB code: 5th6:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 1 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:16.6
occ:1.00
|
O
|
A:HOH629
|
2.3
|
13.3
|
1.0
|
|
O
|
A:GLY197
|
2.4
|
18.1
|
1.0
|
|
O
|
A:GLN199
|
2.4
|
14.2
|
1.0
|
|
O
|
A:ASP165
|
2.4
|
11.2
|
1.0
|
|
OD1
|
A:ASP201
|
2.4
|
12.4
|
1.0
|
|
O
|
A:HOH610
|
2.5
|
15.4
|
1.0
|
|
CG
|
A:ASP201
|
3.4
|
14.7
|
1.0
|
|
C
|
A:ASP165
|
3.5
|
12.8
|
1.0
|
|
C
|
A:GLY197
|
3.5
|
14.4
|
1.0
|
|
C
|
A:GLN199
|
3.6
|
14.6
|
1.0
|
|
OD2
|
A:ASP201
|
3.8
|
14.2
|
1.0
|
|
O
|
A:ALA164
|
4.1
|
17.6
|
1.0
|
|
C
|
A:ILE198
|
4.1
|
15.0
|
1.0
|
|
O
|
A:HOH618
|
4.1
|
21.2
|
1.0
|
|
N
|
A:ASP201
|
4.1
|
11.1
|
1.0
|
|
N
|
A:GLN199
|
4.2
|
11.8
|
1.0
|
|
O
|
A:ILE198
|
4.3
|
13.4
|
1.0
|
|
C
|
A:GLY200
|
4.3
|
12.3
|
1.0
|
|
N
|
A:GLY197
|
4.3
|
14.8
|
1.0
|
|
CA
|
A:GLY200
|
4.3
|
10.7
|
1.0
|
|
CA
|
A:ASP165
|
4.3
|
13.9
|
1.0
|
|
O
|
A:GLY195
|
4.4
|
13.7
|
1.0
|
|
CA
|
A:GLY197
|
4.4
|
17.8
|
1.0
|
|
N
|
A:GLY200
|
4.4
|
11.8
|
1.0
|
|
O
|
A:HOH779
|
4.4
|
28.1
|
1.0
|
|
N
|
A:ILE166
|
4.5
|
12.9
|
1.0
|
|
N
|
A:ILE198
|
4.5
|
15.6
|
1.0
|
|
CA
|
A:GLN199
|
4.5
|
12.8
|
1.0
|
|
CA
|
A:ILE198
|
4.5
|
14.4
|
1.0
|
|
CB
|
A:ASP201
|
4.6
|
12.5
|
1.0
|
|
N
|
A:VAL167
|
4.6
|
12.9
|
1.0
|
|
CA
|
A:ILE166
|
4.7
|
12.4
|
1.0
|
|
CA
|
A:ASP201
|
4.7
|
11.2
|
1.0
|
|
CG2
|
A:VAL167
|
4.8
|
16.4
|
1.0
|
|
C
|
A:PRO196
|
4.8
|
17.3
|
1.0
|
|
O
|
A:HOH686
|
4.9
|
17.5
|
1.0
|
|
CH2
|
A:TRP116
|
4.9
|
14.3
|
1.0
|
|
O
|
A:GLY200
|
5.0
|
10.8
|
1.0
|
|
Calcium binding site 2 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 2 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:13.0
occ:1.00
|
OE2
|
A:GLU208
|
2.2
|
12.5
|
1.0
|
|
O
|
A:GLY183
|
2.3
|
14.9
|
1.0
|
|
O
|
A:ASP185
|
2.3
|
14.4
|
1.0
|
|
O
|
A:LEU187
|
2.3
|
11.2
|
1.0
|
|
OD1
|
A:ASP182
|
2.3
|
13.5
|
1.0
|
|
OD2
|
A:ASP205
|
2.4
|
12.1
|
1.0
|
|
CG
|
A:ASP205
|
