Zinc in PDB 1q3a: Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10:
3.4.24.22;
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10, PDB code: 1q3a
was solved by
V.Calderone,
I.Bertini,
M.Fragai,
C.Luchinat,
S.Mangani,
B.Terni,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.30 /
2.10
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.152,
61.141,
68.588,
90.00,
108.68,
90.00
|
R / Rfree (%)
|
27.6 /
29.8
|
Other elements in 1q3a:
The structure of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
(pdb code 1q3a). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10, PDB code: 1q3a:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 1q3a
Go back to
Zinc Binding Sites List in 1q3a
Zinc binding site 1 out
of 6 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn464
b:33.8
occ:1.00
|
NE2
|
A:HIS227
|
2.1
|
33.3
|
1.0
|
NE2
|
A:HIS217
|
2.1
|
20.9
|
1.0
|
O4
|
A:NGH480
|
2.2
|
43.0
|
1.0
|
NE2
|
A:HIS221
|
2.3
|
26.0
|
1.0
|
O5
|
A:NGH480
|
2.5
|
45.2
|
1.0
|
CD2
|
A:HIS227
|
2.9
|
33.7
|
1.0
|
CD2
|
A:HIS221
|
3.0
|
24.8
|
1.0
|
CD2
|
A:HIS217
|
3.1
|
19.8
|
1.0
|
CE1
|
A:HIS227
|
3.1
|
33.2
|
1.0
|
N1
|
A:NGH480
|
3.1
|
44.9
|
1.0
|
CE1
|
A:HIS217
|
3.1
|
21.1
|
1.0
|
C11
|
A:NGH480
|
3.4
|
45.3
|
1.0
|
CE1
|
A:HIS221
|
3.5
|
24.4
|
1.0
|
O
|
A:HOH485
|
3.9
|
36.5
|
1.0
|
CG
|
A:HIS227
|
4.1
|
34.1
|
1.0
|
ND1
|
A:HIS227
|
4.1
|
34.6
|
1.0
|
OE1
|
A:GLU218
|
4.2
|
22.1
|
1.0
|
CG
|
A:HIS221
|
4.2
|
24.6
|
1.0
|
ND1
|
A:HIS217
|
4.2
|
21.1
|
1.0
|
CG
|
A:HIS217
|
4.3
|
23.3
|
1.0
|
ND1
|
A:HIS221
|
4.4
|
25.2
|
1.0
|
C9
|
A:NGH480
|
4.4
|
46.5
|
1.0
|
N
|
A:NGH480
|
4.6
|
46.0
|
1.0
|
C10
|
A:NGH480
|
4.7
|
46.1
|
1.0
|
C2
|
A:NGH480
|
4.8
|
41.3
|
1.0
|
CE
|
A:MET235
|
4.8
|
31.2
|
1.0
|
C1
|
A:NGH480
|
4.9
|
41.9
|
1.0
|
OE2
|
A:GLU218
|
4.9
|
25.7
|
1.0
|
C3
|
A:NGH480
|
4.9
|
40.3
|
1.0
|
CD
|
A:GLU218
|
5.0
|
23.6
|
1.0
|
|
Zinc binding site 2 out
of 6 in 1q3a
Go back to
Zinc Binding Sites List in 1q3a
Zinc binding site 2 out
of 6 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn465
b:29.3
occ:1.00
|
NE2
|
A:HIS182
|
1.9
|
25.7
|
1.0
|
NE2
|
A:HIS167
|
2.0
|
22.6
|
1.0
|
OD2
|
A:ASP169
|
2.0
|
22.2
|
1.0
|
ND1
|
A:HIS195
|
2.2
|
19.3
|
1.0
|
CE1
|
A:HIS182
|
2.9
|
24.6
|
1.0
|
CG
|
A:ASP169
|
3.0
|
26.7
|
1.0
|
CD2
|
A:HIS182
|
3.0
|
23.8
|
1.0
|
CE1
|
A:HIS167
|
3.0
|
20.0
|
1.0
|
CD2
|
A:HIS167
|
3.0
|
22.2
|
1.0
|
CE1
|
A:HIS195
|
3.0
|
16.8
|
1.0
|
OD1
|
A:ASP169
|
3.3
|
23.8
|
1.0
|
CG
|
A:HIS195
|
3.3
|
17.1
|
1.0
|
CB
|
A:HIS195
|
3.7
|
18.7
|
1.0
|
OH
|
A:TYR184
|
3.9
|
29.7
|
1.0
|
O
|
A:TYR171
|
3.9
|
37.0
|
1.0
|
ND1
|
A:HIS182
|
4.0
