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Calcium 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:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1y93

Go back to Calcium Binding Sites List in 1y93
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca266

b:7.9
occ:1.00
 H2 A:HOH346 2.0 13.1 0.0
O A:GLY192 2.2 7.1 1.0
O A:GLY190 2.3 10.6 1.0
O A:HOH346 2.3 12.3 1.0
O A:ASP158 2.3 7.3 1.0
O A:HOH308 2.4 8.1 1.0
OD2 A:ASP194 2.4 6.9 1.0
H2 A:HOH308 2.9 8.4 0.0
H1 A:HOH346 3.0 13.1 0.0
H1 A:HOH308 3.2 8.4 0.0
H2 A:HOH407 3.2 18.2 0.0
CG A:ASP194 3.4 5.9 1.0
C A:GLY192 3.4 6.7 1.0
C A:ASP158 3.4 6.0 1.0
C A:GLY190 3.5 10.2 1.0
OD1 A:ASP194 3.8 7.4 1.0
HA A:ASP158 3.9 6.1 1.0
HA A:ILE159 3.9 5.5 1.0
C A:ILE191 3.9 8.1 1.0
H A:LEU160 3.9 5.7 1.0
H A:ASP194 4.0 5.3 1.0
HA A:ILE191 4.0 9.9 1.0
HA3 A:GLY193 4.0 5.8 1.0
N A:GLY192 4.0 7.6 1.0
O A:ALA157 4.0 8.5 1.0
O A:ILE191 4.1 7.5 1.0
O A:HOH407 4.1 17.2 1.0
HH2 A:TRP109 4.2 7.4 1.0
N A:ASP194 4.2 5.3 1.0
CA A:ASP158 4.3 6.2 1.0
CA A:GLY192 4.3 7.2 1.0
CA A:ILE191 4.3 10.2 1.0
H1 A:HOH407 4.3 18.2 0.0
H A:GLY192 4.3 7.5 1.0
H2 A:HOH464 4.3 33.2 0.0
N A:ILE191 4.4 9.6 1.0
N A:ILE159 4.4 5.5 1.0
O A:GLY188 4.4 10.4 1.0
N A:GLY193 4.4 6.2 1.0
N A:GLY190 4.4 11.4 1.0
CA A:GLY190 4.5 11.2 1.0
CA A:GLY193 4.5 5.7 1.0
H A:GLY190 4.5 11.4 1.0
CA A:ILE159 4.6 5.5 1.0
HA3 A:GLY192 4.6 7.2 1.0
C A:GLY193 4.6 5.4 1.0
HA2 A:GLY190 4.6 11.0 1.0
CB A:ASP194 4.6 5.4 1.0
N A:LEU160 4.6 5.6 1.0
HA A:ASP194 4.7 5.2 1.0
O A:HOH338 4.7 10.8 1.0
CA A:ASP194 4.8 5.2 1.0
C A:SER189 4.8 11.5 1.0
HB2 A:LEU160 4.8 6.1 1.0
C A:ALA157 4.9 7.2 1.0
HB2 A:ASP194 5.0 5.4 1.0

Calcium binding site 2 out of 3 in 1y93

Go back to Calcium Binding Sites List in 1y93
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca267

b:5.9
occ:1.00
 H2 A:HOH319 1.5 8.9 0.0
H1 A:HOH310 1.6 8.2 0.0
O A:GLU199 2.3 6.2 1.0
OE2 A:GLU199 2.3 6.4 1.0
OD2 A:ASP124 2.4 6.1 1.0
O A:HOH310 2.4 8.0 1.0
O A:GLU201 2.4 6.8 1.0
O A:HOH319 2.4 8.7 1.0
H2 A:HOH310 2.4 8.2 0.0
OD1 A:ASP124 2.5 6.4 1.0
H1 A:HOH319 2.8 8.9 0.0
CG A:ASP124 2.8 5.5 1.0
HG3 A:GLU199 3.3 6.3 1.0
HA A:PHE202 3.3 6.8 1.0
C A:GLU199 3.4 6.3 1.0
CD A:GLU199 3.4 5.9 1.0
C A:GLU201 3.6 6.6 1.0
HA A:GLU199 3.6 5.9 1.0
HD1 A:TRP203 3.7 5.6 1.0
HG1 A:THR122 3.8 5.9 0.0
CG A:GLU199 3.8 6.5 1.0
HD1 A:PHE202 3.9 8.9 1.0
H1 A:HOH323 4.0 10.0 0.0
CA A:GLU199 4.0 5.7 1.0
H A:TRP203 4.1 6.1 1.0
OG1 A:THR122 4.1 5.6 1.0
CA A:PHE202 4.2 6.6 1.0
HH22 A:ARG165 4.2 13.9 1.0
HA A:ASP200 4.2 6.9 1.0
CB A:ASP124 4.3 5.7 1.0
N A:PHE202 4.3 6.7 1.0
CD1 A:TRP203 4.4 5.5 1.0
N A:GLU201 4.4 6.3 1.0
HD2 A:PRO123 4.4 6.8 1.0
N A:ASP200 4.5 6.7 1.0
HG2 A:PRO123 4.5 8.2 1.0
C A:ASP200 4.5 6.8 1.0
OE1 A:GLU199 4.5 6.3 1.0
H A:GLU201 4.5 6.4 1.0
CB A:GLU199 4.5 6.0 1.0
HE1 A:TRP203 4.6 5.7 1.0
CA A:ASP200 4.6 6.9 1.0
HB2 A:ASP124 4.6 5.6 1.0
HG2 A:GLU199 4.6 6.6 1.0
CA A:GLU201 4.7 6.5 1.0
HB3 A:ASP124 4.7 5.9 1.0
H A:ASP124 4.7 5.9 1.0
NH2 A:ARG165 4.7 14.7 1.0
O A:HOH323 4.7 9.6 1.0
HH21 A:ARG165 4.8 14.2 1.0
CD1 A:PHE202 4.8 8.2 1.0
NE1 A:TRP203 4.8 5.8 1.0
N A:TRP203 4.8 5.9 1.0
H2 A:HOH323 4.9 10.0 0.0
HB2 A:PHE202 4.9 6.9 1.0

Calcium binding site 3 out of 3 in 1y93

Go back to Calcium Binding Sites List in 1y93
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca268

b:9.8
occ:1.00
 OE2 A:GLU201 2.2 14.4 1.0
O A:ILE180 2.2 10.1 1.0
OD2 A:ASP175 2.3 10.2 1.0
O A:GLY176 2.3 9.9 1.0
OD1 A:ASP198 2.3 9.1 1.0
O A:GLY178 2.4 10.9 1.0
C A:ILE180 3.4 9.3 1.0
CD A:GLU201 3.4 10.7 1.0
CG A:ASP175 3.4 10.9 1.0
H A:ASP175 3.4 8.9 1.0
CG A:ASP198 3.5 7.3 1.0
C A:GLY176 3.5 10.1 1.0
C A:GLY178 3.6 11.7 1.0
H A:GLY178 3.8 11.5 1.0
HA A:LEU181 3.8 7.3 1.0
N A:GLY178 3.8 11.4 1.0
HB3 A:ASP198 3.8 6.1 1.0
H A:ILE180 3.9 10.1 1.0
N A:ILE180 3.9 10.0 1.0
HB A:ILE180 4.0 10.2 1.0
HA A:LYS177 4.0 10.6 1.0
OD1 A:ASP175 4.0 11.8 1.0
N A:GLY176 4.1 9.7 1.0
CB A:ASP198 4.1 6.1 1.0
HD23 A:LEU181 4.1 10.5 1.0
HG2 A:GLU201 4.1 8.6 1.0
HB2 A:ASP198 4.1 5.7 1.0
C A:LYS177 4.1 11.1 1.0
H A:GLY176 4.2 9.9 1.0
CA A:ILE180 4.2 9.7 1.0
OE1 A:GLU201 4.2 12.2 1.0
HB3 A:PHE174 4.2 8.0 1.0
N A:ASP175 4.2 8.9 1.0
C A:ASP175 4.2 10.1 1.0
H2 A:HOH311 4.2 8.9 0.0
CA A:GLY178 4.3 12.0 1.0
C A:GLY179 4.3 10.7 1.0
CG A:GLU201 4.3 8.0 1.0
CA A:GLY176 4.4 10.1 1.0
CA A:LYS177 4.4 10.6 1.0
N A:LYS177 4.4 9.9 1.0
N A:LEU181 4.4 7.9 1.0
OD2 A:ASP198 4.4 7.2 1.0
HB2 A:ASP200 4.5 7.1 1.0
CA A:LEU181 4.5 7.4 1.0
CA A:ASP175 4.6 9.9 1.0
HA3 A:GLY179 4.6 11.5 1.0
N A:GLY179 4.6 11.9 1.0
CB A:ILE180 4.6 10.3 1.0
CB A:ASP175 4.6 10.2 1.0
HG3 A:GLU201 4.6 8.1 1.0
O A:ASP175 4.7 10.7 1.0
CA A:GLY179 4.7 11.5 1.0
O A:LYS177 4.7 12.6 1.0
HA2 A:GLY178 4.8 11.8 1.0
HA2 A:GLY176 4.8 10.0 1.0
O A:GLY179 4.9 12.3 1.0
HG21 A:ILE180 4.9 10.0 1.0
HD2 A:PHE174 4.9 7.8 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: Sat Dec 12 03:28:31 2020

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