3.4
|
13.5
|
1.0
|
|
CG
|
A:ASP182
|
3.5
|
16.0
|
1.0
|
|
C
|
A:ASP185
|
3.5
|
15.8
|
1.0
|
|
CD
|
A:GLU208
|
3.5
|
12.6
|
1.0
|
|
C
|
A:GLY183
|
3.5
|
20.4
|
1.0
|
|
C
|
A:LEU187
|
3.5
|
11.9
|
1.0
|
|
N
|
A:ASP185
|
3.9
|
14.3
|
1.0
|
|
N
|
A:LEU187
|
3.9
|
11.0
|
1.0
|
|
C
|
A:LYS184
|
4.0
|
14.6
|
1.0
|
|
OD2
|
A:ASP182
|
4.0
|
16.5
|
1.0
|
|
CB
|
A:ASP205
|
4.1
|
12.4
|
1.0
|
|
N
|
A:GLY183
|
4.1
|
16.2
|
1.0
|
|
CA
|
A:ASP185
|
4.2
|
15.4
|
1.0
|
|
OE1
|
A:GLU208
|
4.2
|
13.4
|
1.0
|
|
OD1
|
A:ASP205
|
4.3
|
15.2
|
1.0
|
|
C
|
A:ASP182
|
4.3
|
16.4
|
1.0
|
|
CA
|
A:LEU187
|
4.3
|
11.3
|
1.0
|
|
C
|
A:GLY186
|
4.3
|
13.7
|
1.0
|
|
O
|
A:LYS184
|
4.3
|
15.3
|
1.0
|
|
CA
|
A:LYS184
|
4.4
|
17.7
|
1.0
|
|
N
|
A:ASP182
|
4.4
|
12.5
|
1.0
|
|
N
|
A:LYS184
|
4.4
|
16.5
|
1.0
|
|
CG
|
A:GLU208
|
4.4
|
14.1
|
1.0
|
|
CA
|
A:GLY183
|
4.4
|
19.1
|
1.0
|
|
N
|
A:LEU188
|
4.5
|
10.5
|
1.0
|
|
N
|
A:GLY186
|
4.5
|
16.1
|
1.0
|
|
CA
|
A:LEU188
|
4.6
|
9.7
|
1.0
|
|
CA
|
A:GLY186
|
4.6
|
16.0
|
1.0
|
|
CB
|
A:ASP182
|
4.6
|
19.4
|
1.0
|
|
CA
|
A:ASP182
|
4.7
|
14.2
|
1.0
|
|
CG
|
A:LEU187
|
4.7
|
17.0
|
1.0
|
|
O
|
A:HOH624
|
4.7
|
26.8
|
1.0
|
|
O
|
A:ASP182
|
4.8
|
21.0
|
1.0
|
|
CD1
|
A:LEU187
|
4.8
|
19.9
|
1.0
|
|
CD2
|
A:LEU188
|
4.9
|
13.5
|
1.0
|
|
O
|
A:GLY186
|
5.0
|
13.0
|
1.0
|
|
Calcium binding site 3 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 3 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca505
b:25.7
occ:1.00
|
O
|
A:GLU208
|
2.3
|
17.2
|
1.0
|
|
O
|
A:ASP206
|
2.4
|
15.6
|
1.0
|
|
O
|
A:HOH648
|
2.4
|
21.2
|
1.0
|
|
OD2
|
A:ASP131
|
2.4
|
20.4
|
1.0
|
|
OD1
|
A:ASP206
|
2.5
|
17.4
|
1.0
|
|
C
|
A:ASP206
|
3.2
|
13.9
|
1.0
|
|
CG
|
A:ASP131
|
3.3
|
22.0
|
1.0
|
|
C
|
A:GLU208
|
3.4
|
14.5
|
1.0
|
|
CG
|
A:ASP206
|
3.5
|
19.0
|
1.0
|
|
OD1
|
A:ASP131
|
3.5
|
23.9
|
1.0
|
|
CA
|
A:ASP206
|
3.7
|
14.6
|
1.0
|
|
OG
|
A:SER129
|
3.8
|
16.5
|
1.0
|
|
CB
|
A:ASP206