|
24.5
|
1.0
|
CG
|
A:HIS182
|
4.1
|
25.7
|
1.0
|
ND1
|
A:HIS167
|
4.1
|
22.3
|
1.0
|
CG
|
A:HIS167
|
4.1
|
25.9
|
1.0
|
NE2
|
A:HIS195
|
4.2
|
15.9
|
1.0
|
CB
|
A:ASP169
|
4.3
|
29.5
|
1.0
|
CD2
|
A:HIS195
|
4.3
|
15.9
|
1.0
|
CE1
|
A:TYR184
|
4.5
|
27.7
|
1.0
|
CE1
|
A:PHE173
|
4.6
|
26.4
|
1.0
|
CZ
|
A:TYR184
|
4.7
|
28.2
|
1.0
|
CB
|
A:TYR171
|
4.8
|
38.8
|
1.0
|
CZ
|
A:PHE173
|
4.9
|
26.9
|
1.0
|
O
|
A:HOH490
|
5.0
|
22.3
|
1.0
|
C
|
A:TYR171
|
5.0
|
37.1
|
1.0
|
|
Zinc binding site 3 out
of 6 in 1q3a
Go back to
Zinc Binding Sites List in 1q3a
Zinc binding site 3 out
of 6 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn469
b:33.9
occ:1.00
|
NE2
|
B:HIS221
|
2.0
|
28.6
|
1.0
|
O4
|
B:NGH479
|
2.0
|
35.3
|
1.0
|
O5
|
B:NGH479
|
2.1
|
33.4
|
1.0
|
NE2
|
B:HIS217
|
2.2
|
28.9
|
1.0
|
NE2
|
B:HIS227
|
2.3
|
37.7
|
1.0
|
C11
|
B:NGH479
|
2.5
|
34.4
|
1.0
|
CE1
|
B:HIS217
|
2.6
|
29.5
|
1.0
|
N1
|
B:NGH479
|
2.6
|
33.4
|
1.0
|
CE1
|
B:HIS221
|
2.8
|
27.2
|
1.0
|
CD2
|
B:HIS221
|
3.1
|
27.6
|
1.0
|
CE1
|
B:HIS227
|
3.2
|
38.8
|
1.0
|
CD2
|
B:HIS227
|
3.2
|
37.5
|
1.0
|
CD2
|
B:HIS217
|
3.5
|
30.7
|
1.0
|
ND1
|
B:HIS217
|
3.9
|
31.5
|
1.0
|
ND1
|
B:HIS221
|
4.0
|
29.1
|
1.0
|
C10
|
B:NGH479
|
4.0
|
34.9
|
1.0
|
CG
|
B:HIS221
|
4.1
|
26.8
|
1.0
|
OE2
|
B:GLU218
|
4.2
|
33.3
|
1.0
|
CG
|
B:HIS217
|
4.3
|
30.8
|
1.0
|
ND1
|
B:HIS227
|
4.3
|
38.5
|
1.0
|
CG
|
B:HIS227
|
4.4
|
38.8
|
1.0
|
O
|
B:HOH585
|
4.4
|
50.9
|
1.0
|
C6
|
B:NGH479
|
4.9
|
34.1
|
1.0
|
|
Zinc binding site 4 out
of 6 in 1q3a
Go back to
Zinc Binding Sites List in 1q3a
Zinc binding site 4 out
of 6 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn470
b:20.4
occ:1.00
|
OD1
|
B:ASP169
|
1.9
|
24.9
|
1.0
|
ND1
|
B:HIS195
|
2.0
|
25.0
|
1.0
|
NE2
|
B:HIS182
|
2.1
|
21.6
|
1.0
|
NE2
|
B:HIS167
|
2.3
|
17.2
|
1.0
|
CE1
|
B:HIS195
|
2.9
|
25.9
|
1.0
|
CD2
|
B:HIS182
|
2.9
|
23.6
|
1.0
|
CD2
|
B:HIS167
|
2.9
|
20.7
|
1.0
|
CG
|
B:ASP169
|
2.9
|
28.6
|
1.0
|
CG
|
B:HIS195
|
3.1
|
24.1
|
1.0
|
CE1
|
B:HIS182
|
3.3
|
20.5
|
1.0
|
OD2
|
B:ASP169
|
3.3
|
26.9
|
1.0
|
CE1
|
B:HIS167
|
3.5
|
20.8
|
1.0
|
CB
|
B:HIS195
|
3.5
|
25.0
|
1.0
|
NE2
|
B:HIS195
|
4.0
|
24.5
|
1.0
|
CD2
|
B:HIS195
|
4.1
|
23.7
|
1.0
|
CG
|
B:HIS182
|
4.1
|
21.9
|
1.0
|
OH
|
B:TYR184
|
4.1
|
27.1
|
1.0
|
CB
|
B:ASP169
|
4.2
|
30.8
|
1.0
|
CG
|
B:HIS167
|
4.2
|
23.4
|
1.0
|
ND1
|
B:HIS182
|
4.3
|
21.0
|
1.0
|
O
|
B:TYR171
|
4.3
|
33.4
|
1.0
|
ND1
|
B:HIS167
|
4.4
|
21.5
|
1.0
|
CE2
|
B:PHE173
|
4.5
|
28.7
|
1.0
|
CE2
|
B:TYR184
|
4.5
|
24.0
|
1.0
|
CZ
|
B:TYR184
|
4.8
|
25.1
|
1.0
|
CZ
|
B:PHE173
|
4.8
|
28.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 1q3a
