Calcium in PDB 4fvl: Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
Protein crystallography data
The structure of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4fvl
was solved by
E.A.Stura,
L.Vera,
R.Visse,
H.Nagase,
V.Dive,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.11 /
2.44
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.780,
157.270,
105.550,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.6 /
22.3
|
Other elements in 4fvl:
The structure of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
(pdb code 4fvl). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the
Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4fvl:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 1 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:39.7
occ:1.00
|
O
|
A:LEU184
|
2.2
|
34.7
|
1.0
|
|
OD2
|
A:ASP202
|
2.2
|
38.5
|
1.0
|
|
OE2
|
A:GLU205
|
2.3
|
37.2
|
1.0
|
|
O
|
A:GLY180
|
2.3
|
40.8
|
1.0
|
|
OD1
|
A:ASP179
|
2.5
|
36.0
|
1.0
|
|
O
|
A:SER182
|
2.5
|
42.0
|
1.0
|
|
CG
|
A:ASP202
|
3.3
|
35.2
|
1.0
|
|
C
|
A:LEU184
|
3.4
|
34.4
|
1.0
|
|
CD
|
A:GLU205
|
3.5
|
29.8
|
1.0
|
|
C
|
A:GLY180
|
3.5
|
44.1
|
1.0
|
|
CG
|
A:ASP179
|
3.6
|
40.6
|
1.0
|
|
C
|
A:SER182
|
3.6
|
34.5
|
1.0
|
|
N
|
A:LEU184
|
3.9
|
30.4
|
1.0
|
|
CB
|
A:ASP202
|
3.9
|
32.5
|
1.0
|
|
N
|
A:GLY180
|
4.0
|
37.9
|
1.0
|
|
CA
|
A:LEU184
|
4.0
|
32.0
|
1.0
|
|
N
|
A:SER182
|
4.1
|
46.0
|
1.0
|
|
OD2
|
A:ASP179
|
4.1
|
48.0
|
1.0
|
|
N
|
A:ASP179
|
4.2
|
39.1
|
1.0
|
|
C
|
A:PRO181
|
4.2
|
51.5
|
1.0
|
|
CB
|
A:LEU184
|
4.2
|
35.0
|
1.0
|
|
C
|
A:ASP179
|
4.2
|
41.7
|
1.0
|
|
C
|
A:GLY183
|
4.2
|
37.9
|
1.0
|
|
OD1
|
A:ASP202
|
4.3
|
39.6
|
1.0
|
|
OE1
|
A:GLU205
|
4.3
|
37.0
|
1.0
|
|
CA
|
A:SER182
|
4.3
|
33.9
|
1.0
|
|
CG
|
A:GLU205
|
4.3
|
32.7
|
1.0
|
|
CA
|
A:GLY180
|
4.3
|
40.3
|
1.0
|
|
N
|
A:LEU185
|
4.5
|
29.5
|
1.0
|
|
N
|
A:PRO181
|
4.5
|
42.0
|
1.0
|
|
O
|
A:PRO181
|
4.5
|
46.2
|
1.0
|
|
CA
|
A:PRO181
|
4.6
|
49.5
|
1.0
|
|
CA
|
A:ASP179
|
4.6
|
40.3
|
1.0
|
|
N
|
A:GLY183
|
4.6
|
31.6
|
1.0
|
|
O
|
A:GLY183
|
4.7
|
32.4
|
1.0
|
|
CB
|
A:ASP179
