Calcium in PDB 5ue3: Prommp-9DESFNII

Enzymatic activity of Prommp-9DESFNII

All present enzymatic activity of Prommp-9DESFNII:
3.4.24.35;

Protein crystallography data

The structure of Prommp-9DESFNII, PDB code: 5ue3 was solved by R.S.Alexander, J.Spurlino, C.Milligan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.84 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.300, 73.200, 77.500, 90.00, 106.30, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 5ue3:

The structure of Prommp-9DESFNII also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Prommp-9DESFNII (pdb code 5ue3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Prommp-9DESFNII, PDB code: 5ue3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5ue3

Go back to Calcium Binding Sites List in 5ue3
Calcium binding site 1 out of 5 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prommp-9DESFNII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.5
occ:1.00
 O A:GLY183 2.3 13.6 1.0
O A:LEU187 2.3 13.7 1.0
OE2 A:GLU208 2.3 18.9 1.0
OD1 A:ASP182 2.3 13.8 1.0
O A:ASP185 2.3 15.1 1.0
OD2 A:ASP205 2.4 12.8 1.0
C A:LEU187 3.4 14.0 1.0
CG A:ASP182 3.5 15.4 1.0
CG A:ASP205 3.5 13.0 1.0
C A:GLY183 3.5 13.9 1.0
C A:ASP185 3.5 19.7 1.0
CD A:GLU208 3.5 15.8 1.0
N A:ASP185 3.8 18.2 1.0
N A:LEU187 3.8 12.2 1.0
C A:LYS184 4.0 18.2 1.0
OD2 A:ASP182 4.0 17.9 1.0
N A:GLY183 4.1 13.4 1.0
CA A:LEU187 4.1 16.2 1.0
CB A:ASP205 4.2 9.6 1.0
CA A:ASP185 4.2 19.2 1.0
C A:ASP182 4.3 16.1 1.0
C A:GLY186 4.3 13.3 1.0
OE1 A:GLU208 4.3 14.3 1.0
OD1 A:ASP205 4.3 11.8 1.0
CG A:GLU208 4.4 14.6 1.0
CA A:LYS184 4.4 16.2 1.0
N A:ASP182 4.4 15.0 1.0
N A:LYS184 4.4 16.5 1.0
CA A:GLY183 4.4 14.7 1.0
CB A:LEU187 4.4 21.8 1.0
O A:LYS184 4.4 19.5 1.0
N A:LEU188 4.5 10.4 1.0
N A:GLY186 4.5 15.4 1.0
O A:HOH546 4.6 24.6 1.0
CA A:LEU188 4.6 10.7 1.0
CA A:GLY186 4.6 13.7 1.0
CB A:ASP182 4.6 12.3 1.0
CA A:ASP182 4.6 13.7 1.0
O A:ASP182 4.7 16.8 1.0
O A:GLY186 4.9 15.4 1.0

Calcium binding site 2 out of 5 in 5ue3

Go back to Calcium Binding Sites List in 5ue3
Calcium binding site 2 out of 5 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prommp-9DESFNII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:40.6
occ:1.00
 OD2 A:ASP206 2.6 19.5 1.0
O A:HOH691 2.7 33.5 1.0
O A:HOH487 2.8 15.7 1.0
N A:GLU130 2.8 14.6 1.0
CG A:ASP206 3.4 16.2 1.0
OG A:SER129 3.5 14.1 1.0
OD1 A:ASP206 3.5 13.6 1.0
CA A:SER129 3.7 12.7 1.0
CB A:GLU130 3.7 16.8 1.0
C A:SER129 3.7 16.0 1.0
CA A:GLU130 3.8 15.9 1.0
CB A:SER129 4.1 12.7 1.0
CG A:GLU130 4.1 26.1 1.0
N A:ASP131 4.3 13.8 1.0
O A:HOH403 4.4 15.0 1.0
C A:GLU130 4.4 17.2 1.0
OD1 A:ASP131 4.5 17.3 1.0
CB A:ASP206 4.8 13.3 1.0
CG A:ASP131 4.8 14.4 1.0
O A:TYR128 4.8 21.1 1.0
O A:SER129 4.9 15.5 1.0
OD2 A:ASP131 5.0 13.9 1.0
N A:SER129 5.0 14.3 1.0

