Atomistry » Zinc » PDB 1ylk-1z5h » 1you
Atomistry »
  Zinc »
    PDB 1ylk-1z5h »
      1you »

Zinc in PDB 1you: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor, PDB code: 1you was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.089, 108.223, 36.035, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 29.5

Other elements in 1you:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor (pdb code 1you). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor, PDB code: 1you:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1you

Go back to Zinc Binding Sites List in 1you
Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:20.2
occ:1.00
NE2 A:HIS232 2.1 19.8 1.0
NE2 A:HIS222 2.1 17.6 1.0
N9 A:PFD998 2.1 35.0 1.0
NE2 A:HIS226 2.4 17.0 1.0
O10 A:PFD998 2.9 38.4 1.0
C4 A:PFD998 2.9 36.6 1.0
CE1 A:HIS232 3.0 14.4 1.0
CE1 A:HIS222 3.0 14.4 1.0
C14 A:PFD998 3.1 35.1 1.0
CD2 A:HIS222 3.1 19.6 1.0
CD2 A:HIS232 3.2 17.6 1.0
CD2 A:HIS226 3.2 15.3 1.0
O18 A:PFD998 3.2 38.4 1.0
CE1 A:HIS226 3.5 15.3 1.0
ND1 A:HIS232 4.1 10.0 1.0
ND1 A:HIS222 4.2 15.8 1.0
CG A:HIS232 4.3 17.9 1.0
CG A:HIS222 4.3 18.1 1.0
N7 A:PFD998 4.3 36.6 1.0
CG A:HIS226 4.4 16.7 1.0
C1 A:PFD998 4.4 38.3 1.0
ND1 A:HIS226 4.5 17.7 1.0
C19 A:PFD998 4.6 38.0 1.0
OE2 A:GLU223 4.6 20.9 1.0
C21 A:PFD998 4.7 33.2 1.0
O15 A:PFD998 4.7 40.7 1.0
C13 A:PFD998 4.7 28.9 1.0
CE A:MET240 4.8 11.4 1.0
C3 A:PFD998 4.9 36.4 1.0

Zinc binding site 2 out of 4 in 1you

Go back to Zinc Binding Sites List in 1you
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:16.0
occ:1.00
ND1 A:HIS200 1.9 19.4 1.0
OD2 A:ASP174 2.0 16.7 1.0
NE2 A:HIS187 2.1 15.8 1.0
NE2 A:HIS172 2.1 10.3 1.0
CE1 A:HIS200 2.7 15.3 1.0
CG A:ASP174 2.9 15.4 1.0
CD2 A:HIS187 3.0 17.6 1.0
CE1 A:HIS172 3.0 15.2 1.0
CE1 A:HIS187 3.0 20.1 1.0
CG A:HIS200 3.1 16.4 1.0
CD2 A:HIS172 3.1 10.1 1.0
OD1 A:ASP174 3.1 13.5 1.0
CB A:HIS200 3.6 13.9 1.0
NE2 A:HIS200 3.9 10.6 1.0
CD2 A:HIS200 4.1 12.9 1.0
ND1 A:HIS187 4.2 14.7 1.0
ND1 A:HIS172 4.2 10.6 1.0
CG A:HIS187 4.2 15.6 1.0
CG A:HIS172 4.2 12.2 1.0
CB A:ASP174 4.3 14.2 1.0
O A:TYR176 4.3 15.0 1.0
CZ A:PHE178 4.6 11.4 1.0
CE2 A:PHE189 4.6 20.1 1.0
CE2 A:PHE178 4.7 9.3 1.0
O A:HOH6 4.8 12.0 1.0
CZ A:PHE189 4.9 21.7 1.0
CA A:HIS200 5.0 13.0 1.0

