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Calcium in PDB 4ijo: Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases

Enzymatic activity of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases

All present enzymatic activity of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases:
3.4.24.65;

Protein crystallography data

The structure of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases, PDB code: 4ijo was solved by Y.Udi, M.Fragai, M.Grossman, S.Mitternacht, R.Arad-Yellin, V.Calderone, M.Melikian, M.Toccafondi, I.N.Berezovsky, C.Luchinat, I.Sagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.60 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.435, 60.164, 53.777, 90.00, 114.80, 90.00
R / Rfree (%) 18.3 / 23.2

Other elements in 4ijo:

The structure of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases (pdb code 4ijo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases, PDB code: 4ijo:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4ijo

Go back to Calcium Binding Sites List in 4ijo
Calcium binding site 1 out of 3 in the Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:5.0
occ:1.00
 O A:HOH485 2.2 27.9 1.0
O A:ASP158 2.3 13.8 1.0
O A:GLY190 2.3 18.1 1.0
O A:HOH403 2.3 13.2 1.0
O A:GLY192 2.4 19.3 1.0
OD2 A:ASP194 2.5 11.7 1.0
C A:ASP158 3.5 15.9 1.0
CG A:ASP194 3.5 14.8 1.0
C A:GLY190 3.5 18.7 1.0
C A:GLY192 3.5 16.3 1.0
OD1 A:ASP194 3.9 14.3 1.0
C A:ILE191 4.0 16.9 1.0
O A:HOH465 4.0 24.4 1.0
N A:GLY192 4.2 16.8 1.0
O A:ILE191 4.2 15.2 1.0
O A:ALA157 4.2 21.3 1.0
CA A:ASP158 4.3 16.7 1.0
N A:ASP194 4.3 13.2 1.0
N A:ILE191 4.3 18.7 1.0
CA A:ILE191 4.4 18.1 1.0
O A:GLY188 4.4 19.0 1.0
CA A:GLY192 4.4 15.5 1.0
CA A:GLY190 4.4 18.5 1.0
N A:ILE159 4.4 14.9 1.0
N A:GLY190 4.4 18.6 1.0
O A:HOH479 4.5 35.1 1.0
N A:GLY193 4.5 15.4 1.0
CA A:GLY193 4.5 13.4 1.0
CA A:ILE159 4.6 14.0 1.0
CB A:ASP194 4.6 11.5 1.0
C A:GLY193 4.6 13.1 1.0
N A:LEU160 4.7 12.3 1.0
O A:HOH433 4.7 20.3 1.0
C A:SER189 4.8 19.1 1.0
CA A:ASP194 4.8 12.7 1.0
O A:SER189 5.0 18.0 1.0

Calcium binding site 2 out of 3 in 4ijo

Go back to Calcium Binding Sites List in 4ijo
Calcium binding site 2 out of 3 in the Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:4.2
occ:1.00
 OE2 A:GLU199 2.2 11.4 1.0
O A:HOH404 2.3 16.0 1.0
O A:GLU199 2.4 14.1 1.0
OD1 A:ASP124 2.4 9.9 1.0
OD2 A:ASP124 2.4 11.0 1.0
O A:HOH423 2.4 11.8 1.0
O A:GLU201 2.5 11.0 1.0
CG A:ASP124 2.8 13.9 1.0
CD A:GLU199 3.3 14.1 1.0
C A:GLU199 3.5 13.8 1.0
C A:GLU201 3.7 11.4 1.0
CG A:GLU199 3.9 11.3 1.0
OG1 A:THR122 4.1 10.4 1.0
CA A:GLU199 4.1 12.7 1.0
CA A:PHE202 4.2 12.1 1.0
CB A:ASP124 4.3 13.0 1.0
OE1 A:GLU199 4.4 10.5 1.0
CD1 A:TRP203 4.4 13.4 1.0
N A:PHE202 4.4 11.6 1.0
N A:GLU201 4.5 13.1 1.0
N A:ASP200 4.6 15.3 1.0
CB A:GLU199 4.6 13.3 1.0
C A:ASP200 4.7 14.6 1.0
N A:TRP203 4.8 10.5 1.0
CA A:GLU201 4.8 10.5 1.0
CA A:ASP200 4.8 14.6 1.0
O A:HOH427 4.8 16.4 1.0
NE1 A:TRP203 4.9 15.2 1.0

Calcium binding site 3 out of 3 in 4ijo

Go back to Calcium Binding Sites List in 4ijo
Calcium binding site 3 out of 3 in the Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Unraveling Hidden Allosteric Regulatory Sites in Structurally Homologues Metalloproteases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:4.9
occ:1.00
 OD1 A:ASP198 2.2 13.4 1.0
O A:GLY178 2.2 18.7 1.0
O A:GLY176 2.3 18.2 1.0
OD2 A:ASP175 2.3 15.7 1.0
O A:ILE180 2.4 15.2 1.0
OE2 A:GLU201 2.4 16.1 1.0
CG A:ASP198 3.3 15.6 1.0
C A:GLY178 3.4 19.0 1.0
C A:ILE180 3.5 16.1 1.0
CG A:ASP175 3.5 16.9 1.0
C A:GLY176 3.5 17.3 1.0
CD A:GLU201 3.6 17.6 1.0
N A:GLY178 4.0 19.9 1.0
CB A:ASP198 4.0 10.6 1.0
N A:ILE180 4.0 16.3 1.0
OD1 A:ASP175 4.1 21.4 1.0
C A:LYS177 4.1 20.7 1.0
N A:GLY176 4.2 16.6 1.0
N A:ASP175 4.2 15.9 1.0
C A:ASP175 4.2 17.0 1.0
CA A:GLY178 4.3 19.4 1.0
OD2 A:ASP198 4.3 13.1 1.0
CA A:ILE180 4.3 16.9 1.0
CA A:LYS177 4.3 19.3 1.0
C A:GLY179 4.4 17.2 1.0
N A:LYS177 4.4 17.2 1.0
OE1 A:GLU201 4.4 17.1 1.0
CG A:GLU201 4.4 11.7 1.0
CA A:GLY176 4.4 17.5 1.0
N A:GLY179 4.5 18.1 1.0
N A:LEU181 4.5 14.3 1.0
O A:ASP175 4.5 17.3 1.0
CA A:ASP175 4.6 17.0 1.0
CB A:ASP175 4.6 16.9 1.0
O A:LYS177 4.7 22.9 1.0
CB A:ILE180 4.7 16.9 1.0
CA A:GLY179 4.7 18.6 1.0
CA A:LEU181 4.7 14.1 1.0
O A:GLY179 4.9 17.3 1.0

Reference:

Y.Udi, M.Fragai, M.Grossman, S.Mitternacht, R.Arad-Yellin, V.Calderone, M.Melikian, M.Toccafondi, I.N.Berezovsky, C.Luchinat, I.Sagi. Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases J.Mol.Biol. V. 425 2330 2013.
ISSN: ISSN 0022-2836
PubMed: 23583775
DOI: 10.1016/J.JMB.2013.04.009
Page generated: Tue Jul 8 22:55:58 2025

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