Calcium binding site 3 out of 5 in 5ue3

Go back to Calcium Binding Sites List in 5ue3
Calcium binding site 3 out of 5 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Prommp-9DESFNII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:18.9
occ:1.00
 O A:HOH485 2.3 18.0 1.0
O A:GLN199 2.3 15.2 1.0
O A:HOH412 2.3 20.5 1.0
O A:ASP165 2.4 17.1 1.0
O A:GLY197 2.4 18.3 1.0
OD1 A:ASP201 2.4 14.5 1.0
CG A:ASP201 3.5 14.9 1.0
C A:ASP165 3.5 14.5 1.0
C A:GLN199 3.5 16.9 1.0
C A:GLY197 3.6 20.2 1.0
O A:ALA164 4.0 19.6 1.0
OD2 A:ASP201 4.0 15.8 1.0
C A:ILE198 4.1 14.8 1.0
O A:HOH420 4.1 21.7 1.0
N A:ASP201 4.2 10.8 1.0
N A:GLN199 4.2 15.4 1.0
O A:ILE198 4.2 14.2 1.0
O A:GLY195 4.3 18.3 1.0
CA A:ASP165 4.3 13.6 1.0
N A:GLY197 4.3 22.5 1.0
C A:GLY200 4.3 11.7 1.0
CA A:GLY200 4.3 11.8 1.0
N A:GLY200 4.3 11.8 1.0
N A:ILE166 4.4 11.1 1.0
CA A:GLY197 4.5 21.0 1.0
CA A:GLN199 4.5 16.2 1.0
N A:ILE198 4.5 19.7 1.0
CA A:ILE198 4.5 15.8 1.0
N A:VAL167 4.5 12.2 1.0
CA A:ILE166 4.6 10.1 1.0
CB A:ASP201 4.6 14.6 1.0
CA A:ASP201 4.7 11.8 1.0
C A:PRO196 4.7 23.8 1.0
O A:HOH419 4.8 51.6 1.0
CG2 A:VAL167 4.8 15.8 1.0
O A:HOH463 4.8 22.9 1.0
C A:ALA164 4.9 17.2 1.0
CH2 A:TRP116 5.0 14.6 1.0

Calcium binding site 4 out of 5 in 5ue3

Go back to Calcium Binding Sites List in 5ue3
Calcium binding site 4 out of 5 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Prommp-9DESFNII within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:15.6
occ:1.00
 O B:GLY183 2.2 17.4 1.0
O B:LEU187 2.3 13.2 1.0
OE2 B:GLU208 2.3 19.2 1.0
OD2 B:ASP205 2.3 17.2 1.0
OD1 B:ASP182 2.3 16.6 1.0
O B:ASP185 2.3 17.6 1.0
CG B:ASP205 3.4 14.7 1.0
CG B:ASP182 3.4 20.0 1.0
C B:GLY183 3.4 20.8 1.0
C B:LEU187 3.5 13.4 1.0
C B:ASP185 3.5 18.9 1.0
CD B:GLU208 3.5 18.9 1.0
N B:ASP185 3.8 19.3 1.0
OD2 B:ASP182 3.9 21.0 1.0
N B:LEU187 3.9 14.5 1.0
C B:LYS184 4.0 21.9 1.0
N B:GLY183 4.1 20.0 1.0
CB B:ASP205 4.1 12.2 1.0
CA B:ASP185 4.2 19.8 1.0
CA B:LEU187 4.2 15.2 1.0
C B:ASP182 4.2 21.0 1.0
OE1 B:GLU208 4.3 18.0 1.0
N B:ASP182 4.3 19.2 1.0
OD1 B:ASP205 4.3 15.5 1.0
C B:GLY186 4.3 16.1 1.0
CA B:GLY183 4.4 19.6 1.0
N B:LYS184 4.4 23.0 1.0
O B:LYS184 4.4 23.1 1.0
CG B:GLU208 4.4 14.8 1.0
CA B:LYS184 4.4 22.2 1.0
N B:LEU188 4.5 12.0 1.0
N B:GLY186 4.5 17.8 1.0
CB B:LEU187 4.6 25.3 1.0
CA B:ASP182 4.6 18.4 1.0
CB B:ASP182 4.6 20.4 1.0
O B:HOH488 4.6 26.4 1.0
CA B:GLY186 4.6 17.2 1.0
O B:ASP182 4.7 23.1 1.0
CA B:LEU188 4.7 12.2 1.0
O B:GLY186 4.9 17.5 1.0

