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Cobalt 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:

Calcium (Ca) 6 atoms
Zinc (Zn) 6 atoms

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 3 binding sites of Cobalt 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 Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 5th9

Go back to Cobalt Binding Sites List in 5th9
Cobalt binding site 1 out of 3 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 Cobalt with other atoms in the Co 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:Co505

b:22.5
occ:1.00
 CO A:NCO505 0.0 22.5 1.0
N2 A:NCO505 1.8 12.9 1.0
N4 A:NCO505 1.8 13.9 1.0
N3 A:NCO505 1.8 10.5 1.0
N5 A:NCO505 1.8 17.0 1.0
N1 A:NCO505 1.8 14.8 1.0
N6 A:NCO505 1.8 15.8 1.0
O A:ASP206 3.8 11.9 1.0
OD2 A:ASP131 4.0 16.5 1.0
O A:GLU208 4.1 19.1 1.0
OD1 A:ASP131 4.1 15.8 1.0
O A:HOH602 4.1 13.7 1.0
CG A:ASP131 4.4 17.2 1.0
OD1 A:ASP206 4.7 13.3 1.0
OE1 A:GLU130 4.8 32.4 1.0
C A:ASP206 5.0 8.0 1.0

Cobalt binding site 2 out of 3 in 5th9

Go back to Cobalt Binding Sites List in 5th9
Cobalt binding site 2 out of 3 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 Cobalt with other atoms in the Co 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
B:Co505

b:70.8
occ:1.00
 CO B:NCO505 0.0 70.8 1.0
N2 B:NCO505 1.8 33.2 1.0
N4 B:NCO505 1.8 29.0 1.0
N5 B:NCO505 1.8 50.4 1.0
N3 B:NCO505 1.8 27.4 1.0
N1 B:NCO505 1.8 36.5 1.0
N6 B:NCO505 1.8 31.8 1.0
OD1 B:ASP131 3.5 32.8 1.0
O B:ASP206 3.8 20.3 1.0
O B:GLU208 4.0 26.8 1.0
OD2 B:ASP131 4.2 28.1 1.0
CG B:ASP131 4.2 22.2 1.0
O B:HOH614 4.4 23.1 1.0
OD1 B:ASP206 4.5 18.4 1.0
C B:ASP206 5.0 17.8 1.0

Cobalt binding site 3 out of 3 in 5th9

Go back to Cobalt Binding Sites List in 5th9
Cobalt binding site 3 out of 3 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 Cobalt with other atoms in the Co 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
C:Co505

b:0.7
occ:1.00
 CO C:NCO505 0.0 0.7 1.0
N5 C:NCO505 1.8 0.1 1.0
N1 C:NCO505 1.8 0.3 1.0
N4 C:NCO505 1.8 92.5 1.0
N2 C:NCO505 1.8 0.9 1.0
N6 C:NCO505 1.8 0.6 1.0
N3 C:NCO505 1.8 0.4 1.0
O C:ASP206 3.4 0.9 1.0
OD2 C:ASP131 4.0 93.0 1.0
OD1 C:ASP131 4.2 98.2 1.0
O C:GLU208 4.2 99.7 1.0
CG C:ASP131 4.5 92.6 1.0
C C:ASP206 4.6 0.5 1.0
OD1 C:ASP206 4.6 85.0 1.0
C C:ASP207 5.0 1.0 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: Sun Dec 13 10:48:31 2020

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