|
4.1
|
17.1
|
1.0
|
|
CD1
|
A:TRP210
|
4.1
|
15.6
|
1.0
|
|
N
|
A:GLU208
|
4.1
|
15.1
|
1.0
|
|
N
|
A:ASP207
|
4.3
|
13.7
|
1.0
|
|
O
|
A:HOH617
|
4.3
|
22.0
|
1.0
|
|
N
|
A:LEU209
|
4.3
|
14.2
|
1.0
|
|
C
|
A:ASP207
|
4.3
|
18.8
|
1.0
|
|
OD2
|
A:ASP206
|
4.3
|
18.7
|
1.0
|
|
CA
|
A:LEU209
|
4.4
|
13.5
|
1.0
|
|
CA
|
A:GLU208
|
4.4
|
12.5
|
1.0
|
|
CA
|
A:ASP207
|
4.5
|
13.4
|
1.0
|
|
N
|
A:TRP210
|
4.6
|
14.3
|
1.0
|
|
NE1
|
A:TRP210
|
4.7
|
12.2
|
1.0
|
|
CB
|
A:ASP131
|
4.7
|
15.9
|
1.0
|
|
O
|
A:ASP207
|
4.9
|
14.0
|
1.0
|
|
CB
|
A:SER129
|
4.9
|
16.5
|
1.0
|
|
O
|
A:ASP205
|
4.9
|
12.7
|
1.0
|
|
Calcium binding site 4 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 4 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:17.3
occ:1.00
|
O
|
B:GLY197
|
2.3
|
16.8
|
1.0
|
|
O
|
B:HOH613
|
2.4
|
16.7
|
1.0
|
|
O
|
B:HOH642
|
2.4
|
17.0
|
1.0
|
|
O
|
B:GLN199
|
2.4
|
16.3
|
1.0
|
|
O
|
B:ASP165
|
2.4
|
13.6
|
1.0
|
|
OD1
|
B:ASP201
|
2.4
|
15.1
|
1.0
|
|
CG
|
B:ASP201
|
3.4
|
15.5
|
1.0
|
|
C
|
B:ASP165
|
3.5
|
13.0
|
1.0
|
|
C
|
B:GLN199
|
3.5
|
16.2
|
1.0
|
|
C
|
B:GLY197
|
3.6
|
20.2
|
1.0
|
|
OD2
|
B:ASP201
|
3.9
|
17.9
|
1.0
|
|
O
|
B:ALA164
|
4.0
|
18.5
|
1.0
|
|
C
|
B:ILE198
|
4.1
|
16.9
|
1.0
|
|
N
|
B:ASP201
|
4.2
|
14.3
|
1.0
|
|
N
|
B:GLN199
|
4.2
|
18.3
|
1.0
|
|
CA
|
B:ASP165
|
4.3
|
11.8
|
1.0
|
|
CA
|
B:GLY200
|
4.3
|
14.6
|
1.0
|
|
O
|
B:ILE198
|
4.3
|
17.5
|
1.0
|
|
C
|
B:GLY200
|
4.3
|
15.5
|
1.0
|
|
N
|
B:GLY200
|
4.3
|
14.8
|
1.0
|
|
N
|
B:GLY197
|
4.4
|
18.3
|
1.0
|
|
O
|
B:HOH618
|
4.4
|
20.8
|
1.0
|
|
N
|
B:ILE166
|
4.4
|
11.1
|
1.0
|
|
CA
|
B:GLY197
|
4.4
|
21.8
|
1.0
|
|
O
|
B:GLY195
|
4.5
|
18.5
|
1.0
|
|
CA
|
B:GLN199
|
4.5
|
15.5
|
1.0
|
|
N
|
B:ILE198
|
4.5
|
17.7
|
1.0
|
|
N
|
B:VAL167
|
4.5
|
14.0
|
1.0
|
|
CA
|
B:ILE198
|
4.6
|
17.4
|
1.0
|
|
CB
|
B:ASP201
|
4.6
|
13.1
|
1.0
|
|
CA
|
B:ILE166
|
4.6
|
11.9
|
1.0
|
|
O
|
B:HOH662
|
4.7
|
17.4
