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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:

Calcium (Ca) 9 atoms

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

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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

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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
Page generated: Wed Oct 16 18:01:20 2024

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