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Calcium in PDB 5th9: Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)

Enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)

All present enzymatic activity of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9):
3.4.24.35;

Protein crystallography data

The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9), PDB code: 5th9 was solved by T.C.Appleby, A.E.Greenstein, H.J.Kwon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.64 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 168.167, 168.167, 234.735, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.7

Other elements in 5th9:

The structure of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) (pdb code 5th9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9), PDB code: 5th9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5th9

Go back to Calcium Binding Sites List in 5th9
Calcium binding site 1 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:26.8
occ:1.00
 O A:ASP165 2.3 18.6 1.0
O A:GLN199 2.5 9.4 1.0
O A:GLY197 2.6 12.9 1.0
OD1 A:ASP201 2.6 7.3 1.0
C A:ASP165 3.4 12.3 1.0
CG A:ASP201 3.7 7.9 1.0
C A:GLN199 3.7 8.2 1.0
C A:GLY197 3.7 7.7 1.0
O A:HOH614 3.9 19.8 1.0
OH H:TYR99 3.9 7.5 1.0
O A:ALA164 3.9 11.6 1.0
CA A:ASP165 4.1 11.1 1.0
O A:GLY195 4.1 15.2 1.0
OD2 A:ASP201 4.1 7.3 1.0
N A:GLN199 4.3 11.5 1.0
N A:GLY197 4.3 16.9 1.0
N A:ILE166 4.4 12.1 1.0
N A:ASP201 4.4 13.0 1.0
CA A:GLY197 4.5 10.5 1.0
C A:ILE198 4.5 8.1 1.0
CA A:GLY200 4.5 10.1 1.0
N A:GLY200 4.6 8.0 1.0
C A:GLY200 4.6 10.4 1.0
CA A:GLN199 4.6 8.6 1.0
C A:PRO196 4.7 19.1 1.0
CA A:ILE166 4.7 8.9 1.0
CZ H:TYR99 4.8 4.7 1.0
N A:ILE198 4.8 8.2 1.0
N A:VAL167 4.8 12.5 1.0
C A:ALA164 4.8 11.3 1.0
O A:ILE198 4.8 7.8 1.0
CG2 A:VAL167 4.8 11.6 1.0
CB A:ASP201 4.9 12.6 1.0
N A:ASP165 5.0 13.3 1.0
CA A:ILE198 5.0 10.7 1.0
O A:PRO196 5.0 12.7 1.0

Calcium binding site 2 out of 6 in 5th9

Go back to Calcium Binding Sites List in 5th9
Calcium binding site 2 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:13.9
occ:1.00
 OD2 A:ASP205 2.1 5.8 1.0
O A:GLY183 2.2 13.1 1.0
OE2 A:GLU208 2.2 7.9 1.0
OD1 A:ASP182 2.3 8.0 1.0
O A:ASP185 2.3 13.8 1.0
O A:LEU187 2.5 10.6 1.0
CG A:ASP205 3.3 8.5 1.0
C A:GLY183 3.4 10.9 1.0
CG A:ASP182 3.4 9.7 1.0
CD A:GLU208 3.4 8.3 1.0
C A:ASP185 3.5 11.4 1.0
C A:LEU187 3.6 7.8 1.0
N A:ASP185 3.9 13.7 1.0
OD2 A:ASP182 3.9 8.6 1.0
N A:LEU187 4.0 11.1 1.0
CB A:ASP205 4.0 8.4 1.0
N A:GLY183 4.0 6.6 1.0
C A:LYS184 4.1 10.6 1.0
OD1 A:ASP205 4.2 14.1 1.0
CA A:ASP185 4.2 14.2 1.0
CG A:GLU208 4.3 10.2 1.0
OE1 A:GLU208 4.3 6.7 1.0
CA A:GLY183 4.3 11.2 1.0
N A:LYS184 4.3 7.0 1.0
C A:ASP182 4.4 7.7 1.0
N A:ASP182 4.4 8.5 1.0
CA A:LEU187 4.4 10.4 1.0
CA A:LYS184 4.4 6.6 1.0
C A:GLY186 4.5 10.7 1.0
N A:GLY186 4.5 9.5 1.0
N A:LEU188 4.5 8.0 1.0
O A:LYS184 4.6 12.6 1.0
CB A:ASP182 4.6 6.5 1.0
CA A:LEU188 4.6 5.2 1.0
CA A:GLY186 4.7 11.7 1.0
CA A:ASP182 4.7 9.6 1.0
CG A:LEU187 4.9 9.0 1.0