|
1.0
|
|
CA
|
B:ASP201
|
4.7
|
12.7
|
1.0
|
|
C
|
B:PRO196
|
4.8
|
19.4
|
1.0
|
|
CG2
|
B:VAL167
|
4.8
|
15.8
|
1.0
|
|
O
|
B:HOH612
|
4.8
|
25.8
|
1.0
|
|
C
|
B:ALA164
|
5.0
|
15.6
|
1.0
|
|
Calcium binding site 5 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 5 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca504
b:13.8
occ:1.00
|
OE2
|
B:GLU208
|
2.2
|
14.9
|
1.0
|
|
O
|
B:GLY183
|
2.3
|
17.4
|
1.0
|
|
OD2
|
B:ASP205
|
2.3
|
14.4
|
1.0
|
|
O
|
B:LEU187
|
2.3
|
12.2
|
1.0
|
|
OD1
|
B:ASP182
|
2.4
|
22.6
|
1.0
|
|
O
|
B:ASP185
|
2.4
|
17.8
|
1.0
|
|
CD
|
B:GLU208
|
3.4
|
13.8
|
1.0
|
|
CG
|
B:ASP205
|
3.4
|
17.4
|
1.0
|
|
C
|
B:ASP185
|
3.5
|
16.1
|
1.0
|
|
CG
|
B:ASP182
|
3.5
|
22.1
|
1.0
|
|
C
|
B:LEU187
|
3.5
|
17.1
|
1.0
|
|
C
|
B:GLY183
|
3.5
|
21.4
|
1.0
|
|
N
|
B:ASP185
|
3.9
|
19.4
|
1.0
|
|
C
|
B:LYS184
|
4.0
|
21.2
|
1.0
|
|
N
|
B:LEU187
|
4.0
|
14.5
|
1.0
|
|
OD2
|
B:ASP182
|
4.1
|
22.7
|
1.0
|
|
CB
|
B:ASP205
|
4.1
|
13.2
|
1.0
|
|
N
|
B:GLY183
|
4.1
|
16.6
|
1.0
|
|
CA
|
B:ASP185
|
4.2
|
17.4
|
1.0
|
|
OE1
|
B:GLU208
|
4.2
|
18.2
|
1.0
|
|
N
|
B:ASP182
|
4.3
|
18.4
|
1.0
|
|
C
|
B:ASP182
|
4.3
|
18.9
|
1.0
|
|
O
|
B:LYS184
|
4.3
|
20.6
|
1.0
|
|
C
|
B:GLY186
|
4.3
|
18.4
|
1.0
|
|
CG
|
B:GLU208
|
4.3
|
13.4
|
1.0
|
|
OD1
|
B:ASP205
|
4.4
|
16.1
|
1.0
|
|
CA
|
B:LEU187
|
4.4
|
16.1
|
1.0
|
|
N
|
B:LYS184
|
4.5
|
15.9
|
1.0
|
|
CA
|
B:GLY183
|
4.5
|
17.0
|
1.0
|
|
N
|
B:LEU188
|
4.5
|
14.7
|
1.0
|
|
N
|
B:GLY186
|
4.5
|
16.1
|
1.0
|
|
CA
|
B:LYS184
|
4.5
|
21.0
|
1.0
|
|
CA
|
B:LEU188
|
4.5
|
13.0
|
1.0
|
|
O
|
B:HOH699
|
4.6
|
23.2
|
1.0
|
|
CA
|
B:GLY186
|
4.6
|
17.3
|
1.0
|
|
CA
|
B:ASP182
|
4.6
|
20.1
|
1.0
|
|
CD1
|
B:LEU187
|
4.6
|
26.8
|
1.0
|
|
CB
|
B:ASP182
|
4.7
|
16.9
|
1.0
|
|
O
|
B:ASP182
|
4.7
|
20.0
|
1.0
|
|
CD2
|
B:LEU188
|
4.9
|
13.8
|
1.0
|
|
O
|
B:GLY186
|
4.9
|
18.4
|
1.0
|
|