|
4.7
|
49.7
|
1.0
|
|
CA
|
A:LEU185
|
4.7
|
28.8
|
1.0
|
|
O
|
A:ASP179
|
4.7
|
51.1
|
1.0
|
|
CA
|
A:GLY183
|
4.7
|
37.3
|
1.0
|
|
CB
|
A:PHE178
|
4.9
|
39.1
|
1.0
|
|
CD1
|
A:LEU185
|
5.0
|
33.7
|
1.0
|
|
Calcium binding site 2 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 2 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:43.7
occ:1.00
|
O
|
A:ASN194
|
2.3
|
43.7
|
1.0
|
|
O
|
A:ASP162
|
2.3
|
33.4
|
1.0
|
|
O
|
A:HOH663
|
2.4
|
42.1
|
1.0
|
|
O
|
A:HOH619
|
2.5
|
37.1
|
1.0
|
|
O
|
A:GLY196
|
2.6
|
47.7
|
1.0
|
|
OD1
|
A:ASP198
|
2.6
|
37.0
|
1.0
|
|
C
|
A:ASP162
|
3.4
|
35.8
|
1.0
|
|
C
|
A:ASN194
|
3.5
|
43.2
|
1.0
|
|
C
|
A:GLY196
|
3.5
|
41.1
|
1.0
|
|
CG
|
A:ASP198
|
3.6
|
44.8
|
1.0
|
|
N
|
A:GLY196
|
4.0
|
41.0
|
1.0
|
|
C
|
A:TYR195
|
4.0
|
44.5
|
1.0
|
|
O
|
A:ALA161
|
4.1
|
39.0
|
1.0
|
|
N
|
A:ASP198
|
4.1
|
27.4
|
1.0
|
|
O
|
A:HOH629
|
4.1
|
41.0
|
1.0
|
|
CA
|
A:ASP162
|
4.2
|
37.0
|
1.0
|
|
OD2
|
A:ASP198
|
4.2
|
42.6
|
1.0
|
|
CA
|
A:GLY196
|
4.2
|
41.9
|
1.0
|
|
O
|
A:TYR195
|
4.3
|
41.1
|
1.0
|
|
CA
|
A:ASN194
|
4.4
|
50.3
|
1.0
|
|
N
|
A:ILE163
|
4.4
|
34.7
|
1.0
|
|
N
|
A:TYR195
|
4.4
|
37.3
|
1.0
|
|
N
|
A:GLY197
|
4.4
|
39.8
|
1.0
|
|
N
|
A:ASN194
|
4.4
|
47.7
|
1.0
|
|
CA
|
A:TYR195
|
4.4
|
39.1
|
1.0
|
|
O
|
A:GLY192
|
4.5
|
50.6
|
1.0
|
|
N
|
A:MET164
|
4.5
|
29.2
|
1.0
|
|
CA
|
A:ILE163
|
4.5
|
32.8
|
1.0
|
|
CA
|
A:GLY197
|
4.5
|
34.4
|
1.0
|
|
C
|
A:GLY197
|
4.6
|
30.6
|
1.0
|
|
CB
|
A:ASP198
|
4.7
|
35.1
|
1.0
|
|
CG
|
A:MET164
|
4.8
|
35.8
|
1.0
|
|
C
|
A:PRO193
|
4.8
|
49.6
|
1.0
|
|
CA
|
A:ASP198
|
4.8
|
29.4
|
1.0
|
|
CH2
|
A:TRP113
|
4.9
|
38.4
|
1.0
|
|
Calcium binding site 3 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 3 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca505
b:17.6
occ:1.00
|
O
|
A:ASP291
|
2.3
|
19.5
|
1.0
|
|
O
|
A:ASP432
|
2.3
|
17.4
|
1.0
|
|
O
|
A:ASP335
|
2.4
|
16.1
|
1.0
|
|
O
|
A:HOH669
|
2.4
|
23.2
|
1.0
|
|
O
|
A:SER383
|
2.5
|
18.9
|
1.0
|
|
O
|
A:HOH605
|
2.5
|
30.2
|
1.0
|
|
O
|
A:HOH612
|
2.6
|
23.4
|
1.0
|
|
C
|
A:ASP291
|
3.4
|
18.1
|
1.0
|
|
C
|
A:ASP432