Calcium binding site 3 out of 6 in 5th9

Go back to Calcium Binding Sites List in 5th9
Calcium binding site 3 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:24.3
occ:1.00
 O B:ASP165 2.4 18.3 1.0
O B:GLN199 2.6 12.8 1.0
OD1 B:ASP201 2.6 6.9 1.0
O B:GLY197 2.7 10.1 1.0
O B:HOH609 3.4 15.4 1.0
C B:ASP165 3.5 7.6 1.0
C B:GLN199 3.7 8.4 1.0
CG B:ASP201 3.7 19.7 1.0
C B:GLY197 3.9 7.0 1.0
O B:ALA164 3.9 7.2 1.0
OH I:TYR99 3.9 7.7 1.0
O B:GLY195 4.0 20.6 1.0
CA B:ASP165 4.1 10.0 1.0
OD2 B:ASP201 4.3 8.3 1.0
N B:ASP201 4.4 11.5 1.0
N B:GLN199 4.4 8.0 1.0
N B:GLY197 4.4 6.0 1.0
N B:ILE166 4.4 8.5 1.0
CA B:GLY200 4.5 10.0 1.0
C B:ILE198 4.5 7.4 1.0
N B:GLY200 4.5 7.9 1.0
C B:PRO196 4.6 5.4 1.0
C B:GLY200 4.6 13.4 1.0
CA B:GLY197 4.7 6.8 1.0
CA B:GLN199 4.7 6.9 1.0
CA B:ILE166 4.7 9.2 1.0
O B:PRO196 4.8 7.5 1.0
N B:ILE198 4.8 8.7 1.0
O B:ILE198 4.8 6.7 1.0
C B:ALA164 4.8 7.2 1.0
CZ I:TYR99 4.8 4.2 1.0
CA B:ILE198 4.9 7.9 1.0
N B:VAL167 4.9 7.4 1.0
CH2 B:TRP116 4.9 7.5 1.0
CB B:ASP201 5.0 7.3 1.0

Calcium binding site 4 out of 6 in 5th9

Go back to Calcium Binding Sites List in 5th9
Calcium binding site 4 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:12.6
occ:1.00
 O B:LEU187 2.2 13.5 1.0
OD2 B:ASP205 2.2 16.2 1.0
O B:ASP185 2.2 26.3 1.0
O B:GLY183 2.3 18.3 1.0
OD1 B:ASP182 2.4 16.4 1.0
OE2 B:GLU208 2.4 15.5 1.0
CG B:ASP205 3.4 12.4 1.0
C B:LEU187 3.4 14.7 1.0
C B:ASP185 3.4 21.6 1.0
C B:GLY183 3.5 17.2 1.0
CG B:ASP182 3.6 15.7 1.0
CD B:GLU208 3.6 17.4 1.0
N B:LEU187 3.9 15.8 1.0
N B:ASP185 4.0 19.7 1.0
N B:GLY183 4.1 11.5 1.0
CA B:LEU187 4.1 13.4 1.0
OD2 B:ASP182 4.1 16.6 1.0
C B:LYS184 4.2 20.3 1.0
CB B:ASP205 4.2 10.0 1.0
OD1 B:ASP205 4.2 16.5 1.0
N B:ASP182 4.2 9.3 1.0
CA B:ASP185 4.2 20.4 1.0
C B:ASP182 4.3 13.9 1.0
C B:GLY186 4.3 15.2 1.0
N B:GLY186 4.4 19.0 1.0
CA B:GLY183 4.4 12.8 1.0
N B:LEU188 4.4 10.4 1.0
CA B:GLY186 4.4 16.1 1.0
CG B:GLU208 4.5 12.5 1.0
OE1 B:GLU208 4.5 18.6 1.0
CB B:LEU187 4.5 15.7 1.0
O B:LYS184 4.5 19.6 1.0
N B:LYS184 4.5 17.8 1.0
CA B:ASP182 4.6 11.5 1.0
CA B:LYS184 4.6 23.1 1.0
CA B:LEU188 4.6 9.8 1.0
CB B:ASP182 4.7 11.3 1.0
O B:ASP182 4.7 24.8 1.0