Calcium binding site 6 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 6 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca505
b:35.3
occ:1.00
|
O
|
B:GLU208
|
2.3
|
18.4
|
1.0
|
|
OD2
|
B:ASP131
|
2.3
|
25.2
|
1.0
|
|
O
|
B:ASP206
|
2.5
|
21.7
|
1.0
|
|
OD1
|
B:ASP206
|
2.6
|
20.6
|
1.0
|
|
CG
|
B:ASP131
|
3.1
|
26.1
|
1.0
|
|
OD1
|
B:ASP131
|
3.3
|
24.2
|
1.0
|
|
C
|
B:GLU208
|
3.4
|
15.9
|
1.0
|
|
C
|
B:ASP206
|
3.5
|
18.8
|
1.0
|
|
CG
|
B:ASP206
|
3.6
|
17.5
|
1.0
|
|
OG
|
B:SER129
|
3.7
|
15.6
|
1.0
|
|
CA
|
B:ASP206
|
4.0
|
15.5
|
1.0
|
|
CD1
|
B:TRP210
|
4.0
|
14.8
|
1.0
|
|
N
|
B:GLU208
|
4.2
|
14.9
|
1.0
|
|
N
|
B:LEU209
|
4.3
|
14.5
|
1.0
|
|
CA
|
B:LEU209
|
4.3
|
18.2
|
1.0
|
|
O
|
B:HOH629
|
4.3
|
30.6
|
1.0
|
|
CB
|
B:ASP206
|
4.3
|
18.1
|
1.0
|
|
OD2
|
B:ASP206
|
4.4
|
20.7
|
1.0
|
|
N
|
B:TRP210
|
4.5
|
18.0
|
1.0
|
|
CA
|
B:GLU208
|
4.5
|
16.7
|
1.0
|
|
C
|
B:ASP207
|
4.5
|
21.0
|
1.0
|
|
O
|
B:HOH648
|
4.5
|
20.3
|
1.0
|
|
CB
|
B:ASP131
|
4.5
|
23.7
|
1.0
|
|
N
|
B:ASP207
|
4.5
|
19.9
|
1.0
|
|
NE1
|
B:TRP210
|
4.7
|
15.4
|
1.0
|
|
CA
|
B:ASP207
|
4.7
|
18.7
|
1.0
|
|
CB
|
B:SER129
|
4.8
|
16.0
|
1.0
|
|
C
|
B:LEU209
|
4.9
|
16.5
|
1.0
|
|
O
|
B:ASP207
|
5.0
|
20.4
|
1.0
|
|
CG
|
B:TRP210
|
5.0
|
16.3
|
1.0
|
|
Calcium binding site 7 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 7 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca503
b:12.6
occ:1.00
|
O
|
C:GLN199
|
2.3
|
9.8
|
1.0
|
|
O
|
C:ASP165
|
2.4
|
8.0
|
1.0
|
|
O
|
C:GLY197
|
2.4
|
15.4
|
1.0
|
|
O
|
C:HOH656
|
2.4
|
11.3
|
1.0
|
|
O
|
C:HOH632
|
2.4
|
13.3
|
1.0
|
|
OD1
|
C:ASP201
|
2.5
|
9.9
|
1.0
|
|
CG
|
C:ASP201
|
3.4
|
12.3
|
1.0
|
|
C
|
C:ASP165
|
3.5
|
10.3
|
1.0
|
|
C
|
C:GLN199
|
3.5
|
11.6
|
1.0
|
|
C
|
C:GLY197
|
3.6
|
14.6
|
1.0
|
|
OD2
|
C:ASP201
|
3.9
|
11.1
|
1.0
|
|
O
|
C:ALA164
|
4.1
|
14.5
|
1.0
|
|
O
|
C:HOH646
|
4.1
|
17.5
|
1.0
|
|
C
|
C:ILE198
|
4.1
|
12.1
|
1.0
|
|
N
|
C:ASP201
|
4.1
|
8.7
|
1.0
|
|
O
|
C:ILE198
|