Zinc binding site 3 out of 4 in 1you

Go back to Zinc Binding Sites List in 1you
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:21.3
occ:1.00
NE2 B:HIS232 2.0 21.5 1.0
NE2 B:HIS226 2.0 18.3 1.0
N9 B:PFD999 2.1 34.5 1.0
NE2 B:HIS222 2.3 17.5 1.0
CD2 B:HIS226 2.9 19.5 1.0
C14 B:PFD999 2.9 32.3 1.0
CE1 B:HIS232 3.0 20.6 1.0
CD2 B:HIS232 3.0 20.9 1.0
O18 B:PFD999 3.0 35.2 1.0
C4 B:PFD999 3.0 35.8 1.0
CE1 B:HIS226 3.1 19.2 1.0
O10 B:PFD999 3.1 32.8 1.0
CE1 B:HIS222 3.2 15.2 1.0
CD2 B:HIS222 3.3 15.9 1.0
ND1 B:HIS232 4.1 18.0 1.0
CG B:HIS226 4.1 20.5 1.0
CG B:HIS232 4.1 20.5 1.0
ND1 B:HIS226 4.2 20.5 1.0
N7 B:PFD999 4.2 32.1 1.0
ND1 B:HIS222 4.3 12.3 1.0
CG B:HIS222 4.4 16.3 1.0
C1 B:PFD999 4.5 35.4 1.0
CE B:MET240 4.8 8.8 1.0
OE2 B:GLU223 4.8 15.3 1.0
C3 B:PFD999 4.8 32.6 1.0
C13 B:PFD999 4.8 31.8 1.0
CB B:PRO242 4.9 21.6 1.0

Zinc binding site 4 out of 4 in 1you

Go back to Zinc Binding Sites List in 1you
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with A Potent Pyrimidinetrione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:18.1
occ:1.00
NE2 B:HIS172 1.9 2.0 1.0
OD2 B:ASP174 1.9 7.5 1.0
ND1 B:HIS200 2.0 15.6 1.0
NE2 B:HIS187 2.1 17.7 1.0
CE1 B:HIS187 2.8 19.8 1.0
CE1 B:HIS172 2.8 6.2 1.0
CG B:ASP174 2.9 11.7 1.0
CE1 B:HIS200 2.9 11.3 1.0
CD2 B:HIS172 3.0 7.3 1.0
OD1 B:ASP174 3.2 11.4 1.0
CG B:HIS200 3.2 13.8 1.0
CD2 B:HIS187 3.3 16.5 1.0
CB B:HIS200 3.7 11.1 1.0
ND1 B:HIS172 3.9 2.0 1.0
ND1 B:HIS187 4.0 19.8 1.0
NE2 B:HIS200 4.0 6.2 1.0
CG B:HIS172 4.1 6.7 1.0
CD2 B:HIS200 4.2 12.4 1.0
CB B:ASP174 4.2 13.3 1.0
CG B:HIS187 4.2 17.8 1.0
O B:TYR176 4.3 18.5 1.0
CB B:TYR176 4.3 20.3 1.0
CZ B:PHE178 4.8 7.3 1.0
CZ B:PHE189 4.8 22.4 1.0
O B:HOH15 4.9 11.3 1.0
C B:TYR176 5.0 18.3 1.0
CD2 B:TYR176 5.0 21.5 1.0
CE2 B:PHE189 5.0 21.2 1.0
CE2 B:PHE178 5.0 5.9 1.0

Reference:

J.A.Blagg, M.C.Noe, L.A.Wolf-Gouveia, L.A.Reiter, E.R.Laird, S.P.Chang, D.E.Danley, J.T.Downs, N.C.Elliott, J.D.Eskra, R.J.Griffiths, J.R.Hardink, A.I.Haugeto, C.S.Jones, J.L.Liras, L.L.Lopresti-Morrow, P.G.Mitchell, J.Pandit, R.P.Robinson, C.Subramanyam, M.L.Vaughn-Bowser, S.A.Yocum. Potent Pyrimidinetrione-Based Inhibitors of Mmp-13 with Enhanced Selectivity Over Mmp-14. Bioorg.Med.Chem.Lett. V. 15 1807 2005.
ISSN: ISSN 0960-894X
PubMed: 15780611
DOI: 10.1016/J.BMCL.2005.02.038
Page generated: Wed Oct 16 21:01:58 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy