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Zinc in PDB 1y93: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution, PDB code: 1y93 was solved by I.Bertini, V.Calderone, M.Cosenza, M.Fragai, Y.-M.Lee, C.Luchinat, S.Mangani, B.Terni, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.99 / 1.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.913, 59.552, 53.497, 90.00, 115.14, 90.00
R / Rfree (%) 15.6 / 16.8

Other elements in 1y93:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution (pdb code 1y93). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution, PDB code: 1y93:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y93

Go back to Zinc Binding Sites List in 1y93
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution


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 MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:6.4
occ:1.00
HE2 A:HIS218 1.2 5.7 0.0
HE2 A:HIS228 1.2 7.1 0.0
HE2 A:HIS222 1.2 6.4 0.0
H1 A:HOH408 1.9 18.0 0.0
NE2 A:HIS218 2.0 6.2 1.0
NE2 A:HIS228 2.0 6.3 1.0
NE2 A:HIS222 2.1 6.1 1.0
O A:HAE301 2.1 11.9 1.0
O2 A:HAE301 2.1 12.2 1.0
HO A:HAE301 2.3 13.2 1.0
O A:HOH408 2.6 17.3 0.3
H2 A:HOH408 2.7 18.0 0.0
C2 A:HAE301 2.9 12.2 1.0
N A:HAE301 2.9 8.4 1.0
CE1 A:HIS228 3.0 6.3 1.0
CD2 A:HIS218 3.0 5.9 1.0
CE1 A:HIS222 3.0 6.6 1.0
CE1 A:HIS218 3.0 7.5 1.0
CD2 A:HIS222 3.1 5.5 1.0
CD2 A:HIS228 3.1 7.0 1.0
HD2 A:HIS218 3.1 6.1 1.0
HE1 A:HIS228 3.2 6.8 1.0
HE1 A:HIS222 3.2 6.0 1.0
HD2 A:HIS222 3.2 5.8 1.0
HE1 A:HIS218 3.3 6.3 1.0
HD2 A:HIS228 3.3 6.7 1.0
H2 A:HOH328 3.6 9.9 0.0
H2 A:HOH450 3.7 14.9 0.0
H1 A:HOH556 3.8 31.9 0.0
HN A:HAE301 3.9 10.3 1.0
ND1 A:HIS228 4.1 6.5 1.0
HE3 A:MET236 4.1 5.8 1.0
O A:HOH450 4.1 24.7 1.0
ND1 A:HIS218 4.1 6.6 1.0
CG A:HIS218 4.1 5.8 1.0
CG A:HIS228 4.2 6.6 1.0
ND1 A:HIS222 4.2 6.5 1.0
HA A:PRO238 4.2 10.7 1.0
H2 A:HOH556 4.2 31.9 0.0
CG A:HIS222 4.2 5.3 1.0
O A:HOH328 4.3 9.7 1.0
OE1 A:GLU219 4.3 8.8 1.0
C1 A:HAE301 4.3 14.6 1.0
H2 A:HOH583 4.5 31.0 0.0
O A:HOH556 4.6 32.9 1.0
H1 A:HOH450 4.7 14.9 0.0
O A:HOH583 4.8 29.7 1.0
H1 A:HOH574 4.8 39.5 0.0
OE2 A:GLU219 4.8 9.1 1.0
H12 A:HAE301 4.9 15.8 1.0
HD1 A:HIS228 4.9 6.9 0.0
HD1 A:HIS218 4.9 6.6 0.0
H11 A:HAE301 4.9 15.7 1.0
CD A:GLU219 4.9 6.9 1.0
HE2 A:MET236 4.9 5.9 1.0
CE A:MET236 4.9 5.8 1.0
HD1 A:HIS222 5.0 6.4 0.0

Zinc binding site 2 out of 2 in 1y93

Go back to Zinc Binding Sites List in 1y93
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution


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 MMP12 Complexed with Acetohydroxamic Acid at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:7.3
occ:1.00
HE2 A:HIS168 1.1 8.5 0.0
HE2 A:HIS183 1.1 7.5 0.0
HD1 A:HIS196 1.2 7.0 0.0
OD1 A:ASP170 1.9 6.2 0.7
NE2 A:HIS168 2.0 7.6 1.0
NE2 A:HIS183 2.0 8.0 1.0
ND1 A:HIS196 2.0 6.7 1.0
CE1 A:HIS183 2.8 9.6 1.0
CG A:ASP170 2.9 7.5 0.7
CD2 A:HIS168 2.9 7.4 1.0
HE1 A:HIS183 2.9 8.4 1.0
CE1 A:HIS196 2.9 7.2 1.0
CE1 A:HIS168 3.0 7.5 1.0
HD2 A:HIS168 3.0 8.1 1.0
CG A:HIS196 3.1 6.0 1.0
HE1 A:HIS196 3.1 6.4 1.0
CD2 A:HIS183 3.1 9.2 1.0
OD2 A:ASP170 3.1 7.6 0.7
HB2 A:HIS196 3.2 5.3 1.0
HE1 A:HIS168 3.3 8.5 1.0
HD2 A:HIS183 3.4 8.7 1.0
CB A:HIS196 3.5 5.6 1.0
HB3 A:HIS196 3.5 5.2 1.0
HE2 A:PHE185 3.6 9.8 1.0
HB2 A:HIS172 3.8 15.0 1.0
ND1 A:HIS183 4.0 10.1 1.0
CG A:HIS168 4.1 8.4 1.0
NE2 A:HIS196 4.1 6.6 1.0
ND1 A:HIS168 4.1 8.1 1.0
O A:HIS172 4.1 11.4 1.0
H2 A:HOH325 4.1 11.6 0.0
CG A:HIS183 4.2 6.9 1.0
CD2 A:HIS196 4.2 6.2 1.0
HZ A:PHE185 4.2 9.9 1.0
CB A:ASP170 4.2 11.6 0.7
HB3 A:ASP170 4.3 11.8 0.7
CE2 A:PHE185 4.4 12.1 1.0
H2 A:HOH476 4.4 32.3 0.0
HZ A:PHE174 4.4 7.5 1.0
HE1 A:PHE174 4.6 7.6 1.0
HB2 A:ASP170 4.6 11.7 0.7
CZ A:PHE174 4.6 7.1 1.0
CZ A:PHE185 4.7 11.8 1.0
CE1 A:PHE174 4.7 7.2 1.0
CB A:HIS172 4.8 15.3 1.0
HD12 A:ILE191 4.8 14.1 1.0
H2 A:HOH452 4.8 27.9 0.0
HD1 A:HIS183 4.8 11.7 0.0
HE2 A:HIS196 4.8 6.5 0.0
H A:HIS172 4.9 15.1 1.0
H A:ASP170 4.9 13.2 0.7
HD1 A:HIS168 4.9 8.3 0.0
O A:HOH325 4.9 11.0 1.0
CA A:HIS196 5.0 4.9 1.0
O A:HOH476 5.0 30.6 1.0
HB3 A:HIS172 5.0 15.1 1.0

Reference:

I.Bertini, V.Calderone, M.Cosenza, M.Fragai, Y.-M.Lee, C.Luchinat, S.Mangani, B.Terni, P.Turano. Conformational Variability of Matrix Metalloproteinases: Beyond A Single 3D Structure Proc.Natl.Acad.Sci.Usa V. 102 5334 2005.
ISSN: ISSN 0027-8424
PubMed: 15809432
DOI: 10.1073/PNAS.0407106102
Page generated: Wed Dec 16 03:13:55 2020

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