Calcium binding site 5 out of 5 in 5ue3

Go back to Calcium Binding Sites List in 5ue3
Calcium binding site 5 out of 5 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Prommp-9DESFNII within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:16.6
occ:1.00
 O B:GLN199 2.3 14.5 1.0
O B:HOH463 2.3 17.0 1.0
O B:GLY197 2.4 19.2 1.0
O B:ASP165 2.4 14.8 1.0
O B:HOH443 2.4 17.5 1.0
OD1 B:ASP201 2.5 14.1 1.0
CG B:ASP201 3.5 12.7 1.0
C B:GLN199 3.5 13.3 1.0
C B:ASP165 3.6 13.9 1.0
C B:GLY197 3.6 13.7 1.0
OD2 B:ASP201 3.9 14.2 1.0
C B:ILE198 4.0 14.5 1.0
N B:ASP201 4.1 11.7 1.0
N B:GLN199 4.2 14.4 1.0
O B:ILE198 4.2 14.3 1.0
CA B:GLY200 4.3 11.7 1.0
C B:GLY200 4.3 13.2 1.0
N B:GLY200 4.3 10.1 1.0
O B:GLY195 4.3 17.2 1.0
N B:GLY197 4.3 22.1 1.0
O B:ALA164 4.4 18.9 1.0
O B:HOH626 4.4 24.7 1.0
O B:HOH428 4.4 26.6 1.0
N B:ILE166 4.4 11.7 1.0
CA B:ASP165 4.4 11.0 1.0
O B:HOH624 4.4 48.7 1.0
CA B:GLN199 4.4 13.4 1.0
CA B:GLY197 4.5 24.2 1.0
N B:ILE198 4.5 18.4 1.0
CA B:ILE198 4.5 17.0 1.0
CA B:ILE166 4.5 11.8 1.0
N B:VAL167 4.5 12.3 1.0
CB B:ASP201 4.6 10.5 1.0
CA B:ASP201 4.7 11.9 1.0
C B:PRO196 4.8 24.1 1.0
CG2 B:VAL167 4.9 16.9 1.0
CH2 B:TRP116 5.0 15.1 1.0
C B:ILE166 5.0 13.9 1.0

Reference:

R.H.Scannevin, R.Alexander, T.M.Haarlander, S.L.Burke, M.Singer, C.Huo, Y.M.Zhang, D.Maguire, J.Spurlino, I.Deckman, K.I.Carroll, F.Lewandowski, E.Devine, K.Dzordzorme, B.Tounge, C.Milligan, S.Bayoumy, R.Williams, C.Schalk-Hihi, K.Leonard, P.Jackson, M.Todd, L.C.Kuo, K.J.Rhodes. Discovery of A Highly Selective Chemical Inhibitor of Matrix Metalloproteinase-9 (Mmp-9) That Allosterically Inhibits Zymogen Activation. J. Biol. Chem. V. 292 17963 2017.
ISSN: ESSN 1083-351X
PubMed: 28860188
DOI: 10.1074/JBC.M117.806075
Page generated: Sat Dec 12 05:45:58 2020

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