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Calcium in PDB 1rmz: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution, PDB code: 1rmz was solved by I.Bertini, V.Calderone, 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) 20.00 / 1.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.194, 62.564, 37.262, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 1rmz:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Inhibitor Nngh at 1.3 A Resolution (pdb code 1rmz). 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 the Inhibitor Nngh at 1.3 A Resolution, PDB code: 1rmz:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1rmz

Go back to Calcium Binding Sites List in 1rmz
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Inhibitor Nngh at 1.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:17.7
occ:1.00
 O A:GLY190 2.3 19.1 1.0
O A:GLY192 2.3 16.4 1.0
O A:HOH288 2.3 21.3 1.0
O A:ASP158 2.3 15.8 1.0
O A:HOH296 2.4 18.4 1.0
OD2 A:ASP194 2.4 15.7 1.0
CG A:ASP194 3.4 12.9 1.0
C A:ASP158 3.5 16.0 1.0
C A:GLY190 3.5 18.6 1.0
C A:GLY192 3.5 16.2 1.0
OD1 A:ASP194 3.8 14.8 1.0
C A:ILE191 3.9 17.6 1.0
N A:GLY192 4.1 16.6 1.0
O A:ILE191 4.2 16.9 1.0
O A:ALA157 4.2 18.3 1.0
N A:ASP194 4.3 14.4 1.0
CA A:ASP158 4.3 16.2 1.0
CA A:ILE191 4.3 18.6 1.0
O A:GLY188 4.3 20.3 1.0
CA A:GLY192 4.3 16.4 1.0
N A:ILE191 4.3 17.9 1.0
N A:GLY190 4.4 20.3 1.0
CA A:GLY190 4.4 19.2 1.0
N A:ILE159 4.4 15.2 1.0
N A:GLY193 4.4 16.0 1.0
CA A:GLY193 4.5 15.8 1.0
CA A:ILE159 4.6 14.8 1.0
C A:GLY193 4.6 15.0 1.0
N A:LEU160 4.6 14.6 1.0
CB A:ASP194 4.7 13.2 1.0
O A:HOH371 4.7 29.4 1.0
C A:SER189 4.8 21.2 1.0
O A:HOH280 4.8 23.0 1.0
CA A:ASP194 4.8 13.3 1.0
CH2 A:TRP109 4.9 21.4 1.0

Calcium binding site 2 out of 3 in 1rmz

Go back to Calcium Binding Sites List in 1rmz
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Inhibitor Nngh at 1.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:21.8
occ:1.00
 OD2 A:ASP124 2.3 22.7 1.0
O A:HOH297 2.3 27.2 1.0
O A:GLU199 2.4 20.9 1.0
O A:GLU201 2.4 21.0 1.0
OE2 A:GLU199 2.4 18.6 1.0
O A:HOH311 2.5 24.5 1.0
OD1 A:ASP124 2.5 22.9 1.0
CG A:ASP124 2.8 23.3 1.0
CD A:GLU199 3.5 17.6 1.0
C A:GLU199 3.5 19.0 1.0
C A:GLU201 3.6 20.8 1.0
CG A:GLU199 3.9 17.9 1.0
CA A:PHE202 4.2 21.9 1.0
CA A:GLU199 4.2 17.8 1.0
OG1 A:THR122 4.2 20.1 1.0
N A:PHE202 4.3 21.6 1.0
CB A:ASP124 4.3 23.2 1.0
CD1 A:TRP203 4.3 16.4 1.0
N A:GLU201 4.5 19.3 1.0
O A:HOH409 4.5 39.5 1.0
N A:ASP200 4.5 18.8 1.0
C A:ASP200 4.6 20.4 1.0
O A:HOH335 4.6 33.7 1.0
OE1 A:GLU199 4.6 19.4 1.0
O A:HOH365 4.6 29.8 1.0
O A:HOH406 4.6 38.1 1.0
CB A:GLU199 4.7 16.2 1.0
CA A:GLU201 4.7 20.2 1.0
N A:TRP203 4.7 20.4 1.0
CA A:ASP200 4.7 19.6 1.0
O A:HOH501 4.8 31.7 1.0
CD1 A:PHE202 4.8 28.6 1.0
NE1 A:TRP203 4.9 15.8 1.0
O A:HOH283 4.9 25.2 1.0
O A:ASP200 5.0 21.8 1.0

Calcium binding site 3 out of 3 in 1rmz

Go back to Calcium Binding Sites List in 1rmz
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Inhibitor Nngh at 1.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:16.8
occ:1.00
 OE2 A:GLU201 2.3 22.2 1.0
O A:GLY176 2.3 20.0 1.0
O A:ILE180 2.3 16.6 1.0
OD2 A:ASP175 2.3 17.9 1.0
O A:GLY178 2.3 21.4 1.0
OD1 A:ASP198 2.3 16.2 1.0
CG A:ASP198 3.4 16.4 1.0
C A:ILE180 3.4 15.2 1.0
CG A:ASP175 3.5 18.9 1.0
CD A:GLU201 3.5 21.4 1.0
C A:GLY176 3.5 19.8 1.0
C A:GLY178 3.5 21.7 1.0
N A:ILE180 3.9 17.4 1.0
N A:GLY178 4.0 22.1 1.0
CB A:ASP198 4.0 14.5 1.0
OD1 A:ASP175 4.0 18.1 1.0
N A:GLY176 4.1 19.3 1.0
OE1 A:GLU201 4.2 21.6 1.0
C A:LYS177 4.2 23.0 1.0
CA A:ILE180 4.2 16.0 1.0
C A:ASP175 4.2 19.2 1.0
C A:GLY179 4.3 18.9 1.0
N A:ASP175 4.3 18.6 1.0
CA A:GLY178 4.4 22.6 1.0
OD2 A:ASP198 4.4 17.0 1.0
N A:LEU181 4.4 14.4 1.0
CA A:GLY176 4.4 19.8 1.0
N A:LYS177 4.4 21.4 1.0
CA A:LYS177 4.4 22.9 1.0
N A:GLY179 4.5 21.0 1.0
CG A:GLU201 4.6 19.5 1.0
CA A:LEU181 4.6 15.2 1.0
CA A:ASP175 4.6 18.9 1.0
CA A:GLY179 4.6 20.1 1.0
O A:ASP175 4.7 20.5 1.0
CB A:ASP175 4.7 18.9 1.0
CB A:ILE180 4.7 15.6 1.0
O A:LYS177 4.7 23.8 1.0
O A:GLY179 4.8 19.8 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: Tue Jul 8 01:39:54 2025

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