Calcium binding site 5 out of 6 in 5th9

Go back to Calcium Binding Sites List in 5th9
Calcium binding site 5 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:75.5
occ:1.00
 O C:ASP165 2.7 95.9 1.0
O C:GLY197 2.7 95.5 1.0
O C:GLN199 2.8 84.5 1.0
OD1 C:ASP201 2.8 79.8 1.0
C C:ASP165 3.6 77.3 1.0
O C:ALA164 3.6 78.1 1.0
OH J:TYR99 3.7 82.6 1.0
C C:GLY197 3.9 92.0 1.0
CG C:ASP201 3.9 78.6 1.0
O C:GLY195 4.0 96.7 1.0
C C:GLN199 4.0 85.0 1.0
CA C:ASP165 4.2 74.9 1.0
N C:GLY197 4.3 91.4 1.0
N C:ASP201 4.5 89.5 1.0
OD2 C:ASP201 4.5 78.1 1.0
N C:ILE166 4.5 74.1 1.0
C C:PRO196 4.6 94.7 1.0
CZ J:TYR99 4.6 92.6 1.0
CA C:GLY197 4.6 94.3 1.0
N C:GLN199 4.6 92.0 1.0
C C:ILE198 4.6 89.9 1.0
C C:ALA164 4.6 78.0 1.0
C C:GLY200 4.7 80.0 1.0
CA C:GLY200 4.8 78.4 1.0
O C:ILE198 4.8 90.5 1.0
N C:GLY200 4.9 82.0 1.0
CA C:ILE166 4.9 74.7 1.0
CG2 C:VAL167 4.9 71.5 1.0
N C:ILE198 4.9 92.6 1.0
N C:VAL167 4.9 71.8 1.0
N C:ASP165 4.9 81.5 1.0
CA C:GLN199 4.9 87.3 1.0
CA C:PRO196 4.9 0.5 1.0
CA C:ILE198 5.0 89.3 1.0

Calcium binding site 6 out of 6 in 5th9

Go back to Calcium Binding Sites List in 5th9
Calcium binding site 6 out of 6 in the Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9 (Gs-5745 Bound to Mmp-9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:0.6
occ:1.00
 O C:LEU187 2.3 1.0 1.0
O C:ASP185 2.3 1.0 1.0
OD1 C:ASP182 2.5 0.9 1.0
O C:GLY183 2.5 0.4 1.0
OE2 C:GLU208 2.7 0.5 1.0
OD2 C:ASP205 3.0 0.7 1.0
C C:LEU187 3.5 0.1 1.0
C C:ASP185 3.6 0.8 1.0
C C:GLY183 3.7 0.5 1.0
CG C:ASP182 3.7 0.6 1.0
CD C:GLU208 3.9 100.0 1.0
N C:LEU187 4.0 0.6 1.0
CG C:ASP205 4.0 0.6 1.0
N C:GLY183 4.1 91.4 1.0
N C:ASP182 4.2 0.8 1.0
C C:GLY186 4.3 97.8 1.0
C C:ASP182 4.3 97.1 1.0
N C:ASP185 4.3 0.3 1.0
CA C:GLY186 4.3 0.5 1.0
CA C:LEU187 4.3 0.8 1.0
OD2 C:ASP182 4.4 0.2 1.0
N C:LEU188 4.4 90.6 1.0
N C:GLY186 4.4 0.3 1.0
CA C:LEU188 4.5 90.9 1.0
CA C:GLY183 4.5 89.4 1.0
C C:LYS184 4.5 0.5 1.0
CA C:ASP185 4.5 0.4 1.0
CB C:ASP205 4.6 92.9 1.0
CA C:ASP182 4.6 0.1 1.0
CG C:GLU208 4.7 97.5 1.0
N C:LYS184 4.7 97.0 1.0
OE1 C:GLU208 4.8 96.0 1.0
CB C:ASP182 4.8 0.4 1.0
CD1 C:LEU187 4.8 1.0 1.0
O C:ASP182 4.8 97.3 1.0
CG C:LEU187 4.8 89.1 1.0
CA C:LYS184 4.8 0.1 1.0
O C:LYS184 4.9 0.9 1.0
OD1 C:ASP205 4.9 0.9 1.0
CB C:PHE181 5.0 0.2 1.0
O C:GLY186 5.0 0.8 1.0

Reference:

T.C.Appleby, A.E.Greenstein, M.Hung, A.Liclican, M.Velasquez, A.G.Villasenor, R.Wang, M.H.Wong, X.Liu, G.A.Papalia, B.E.Schultz, R.Sakowicz, V.Smith, H.J.Kwon. Biochemical Characterization and Structure Determination of A Potent, Selective Antibody Inhibitor of Human MMP9. J. Biol. Chem. V. 292 6810 2017.
ISSN: ESSN 1083-351X
PubMed: 28235803
DOI: 10.1074/JBC.M116.760579
Page generated: Mon Jul 15 11:17:08 2024

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