|
3.5
|
16.2
|
1.0
|
|
C
|
A:ASP335
|
3.5
|
18.6
|
1.0
|
|
C
|
A:SER383
|
3.5
|
20.2
|
1.0
|
|
CA
|
A:ASP291
|
4.0
|
17.4
|
1.0
|
|
CA
|
A:ASP335
|
4.1
|
19.0
|
1.0
|
|
CA
|
A:ASP432
|
4.1
|
14.2
|
1.0
|
|
CA
|
A:SER383
|
4.2
|
21.0
|
1.0
|
|
N
|
A:ALA292
|
4.5
|
18.9
|
1.0
|
|
N
|
A:ALA433
|
4.6
|
13.2
|
1.0
|
|
N
|
A:ALA336
|
4.6
|
22.6
|
1.0
|
|
N
|
A:ALA384
|
4.6
|
18.6
|
1.0
|
|
O
|
A:LEU290
|
4.7
|
20.3
|
1.0
|
|
CB
|
A:SER383
|
4.7
|
20.7
|
1.0
|
|
O
|
A:ILE334
|
4.8
|
25.5
|
0.3
|
|
CB
|
A:ASP291
|
4.8
|
21.6
|
1.0
|
|
CB
|
A:ASP432
|
4.8
|
19.0
|
1.0
|
|
O
|
A:ILE334
|
4.9
|
25.7
|
0.7
|
|
O
|
A:VAL431
|
4.9
|
19.7
|
1.0
|
|
CB
|
A:ASP335
|
4.9
|
19.0
|
1.0
|
|
CA
|
A:ALA292
|
4.9
|
16.7
|
1.0
|
|
CA
|
A:ALA433
|
4.9
|
14.1
|
1.0
|
|
CA
|
A:ALA384
|
4.9
|
17.1
|
1.0
|
|
CA
|
A:ALA336
|
5.0
|
15.7
|
1.0
|
|
Calcium binding site 4 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 4 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca506
b:34.5
occ:1.00
|
O
|
A:ALA385
|
2.2
|
19.7
|
1.0
|
|
O
|
A:ILE293
|
2.3
|
22.6
|
1.0
|
|
O
|
A:ALA337
|
2.4
|
21.2
|
1.0
|
|
O
|
A:VAL434
|
2.5
|
16.1
|
1.0
|
|
CL
|
A:CL508
|
2.7
|
14.8
|
1.0
|
|
CL
|
A:CL509
|
3.1
|
38.0
|
1.0
|
|
C
|
A:ALA385
|
3.5
|
21.1
|
1.0
|
|
C
|
A:ILE293
|
3.5
|
18.6
|
1.0
|
|
C
|
A:ALA337
|
3.6
|
21.3
|
1.0
|
|
C
|
A:VAL434
|
3.7
|
14.5
|
1.0
|
|
N
|
A:ALA385
|
4.1
|
15.5
|
1.0
|
|
N
|
A:ILE293
|
4.1
|
15.7
|
1.0
|
|
N
|
A:VAL434
|
4.2
|
12.5
|
1.0
|
|
N
|
A:ALA337
|
4.3
|
18.7
|
1.0
|
|
CA
|
A:ALA385
|
4.3
|
17.7
|
1.0
|
|
CA
|
A:ILE293
|
4.4
|
19.3
|
1.0
|
|
CG1
|
A:VAL434
|
4.4
|
13.6
|
1.0
|
|
N
|
A:VAL386
|
4.4
|
20.0
|
1.0
|
|
CA
|
A:VAL386
|
4.5
|
19.1
|
1.0
|
|
CA
|
A:ALA337
|
4.5
|
23.6
|
1.0
|
|
N
|
A:THR294
|
4.5
|
18.1
|
1.0
|
|
CA
|
A:VAL434
|
4.5
|
14.9
|
1.0
|
|
CA
|
A:TYR338
|
4.5
|
24.3
|
1.0
|
|
CB
|
A:TYR338
|
4.5
|
22.9
|
1.0
|
|
N
|
A:TYR338
|
4.5
|
22.6
|
1.0
|
|
CA
|
A:THR294
|
4.6
|
20.0
|
1.0
|
|
N
|
A:TYR435
|
4.7
|
17.2
|
1.0
|
|
CA
|
A:TYR435
|
4.7
|
22.4
|
1.0
|
|
OG1
|
A:THR294
|
4.7
|
30.3
|
1.0
|
|
CB
|
A:VAL386
|
4.7
|
23.4
|
1.0
|
|
CB
|
A:TYR435