Go back to
Zinc Binding Sites List in 1q3a
Zinc binding site 5 out
of 6 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn474
b:36.4
occ:1.00
|
C11
|
C:NGH481
|
2.1
|
49.5
|
1.0
|
NE2
|
C:HIS217
|
2.1
|
33.2
|
1.0
|
NE2
|
C:HIS227
|
2.3
|
28.6
|
1.0
|
NE2
|
C:HIS221
|
2.3
|
31.0
|
1.0
|
O4
|
C:NGH481
|
2.4
|
48.8
|
1.0
|
O
|
C:HOH491
|
2.6
|
48.7
|
1.0
|
N1
|
C:NGH481
|
2.8
|
48.3
|
1.0
|
O5
|
C:NGH481
|
2.8
|
51.3
|
1.0
|
CD2
|
C:HIS217
|
2.9
|
31.7
|
1.0
|
CE1
|
C:HIS217
|
3.1
|
31.6
|
1.0
|
CE1
|
C:HIS227
|
3.2
|
30.8
|
1.0
|
CD2
|
C:HIS227
|
3.2
|
31.6
|
1.0
|
CD2
|
C:HIS221
|
3.3
|
30.2
|
1.0
|
CE1
|
C:HIS221
|
3.3
|
31.1
|
1.0
|
C10
|
C:NGH481
|
3.3
|
48.9
|
1.0
|
CG
|
C:HIS217
|
4.0
|
30.9
|
1.0
|
OE1
|
C:GLU218
|
4.1
|
30.4
|
1.0
|
O
|
C:HOH517
|
4.1
|
26.9
|
1.0
|
ND1
|
C:HIS217
|
4.1
|
31.4
|
1.0
|
CD
|
C:PRO237
|
4.2
|
47.2
|
1.0
|
ND1
|
C:HIS227
|
4.3
|
32.1
|
1.0
|
CG
|
C:HIS227
|
4.4
|
34.1
|
1.0
|
ND1
|
C:HIS221
|
4.4
|
32.0
|
1.0
|
CG
|
C:HIS221
|
4.4
|
31.2
|
1.0
|
N
|
C:NGH481
|
4.4
|
48.0
|
1.0
|
CE
|
C:MET235
|
4.4
|
43.3
|
1.0
|
C5
|
C:NGH481
|
4.5
|
43.3
|
1.0
|
C6
|
C:NGH481
|
4.7
|
45.8
|
1.0
|
N
|
C:PRO237
|
5.0
|
47.5
|
1.0
|
CD
|
C:GLU218
|
5.0
|
29.7
|
1.0
|
|
Zinc binding site 6 out
of 6 in 1q3a
Go back to
Zinc Binding Sites List in 1q3a
Zinc binding site 6 out
of 6 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn475
b:29.3
occ:1.00
|
ND1
|
C:HIS195
|
1.9
|
23.1
|
1.0
|
NE2
|
C:HIS167
|
2.0
|
31.3
|
1.0
|
OD2
|
C:ASP169
|
2.1
|
31.5
|
1.0
|
NE2
|
C:HIS182
|
2.1
|
18.9
|
1.0
|
CE1
|
C:HIS195
|
2.7
|
26.8
|
1.0
|
CD2
|
C:HIS167
|
2.8
|
29.6
|
1.0
|
CG
|
C:ASP169
|
2.9
|
32.1
|
1.0
|
CD2
|
C:HIS182
|
3.0
|
20.8
|
1.0
|
OD1
|
C:ASP169
|
3.0
|
32.6
|
1.0
|
CE1
|
C:HIS182
|
3.1
|
18.3
|
1.0
|
CG
|
C:HIS195
|
3.1
|
24.5
|
1.0
|
CE1
|
C:HIS167
|
3.1
|
30.4
|
1.0
|
CB
|
C:HIS195
|
3.6
|
24.5
|
1.0
|
NE2
|
C:HIS195
|
3.9
|
26.8
|
1.0
|
O
|
C:TYR171
|
3.9
|
31.3
|
1.0
|
OH
|
C:TYR184
|
4.0
|
30.3
|
1.0
|
CG
|
C:HIS167
|
4.0
|
32.2
|
1.0
|
CD2
|
C:HIS195
|
4.1
|
25.7
|
1.0
|
ND1
|
C:HIS167
|
4.1
|
32.8
|
1.0
|
CG
|
C:HIS182
|
4.2
|
22.1
|
1.0
|
ND1
|
C:HIS182
|
4.2
|
21.1
|
1.0
|
CB
|
C:ASP169
|
4.3
|
31.7
|
1.0
|
CE1
|
C:TYR184
|
4.6
|
30.0
|
1.0
|
CE1
|
C:PHE173
|
4.7
|
27.1
|
1.0
|
CZ
|
C:TYR184
|
4.8
|
30.5
|
1.0
|
CZ
|
C:PHE173
|
4.9
|
28.4
|
1.0
|
|
Reference:
I.Bertini,
V.Calderone,
M.Fragai,
C.Luchinat,
S.Mangani,
B.Terni.
Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10. J.Mol.Biol. V. 336 707 2004.
ISSN: ISSN 0022-2836
PubMed: 15095982
DOI: 10.1016/J.JMB.2003.12.033
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