4.2
|
11.7
|
1.0
|
|
N
|
C:GLN199
|
4.2
|
11.3
|
1.0
|
|
CA
|
C:GLY200
|
4.3
|
8.9
|
1.0
|
|
C
|
C:GLY200
|
4.3
|
9.1
|
1.0
|
|
CA
|
C:ASP165
|
4.3
|
11.8
|
1.0
|
|
N
|
C:GLY200
|
4.3
|
8.4
|
1.0
|
|
N
|
C:GLY197
|
4.4
|
13.4
|
1.0
|
|
O
|
C:GLY195
|
4.4
|
11.1
|
1.0
|
|
CA
|
C:GLY197
|
4.4
|
15.3
|
1.0
|
|
N
|
C:ILE166
|
4.4
|
8.2
|
1.0
|
|
CA
|
C:GLN199
|
4.5
|
10.8
|
1.0
|
|
N
|
C:ILE198
|
4.5
|
13.6
|
1.0
|
|
CA
|
C:ILE198
|
4.5
|
14.6
|
1.0
|
|
N
|
C:VAL167
|
4.6
|
7.4
|
1.0
|
|
CB
|
C:ASP201
|
4.6
|
11.3
|
1.0
|
|
CA
|
C:ILE166
|
4.6
|
8.7
|
1.0
|
|
CA
|
C:ASP201
|
4.7
|
6.1
|
1.0
|
|
C
|
C:PRO196
|
4.8
|
11.4
|
1.0
|
|
O
|
C:HOH708
|
4.8
|
13.6
|
1.0
|
|
CH2
|
C:TRP116
|
4.9
|
12.5
|
1.0
|
|
O
|
C:GLY200
|
5.0
|
9.3
|
1.0
|
|
Calcium binding site 8 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 8 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca504
b:12.9
occ:1.00
|
O
|
C:GLY183
|
2.3
|
12.7
|
1.0
|
|
OE2
|
C:GLU208
|
2.3
|
13.5
|
1.0
|
|
O
|
C:ASP185
|
2.3
|
14.0
|
1.0
|
|
O
|
C:LEU187
|
2.4
|
11.6
|
1.0
|
|
OD1
|
C:ASP182
|
2.4
|
13.8
|
1.0
|
|
OD2
|
C:ASP205
|
2.4
|
11.6
|
1.0
|
|
C
|
C:ASP185
|
3.5
|
12.1
|
1.0
|
|
CG
|
C:ASP205
|
3.5
|
14.3
|
1.0
|
|
CG
|
C:ASP182
|
3.5
|
14.7
|
1.0
|
|
CD
|
C:GLU208
|
3.5
|
12.2
|
1.0
|
|
C
|
C:GLY183
|
3.5
|
20.4
|
1.0
|
|
C
|
C:LEU187
|
3.5
|
11.7
|
1.0
|
|
N
|
C:ASP185
|
3.8
|
15.9
|
1.0
|
|
OD2
|
C:ASP182
|
4.0
|
18.1
|
1.0
|
|
C
|
C:LYS184
|
4.0
|
14.9
|
1.0
|
|
N
|
C:LEU187
|
4.0
|
10.2
|
1.0
|
|
CB
|
C:ASP205
|
4.1
|
11.8
|
1.0
|
|
CA
|
C:ASP185
|
4.2
|
13.9
|
1.0
|
|
N
|
C:GLY183
|
4.2
|
13.4
|
1.0
|
|
OE1
|
C:GLU208
|
4.2
|
13.3
|
1.0
|
|
C
|
C:ASP182
|
4.3
|
17.2
|
1.0
|
|
N
|
C:ASP182
|
4.4
|
13.3
|
1.0
|
|
OD1
|
C:ASP205
|
4.4
|
13.1
|
1.0
|
|
CA
|
C:LEU187
|
4.4
|
10.5
|
1.0
|
|
O
|
C:LYS184
|
4.4
|
15.7
|
1.0
|
|
C
|
C:GLY186
|
4.4
|
9.8
|
1.0
|
|
N
|
C:LYS184
|
4.4
|
15.0
|
1.0
|
|
CA
|
C:LYS184
|
4.4
|