|
4.8
|
18.0
|
1.0
|
|
CB
|
A:ALA385
|
4.8
|
21.5
|
1.0
|
|
CB
|
A:ILE293
|
4.8
|
19.8
|
1.0
|
|
CG2
|
A:THR294
|
4.8
|
27.3
|
1.0
|
|
CB
|
A:ALA337
|
4.9
|
17.0
|
1.0
|
|
CB
|
A:THR294
|
5.0
|
25.9
|
1.0
|
|
Calcium binding site 5 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 5 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca507
b:55.2
occ:1.00
|
O
|
A:ASP203
|
2.2
|
36.2
|
1.0
|
|
O
|
A:GLU205
|
2.4
|
39.5
|
1.0
|
|
OD2
|
A:ASP128
|
2.5
|
40.4
|
1.0
|
|
OD2
|
A:ASP203
|
2.9
|
43.6
|
1.0
|
|
C
|
A:ASP203
|
3.2
|
37.7
|
1.0
|
|
CG
|
A:ASP128
|
3.4
|
49.4
|
1.0
|
|
C
|
A:GLU205
|
3.5
|
36.9
|
1.0
|
|
OD1
|
A:ASP128
|
3.5
|
51.2
|
1.0
|
|
CA
|
A:ASP203
|
3.9
|
35.1
|
1.0
|
|
CG
|
A:ASP203
|
3.9
|
42.9
|
1.0
|
|
C
|
A:ASP204
|
4.0
|
43.2
|
1.0
|
|
N
|
A:GLU205
|
4.1
|
33.0
|
1.0
|
|
N
|
A:ASP204
|
4.1
|
39.0
|
1.0
|
|
CB
|
A:ASP203
|
4.2
|
35.6
|
1.0
|
|
CA
|
A:ASP204
|
4.2
|
34.8
|
1.0
|
|
N
|
A:THR206
|
4.3
|
36.2
|
1.0
|
|
CA
|
A:THR206
|
4.3
|
37.6
|
1.0
|
|
O
|
A:ASP204
|
4.4
|
40.5
|
1.0
|
|
OG1
|
A:THR126
|
4.4
|
32.7
|
1.0
|
|
CA
|
A:GLU205
|
4.4
|
34.7
|
1.0
|
|
CD1
|
A:TRP207
|
4.6
|
29.4
|
1.0
|
|
CB
|
A:ASP128
|
4.8
|
40.7
|
1.0
|
|
OD1
|
A:ASP203
|
5.0
|
48.2
|
1.0
|
|
NE1
|
A:TRP207
|
5.0
|
36.9
|
1.0
|
|
Calcium binding site 6 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 6 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:22.5
occ:1.00
|
O
|
B:GLY180
|
2.2
|
33.1
|
1.0
|
|
OE2
|
B:GLU205
|
2.2
|
26.8
|
1.0
|
|
O
|
B:SER182
|
2.2
|
22.7
|
1.0
|
|
OD2
|
B:ASP202
|
2.3
|
21.0
|
1.0
|
|
O
|
B:LEU184
|
2.3
|
23.5
|
1.0
|
|
OD1
|
B:ASP179
|
2.4
|
20.1
|
1.0
|
|
CG
|
B:ASP202
|
3.4
|
23.8
|
1.0
|
|
C
|
B:GLY180
|
3.4
|
26.9
|
1.0
|
|
C
|
B:SER182
|
3.4
|
24.4
|
1.0
|
|
CD
|
B:GLU205
|
3.4
|
24.9
|
1.0
|
|
C
|
B:LEU184
|
3.5
|
25.0
|
1.0
|
|
CG
|
B:ASP179
|
3.5
|
26.3
|
1.0
|
|
N
|
B:LEU184
|
3.9
|
18.9
|
1.0
|
|
N
|
B:SER182
|
3.9
|
33.0
|
1.0
|
|
N
|
B:GLY180
|
3.9
|
29.4
|
1.0
|
|
C
|
B:PRO181
|
4.0
|
27.7
|
1.0
|
|
CB
|
B:ASP202
|
4.0
|
22.9
|
1.0
|
|
OD2
|
B:ASP179
|
4.1
|
23.8
|
1.0
|
|
CA
|
B:LEU184
|
4.1
|
19.9
|
