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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

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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

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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

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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

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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 Dec 16 03:14:52 2020

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