14.1
|
1.0
|
|
O
|
C:HOH609
|
4.4
|
26.5
|
1.0
|
|
CA
|
C:GLY183
|
4.4
|
16.9
|
1.0
|
|
CG
|
C:GLU208
|
4.5
|
12.7
|
1.0
|
|
N
|
C:GLY186
|
4.5
|
11.9
|
1.0
|
|
N
|
C:LEU188
|
4.5
|
6.2
|
1.0
|
|
CD1
|
C:LEU187
|
4.5
|
20.7
|
1.0
|
|
CA
|
C:LEU188
|
4.6
|
7.3
|
1.0
|
|
CA
|
C:GLY186
|
4.6
|
11.7
|
1.0
|
|
CA
|
C:ASP182
|
4.7
|
14.1
|
1.0
|
|
CB
|
C:ASP182
|
4.7
|
15.6
|
1.0
|
|
O
|
C:ASP182
|
4.7
|
18.2
|
1.0
|
|
CG
|
C:LEU187
|
4.9
|
15.7
|
1.0
|
|
CD2
|
C:LEU188
|
4.9
|
13.1
|
1.0
|
|
Calcium binding site 9 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 9 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca505
b:22.4
occ:1.00
|
O
|
C:GLU208
|
2.3
|
13.3
|
1.0
|
|
O
|
C:ASP206
|
2.3
|
13.8
|
1.0
|
|
O
|
C:HOH617
|
2.4
|
24.1
|
1.0
|
|
OD2
|
C:ASP131
|
2.4
|
18.5
|
1.0
|
|
OD1
|
C:ASP206
|
2.6
|
16.2
|
1.0
|
|
O
|
C:HOH783
|
2.6
|
29.8
|
1.0
|
|
CG
|
C:ASP131
|
3.2
|
20.8
|
1.0
|
|
C
|
C:ASP206
|
3.2
|
10.3
|
1.0
|
|
OD1
|
C:ASP131
|
3.3
|
22.5
|
1.0
|
|
CG
|
C:ASP206
|
3.4
|
14.4
|
1.0
|
|
C
|
C:GLU208
|
3.5
|
14.3
|
1.0
|
|
CA
|
C:ASP206
|
3.7
|
11.0
|
1.0
|
|
OG
|
C:SER129
|
3.9
|
15.4
|
1.0
|
|
CB
|
C:ASP206
|
4.1
|
11.2
|
1.0
|
|
N
|
C:GLU208
|
4.2
|
13.9
|
1.0
|
|
CD1
|
C:TRP210
|
4.2
|
9.5
|
1.0
|
|
OD2
|
C:ASP206
|
4.3
|
15.4
|
1.0
|
|
N
|
C:LEU209
|
4.3
|
10.4
|
1.0
|
|
N
|
C:ASP207
|
4.3
|
11.8
|
1.0
|
|
CA
|
C:LEU209
|
4.3
|
14.9
|
1.0
|
|
C
|
C:ASP207
|
4.4
|
16.7
|
1.0
|
|
CA
|
C:GLU208
|
4.5
|
12.4
|
1.0
|
|
O
|
C:HOH648
|
4.5
|
21.9
|
1.0
|
|
CA
|
C:ASP207
|
4.6
|
13.5
|
1.0
|
|
CB
|
C:ASP131
|
4.6
|
14.3
|
1.0
|
|
N
|
C:TRP210
|
4.6
|
12.4
|
1.0
|
|
NE1
|
C:TRP210
|
4.8
|
7.8
|
1.0
|
|
O
|
C:ASP207
|
4.9
|
15.7
|
1.0
|
|
Calcium binding site 10 out
of 12 in 5th6
Go back to
Calcium Binding Sites List in 5th6
Calcium binding site 10 out
of 12 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9)
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Apo MMP9) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca503
b:16.7
occ:1.00
|
O
|
D:ASP165
|
2.3
|
13.6
|
1.0
|
|
O
|
D:GLY197
|
2.4
|
19.1
|
1.0
|
|
O
|
D:GLN199
|
2.4
|
13.2
|
1.0
|
|
O
|
D:HOH640
|
2.4
|
16.9
|
1.0
|
|
OD1
|
D:ASP201
|
2.5
|
11.8
|
1.0
|
|
O
|
D:HOH653
|
2.5
|
14.3
|
1.0
|
|
CG
|
D:ASP201
|
3.5
|
13.2
|
1.0
|
|
C
|
D:ASP165
|
3.5
|
11.8
|
1.0
|
|
C
|
D:GLY197
|
3.6
|
18.8
|
1.0
|
|
C
|
D:GLN199
|
3.6
|
11.7
|
1.0
|
|
OD2
|
D:ASP201
|
3.9
|
11.4
|
1.0
|
|
O
|
D:ALA164
|
4.1
|
17.1
|
1.0
|
|
C
|
D:ILE198
|
4.1
|
16.2
|
1.0
|
|
N
|
D:ASP201
|
4.1
|
10.5
|
1.0
|
|
N
|
D:GLN199
|
4.3
|
15.3
|
1.0
|
|
CA
|
D:ASP165
|
4.3
|
14.2
|
1.0
|
|
O
|
D:ILE198
|
4.3
|
15.1
|
1.0
|
|
O
|
D:HOH779
|
4.3
|
36.8
|
1.0
|
|
O
|
D:HOH613
|
4.3
|
22.1
|
1.0
|
|
CA
|
D:GLY200
|
4.3
|
10.4
|
1.0
|
|
C
|
D:GLY200
|
4.3
|
11.7
|
1.0
|
|
N
|
D:GLY197
|
4.4
|
18.2
|
1.0
|
|
N
|
D:GLY200
|
4.4
|
10.8
|
1.0
|
|
N
|
D:ILE166
|
4.4
|
11.2
|
1.0
|
|
O
|
D:HOH638
|
4.4
|
21.1
|
1.0
|
|
CA
|
D:GLY197
|
4.4
|
21.6
|
1.0
|
|
O
|
D:GLY195
|
4.4
|
15.1
|
1.0
|
|
N
|
D:ILE198
|
4.5
|
18.6
|
1.0
|
|
CA
|
D:GLN199
|
4.6
|
12.8
|
1.0
|
|
CA
|
D:ILE198
|
4.6
|
18.7
|
1.0
|
|
N
|
D:VAL167
|
4.6
|
12.2
|
1.0
|
|
CA
|
D:ILE166
|
4.6
|
8.8
|
1.0
|
|
CB
|
D:ASP201
|
4.6
|
12.0
|
1.0
|
|
CA
|
D:ASP201
|
4.7
|
10.5
|
1.0
|
|
C
|
D:PRO196
|
4.8
|
18.3
|
1.0
|
|
O
|
D:HOH647
|
4.8
|
18.9
|
1.0
|
|
CG2
|
D:VAL167
|
4.9
|
15.7
|
1.0
|
|
CH2
|
D:TRP116
|
4.9
|
13.6
|
1.0
|
|
Reference:
T.C.Appleby,
A.E.Greenstein,
M.Hung,
A.Liclican,
M.Velasquez,
A.G.Villasenor,
R.Wang,
M.H.Wong,
X.Liu,
G.A.Papalia,
B.E.Schultz,
R.Sakowicz,
V.Smith,
H.J.Kwon.
Biochemical Characterization and Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9. J. Biol. Chem. V. 292 6810 2017.
ISSN: ESSN 1083-351X
PubMed: 28235803
DOI: 10.1074/JBC.M116.760579
Page generated: Wed Jul 9 10:18:15 2025
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