1.0
|
|
CA
|
B:SER182
|
4.2
|
29.2
|
1.0
|
|
C
|
B:GLY183
|
4.2
|
23.9
|
1.0
|
|
C
|
B:ASP179
|
4.2
|
21.8
|
1.0
|
|
CA
|
B:GLY180
|
4.2
|
28.1
|
1.0
|
|
OE1
|
B:GLU205
|
4.3
|
25.7
|
1.0
|
|
OD1
|
B:ASP202
|
4.3
|
17.5
|
1.0
|
|
N
|
B:PRO181
|
4.3
|
27.5
|
1.0
|
|
N
|
B:ASP179
|
4.3
|
22.9
|
1.0
|
|
O
|
B:PRO181
|
4.3
|
28.8
|
1.0
|
|
CG
|
B:GLU205
|
4.3
|
24.8
|
1.0
|
|
CB
|
B:LEU184
|
4.4
|
26.9
|
1.0
|
|
CA
|
B:PRO181
|
4.4
|
28.1
|
1.0
|
|
N
|
B:GLY183
|
4.4
|
26.8
|
1.0
|
|
CA
|
B:GLY183
|
4.6
|
22.6
|
1.0
|
|
N
|
B:LEU185
|
4.6
|
21.1
|
1.0
|
|
CA
|
B:ASP179
|
4.6
|
19.9
|
1.0
|
|
CB
|
B:ASP179
|
4.7
|
21.1
|
1.0
|
|
O
|
B:ASP179
|
4.7
|
30.8
|
1.0
|
|
O
|
B:GLY183
|
4.8
|
26.8
|
1.0
|
|
CA
|
B:LEU185
|
4.8
|
19.3
|
1.0
|
|
Calcium binding site 7 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 7 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca504
b:28.8
occ:1.00
|
O
|
B:ASP162
|
2.2
|
22.6
|
1.0
|
|
O
|
B:ASN194
|
2.2
|
35.2
|
1.0
|
|
O
|
B:HOH633
|
2.3
|
29.7
|
1.0
|
|
O
|
B:GLY196
|
2.3
|
20.5
|
1.0
|
|
OD1
|
B:ASP198
|
2.5
|
27.4
|
1.0
|
|
O
|
B:HOH713
|
2.6
|
28.8
|
1.0
|
|
C
|
B:ASP162
|
3.4
|
26.2
|
1.0
|
|
C
|
B:ASN194
|
3.4
|
33.1
|
1.0
|
|
C
|
B:GLY196
|
3.5
|
20.5
|
1.0
|
|
CG
|
B:ASP198
|
3.5
|
26.5
|
1.0
|
|
C
|
B:TYR195
|
3.9
|
31.0
|
1.0
|
|
OD2
|
B:ASP198
|
4.0
|
29.9
|
1.0
|
|
N
|
B:GLY196
|
4.0
|
25.0
|
1.0
|
|
O
|
B:TYR195
|
4.1
|
25.0
|
1.0
|
|
N
|
B:ASP198
|
4.1
|
19.2
|
1.0
|
|
O
|
B:ALA161
|
4.2
|
27.5
|
1.0
|
|
CA
|
B:ASP162
|
4.2
|
32.8
|
1.0
|
|
N
|
B:ILE163
|
4.3
|
23.4
|
1.0
|
|
CA
|
B:GLY196
|
4.3
|
22.1
|
1.0
|
|
CA
|
B:ASN194
|
4.3
|
35.9
|
1.0
|
|
N
|
B:TYR195
|
4.3
|
34.2
|
1.0
|
|
N
|
B:MET164
|
4.3
|
24.3
|
1.0
|
|
CA
|
B:ILE163
|
4.4
|
22.7
|
1.0
|
|
CA
|
B:TYR195
|
4.4
|
33.3
|
1.0
|
|
O
|
B:GLY192
|
4.4
|
32.2
|
1.0
|
|
N
|
B:GLY197
|
4.4
|
24.0
|
1.0
|
|
N
|
B:ASN194
|
4.5
|
39.0
|
1.0
|
|
C
|
B:GLY197
|
4.5
|
18.5
|
1.0
|
|
CA
|
B:GLY197
|
4.5
|
20.5
|
1.0
|
|
CB
|
B:ASP198
|
4.7
|
17.8
|
1.0
|
|
O
|
B:HOH714
|
4.7
|
34.7
|
1.0
|
|
CA
|
B:ASP198
|
4.7
|
21.9
|
1.0
|
|
CG
|
B:MET164
|
4.8
|
19.9
