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Calcium in PDB 1l6j: Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B).

Enzymatic activity of Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B).

All present enzymatic activity of Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B).:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B)., PDB code: 1l6j was solved by P.A.Elkins, Y.S.Ho, W.W.Smith, C.A.Janson, K.J.D'alessio, M.S.Mcqueney, M.D.Cummings, A.M.Romanic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 123.685, 123.685, 89.937, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 23

Other elements in 1l6j:

The structure of Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B). also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B). (pdb code 1l6j). 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 Human Matrix Metalloproteinase MMP9 (Gelatinase B)., PDB code: 1l6j:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1l6j

Go back to Calcium Binding Sites List in 1l6j
Calcium binding site 1 out of 3 in the Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B).


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 Human Matrix Metalloproteinase MMP9 (Gelatinase B). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:26.0
occ:1.00
O A:GLY183 2.4 37.7 1.0
OD2 A:ASP205 2.5 21.6 1.0
OE2 A:GLU208 2.5 21.6 1.0
O A:LEU187 2.5 23.5 1.0
OD1 A:ASP182 2.6 27.4 1.0
N A:GLY186 2.9 37.3 1.0
CG A:ASP182 3.6 29.3 1.0
N A:LEU187 3.6 28.4 1.0
CA A:GLY186 3.6 34.9 1.0
C A:GLY183 3.6 34.9 1.0
CG A:ASP205 3.6 20.5 1.0
C A:LEU187 3.7 26.7 1.0
CD A:GLU208 3.7 25.7 1.0
N A:ASP185 3.7 39.2 1.0
C A:ASP185 3.8 40.6 1.0
C A:GLY186 3.8 31.9 1.0
C A:LYS184 3.9 40.4 1.0
OD2 A:ASP182 4.1 29.2 1.0
CA A:ASP185 4.1 39.7 1.0
N A:GLY183 4.2 29.4 1.0
O A:LYS184 4.3 38.6 1.0
N A:ASP182 4.3 28.8 1.0
C A:ASP182 4.3 31.1 1.0
CA A:LEU187 4.4 26.2 1.0
CA A:LYS184 4.4 40.2 1.0
CB A:ASP205 4.4 18.6 1.0
OE1 A:GLU208 4.4 24.0 1.0
N A:LYS184 4.5 37.3 1.0
OD1 A:ASP205 4.5 21.5 1.0
CA A:ASP182 4.6 29.3 1.0
CA A:GLY183 4.6 32.0 1.0
N A:LEU188 4.6 23.2 1.0
CG A:GLU208 4.6 27.8 1.0
CB A:ASP182 4.7 29.9 1.0
CA A:LEU188 4.7 18.3 1.0
O A:GLY186 4.7 28.7 1.0
O A:ASP182 4.7 31.9 1.0
O A:ASP185 4.8 45.5 1.0
CG A:LEU187 4.9 23.1 1.0

Calcium binding site 2 out of 3 in 1l6j

Go back to Calcium Binding Sites List in 1l6j
Calcium binding site 2 out of 3 in the Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B).


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 Human Matrix Metalloproteinase MMP9 (Gelatinase B). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:61.2
occ:1.00
O A:ASP206 2.5 31.9 1.0
O A:GLU208 2.6 27.5 1.0
OD1 A:ASP206 2.7 35.1 1.0
OD2 A:ASP131 2.8 35.5 1.0
O A:HOH1054 2.8 23.8 1.0
C A:ASP206 3.3 29.6 1.0
CG A:ASP131 3.6 33.9 1.0
CG A:ASP206 3.6 34.5 1.0
OD1 A:ASP131 3.6 37.0 1.0
C A:GLU208 3.7 26.6 1.0
O A:HOH1079 3.7 38.5 1.0
O A:HOH1049 3.8 26.5 1.0
CA A:ASP206 3.9 28.2 1.0
N A:GLU208 4.1 26.4 1.0
CB A:ASP206 4.2 28.6 1.0
C A:ASP207 4.2 29.0 1.0
O A:HOH1078 4.2 36.0 1.0
OG A:SER129 4.3 26.1 1.0
N A:ASP207 4.3 32.0 1.0
OD2 A:ASP206 4.4 37.2 1.0
CA A:ASP207 4.4 29.0 1.0
CA A:LEU209 4.4 24.8 1.0
N A:LEU209 4.5 27.3 1.0
CD1 A:TRP210 4.6 23.9 1.0
CA A:GLU208 4.6 27.2 1.0
O A:ASP207 4.7 33.8 1.0
N A:TRP210 4.8 20.4 1.0
CB A:ASP131 4.9 34.1 1.0

Calcium binding site 3 out of 3 in 1l6j

Go back to Calcium Binding Sites List in 1l6j
Calcium binding site 3 out of 3 in the Crystal Structure of Human Matrix Metalloproteinase MMP9 (Gelatinase B).


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 Human Matrix Metalloproteinase MMP9 (Gelatinase B). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:80.3
occ:1.00
OD1 A:ASP201 2.7 35.8 1.0
O A:ASP165 2.7 32.0 1.0
O A:GLY197 2.9 38.6 1.0
O A:HOH1174 3.0 35.2 1.0
O A:GLN199 3.0 26.0 1.0
O A:HOH1052 3.0 36.3 1.0
O A:HOH1084 3.3 37.8 1.0
O A:ALA164 3.5 41.8 1.0
C A:ASP165 3.5 30.1 1.0
CG A:ASP201 3.7 33.5 1.0
C A:GLY197 4.1 35.5 1.0
OD2 A:ASP201 4.1 34.0 1.0
C A:GLN199 4.2 29.3 1.0
N A:ILE166 4.3 25.9 1.0
N A:VAL167 4.3 26.2 1.0
CA A:ASP165 4.3 32.9 1.0
CG2 A:VAL167 4.4 24.6 1.0
CA A:ILE166 4.4 23.6 1.0
C A:ALA164 4.5 40.0 1.0
O A:HOH1180 4.6 36.6 1.0
C A:ILE198 4.6 33.9 1.0
C A:ILE166 4.7 26.1 1.0
N A:GLN199 4.7 28.7 1.0
N A:ASP201 4.8 20.6 1.0
O A:ILE198 4.8 32.6 1.0
CB A:VAL167 4.8 27.3 1.0
CA A:ILE198 4.9 34.7 1.0
N A:ASP165 4.9 35.9 1.0
N A:ILE198 4.9 36.1 1.0
N A:GLY197 4.9 33.5 1.0
C A:GLY200 4.9 22.6 1.0
O A:GLY195 4.9 29.1 1.0

Reference:

P.A.Elkins, Y.S.Ho, W.W.Smith, C.A.Janson, K.J.D'alessio, M.S.Mcqueney, M.D.Cummings, A.M.Romanic. Structure of the C-Terminally Truncated Human PROMMP9, A Gelatin-Binding Matrix Metalloproteinase. Acta Crystallogr.,Sect.D V. 58 1182 2002.
ISSN: ISSN 0907-4449
PubMed: 12077439
DOI: 10.1107/S0907444902007849
Page generated: Sat Dec 12 03:04:44 2020

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