|
1.0
|
|
C
|
B:ILE163
|
4.9
|
25.8
|
1.0
|
|
C
|
B:PRO193
|
4.9
|
35.1
|
1.0
|
|
CH2
|
B:TRP113
|
4.9
|
28.8
|
1.0
|
|
Calcium binding site 8 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 8 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca505
b:25.3
occ:1.00
|
O
|
B:ASP291
|
2.3
|
26.6
|
1.0
|
|
O
|
B:ASP335
|
2.4
|
24.4
|
1.0
|
|
O
|
B:SER383
|
2.4
|
21.8
|
1.0
|
|
O
|
B:ASP432
|
2.4
|
20.2
|
1.0
|
|
O
|
B:HOH606
|
2.5
|
27.5
|
1.0
|
|
O
|
B:HOH661
|
2.6
|
32.4
|
1.0
|
|
O
|
B:HOH615
|
2.7
|
30.9
|
1.0
|
|
C
|
B:ASP335
|
3.4
|
27.7
|
1.0
|
|
C
|
B:SER383
|
3.4
|
23.0
|
1.0
|
|
C
|
B:ASP291
|
3.5
|
24.4
|
1.0
|
|
C
|
B:ASP432
|
3.6
|
21.7
|
1.0
|
|
CA
|
B:ASP335
|
3.9
|
29.2
|
1.0
|
|
CA
|
B:ASP291
|
4.0
|
25.3
|
1.0
|
|
CA
|
B:SER383
|
4.0
|
29.5
|
1.0
|
|
CA
|
B:ASP432
|
4.2
|
21.5
|
1.0
|
|
N
|
B:ALA336
|
4.5
|
25.7
|
1.0
|
|
N
|
B:ALA384
|
4.5
|
23.1
|
1.0
|
|
N
|
B:ALA292
|
4.6
|
22.1
|
1.0
|
|
CB
|
B:SER383
|
4.6
|
24.5
|
1.0
|
|
N
|
B:ALA433
|
4.7
|
21.9
|
1.0
|
|
O
|
B:ILE334
|
4.7
|
33.9
|
1.0
|
|
CB
|
B:ASP335
|
4.7
|
30.0
|
1.0
|
|
CB
|
B:ASP291
|
4.8
|
22.6
|
1.0
|
|
O
|
B:LEU290
|
4.8
|
30.1
|
1.0
|
|
CB
|
B:ASP432
|
4.9
|
21.5
|
1.0
|
|
CA
|
B:ALA336
|
4.9
|
25.7
|
1.0
|
|
O
|
B:VAL431
|
4.9
|
23.1
|
1.0
|
|
CA
|
B:ALA384
|
4.9
|
19.4
|
1.0
|
|
CA
|
B:ALA292
|
4.9
|
21.5
|
1.0
|
|
Calcium binding site 9 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 9 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca506
b:42.3
occ:1.00
|
O
|
B:ALA385
|
2.3
|
20.9
|
1.0
|
|
O
|
B:ALA337
|
2.4
|
30.9
|
1.0
|
|
O
|
B:ILE293
|
2.4
|
23.4
|
1.0
|
|
O
|
B:VAL434
|
2.4
|
18.0
|
1.0
|
|
O
|
B:HOH617
|
2.7
|
23.8
|
1.0
|
|
CL
|
B:CL508
|
2.8
|
21.3
|
1.0
|
|
C
|
B:ALA385
|
3.5
|
24.0
|
1.0
|
|
C
|
B:ALA337
|
3.6
|
23.7
|
1.0
|
|
C
|
B:ILE293
|
3.6
|
25.8
|
1.0
|
|
C
|
B:VAL434
|
3.6
|
21.3
|
1.0
|
|
CB
|
B:THR294
|
4.2
|
33.8
|
1.0
|
|
CB
|
B:TYR338
|
4.2
|
29.7
|
1.0
|
|
N
|
B:VAL434
|
4.3
|
16.6
|
1.0
|
|
N
|
B:ILE293
|
4.3
|
23.2
|
1.0
|
|
CA
|
B:TYR338
|
4.3
|
30.2
|
1.0
|
|
N
|
B:ALA385
|
4.3
|
21.4
|
1.0
|
|
CG1
|
B:VAL434
|
4.3
|
20.4
|
1.0
|
|
CA
|
B:VAL386
|
4.4
|
25.1
|
1.0
|
|
N
|
B:ALA337
|
4.4
|
17.5
|
1.0
|
|
N
|
B:VAL386
|
4.4
|
25.0
|
1.0
|
|
CA
|
B:THR294
|
4.4
|
28.5
|
1.0
|
|
N
|
B:TYR338
|
4.4
|
32.1
|
1.0
|
|
N
|
B:THR294
|
4.5
|
27.6
|
1.0
|
|
CA
|
B:TYR435
|
4.5
|
28.3
|
1.0
|
|
CA
|
B:ALA385
|
4.5
|
24.1
|
1.0
|
|
N
|
B:TYR435
|
4.5
|
26.4
|
1.0
|
|
CA
|
B:VAL434
|
4.5
|
20.3
|
1.0
|
|
CA
|
B:ILE293
|
4.5
|
24.7
|
1.0
|
|
OG1
|
B:THR294
|
4.5
|
39.5
|
1.0
|
|
CA
|
B:ALA337
|
4.6
|
24.3
|
1.0
|
|
CB
|
B:TYR435
|
4.6
|
28.4
|
1.0
|
|
CB
|
B:VAL386
|
4.6
|
25.9
|
1.0
|
|
CB
|
B:ILE293
|
4.9
|
27.4
|
1.0
|
|
Calcium binding site 10 out
of 10 in 4fvl
Go back to
Calcium Binding Sites List in 4fvl
Calcium binding site 10 out
of 10 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca507
b:47.3
occ:1.00
|
O
|
B:ASP203
|
2.3
|
25.7
|
1.0
|
|
O
|
B:GLU205
|
2.4
|
25.6
|
1.0
|
|
OD2
|
B:ASP128
|
2.5
|
30.6
|
1.0
|
|
OD2
|
B:ASP203
|
2.7
|
27.5
|
1.0
|
|
OD1
|
B:ASP128
|
3.0
|
36.8
|
1.0
|
|
CG
|
B:ASP128
|
3.1
|
26.3
|
1.0
|
|
C
|
B:ASP203
|
3.3
|
21.3
|
1.0
|
|
C
|
B:GLU205
|
3.6
|
26.3
|
1.0
|
|
CG
|
B:ASP203
|
3.7
|
31.7
|
1.0
|
|
CA
|
B:ASP203
|
4.0
|
22.4
|
1.0
|
|
OG1
|
B:THR126
|
4.0
|
23.7
|
1.0
|
|
CB
|
B:ASP203
|
4.2
|
22.4
|
1.0
|
|
N
|
B:GLU205
|
4.3
|
24.4
|
1.0
|
|
N
|
B:ASP204
|
4.3
|
24.9
|
1.0
|
|
CD1
|
B:TRP207
|
4.4
|
19.2
|
1.0
|
|
C
|
B:ASP204
|
4.4
|
33.1
|
1.0
|
|
CA
|
B:THR206
|
4.4
|
24.7
|
1.0
|
|
N
|
B:THR206
|
4.5
|
26.0
|
1.0
|
|
CA
|
B:ASP204
|
4.6
|
21.5
|
1.0
|
|
OD1
|
B:ASP203
|
4.6
|
34.1
|
1.0
|
|
CB
|
B:ASP128
|
4.6
|
26.8
|
1.0
|
|
CA
|
B:GLU205
|
4.6
|
29.3
|
1.0
|
|
N
|
B:TRP207
|
4.8
|
25.7
|
1.0
|
|
O
|
B:ASP204
|
4.8
|
31.8
|
1.0
|
|
CD
|
B:PRO127
|
4.9
|
32.4
|
1.0
|
|
NE1
|
B:TRP207
|
4.9
|
23.9
|
1.0
|
|
Reference:
E.A.Stura,
R.Visse,
P.Cuniasse,
V.Dive,
H.Nagase.
Crystal Structure of Full-Length Human Collagenase 3 (Mmp-13) with Peptides in the Active Site Defines Exosites in the Catalytic Domain. Faseb J. V. 27 4395 2013.
ISSN: ISSN 0892-6638
PubMed: 23913860
DOI: 10.1096/FJ.13-233601
Page generated: Tue Jul 8 20:09:15 2025
|
