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Zinc in PDB 5uwn: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D

Protein crystallography data

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D, PDB code: 5uwn was solved by A.B.Taylor, X.Cao, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.80 / 3.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.727, 131.727, 418.722, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.4

Other elements in 5uwn:

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D (pdb code 5uwn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D, PDB code: 5uwn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5uwn

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Zinc binding site 1 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:43.2
occ:1.00
 NE2 A:HIS232 2.0 44.4 1.0
NE2 A:HIS226 2.2 36.0 1.0
NE2 A:HIS222 2.2 39.4 1.0
CE1 A:HIS232 2.7 51.3 1.0
CD2 A:HIS222 3.0 39.9 1.0
CD2 A:HIS226 3.1 39.2 1.0
CE1 A:HIS226 3.2 42.3 1.0
CD2 A:HIS232 3.2 50.1 1.0
CE1 A:HIS222 3.4 44.9 1.0
OE2 A:GLU223 3.7 44.1 1.0
ND1 A:HIS232 4.0 55.3 1.0
CG A:HIS232 4.2 52.7 1.0
ND1 A:HIS226 4.2 42.5 1.0
CG A:HIS226 4.2 40.3 1.0
CG A:HIS222 4.2 40.3 1.0
C11 A:8O7305 4.4 44.7 1.0
ND1 A:HIS222 4.4 42.4 1.0
CD A:GLU223 4.5 42.7 1.0
C12 A:8O7305 4.6 48.4 1.0
C10 A:8O7305 4.7 42.3 1.0
OE1 A:GLU223 4.7 38.7 1.0

Zinc binding site 2 out of 10 in 5uwn

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Zinc binding site 2 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:42.7
occ:1.00
 OD2 A:ASP174 2.0 39.6 1.0
NE2 A:HIS172 2.0 41.2 1.0
ND1 A:HIS200 2.0 37.3 1.0
NE2 A:HIS187 2.0 39.2 1.0
CG A:ASP174 2.8 39.2 1.0
CE1 A:HIS187 2.9 41.9 1.0
CE1 A:HIS200 2.9 37.7 1.0
CD2 A:HIS172 2.9 40.9 1.0
CE1 A:HIS172 3.0 45.7 1.0
OD1 A:ASP174 3.1 45.0 1.0
CG A:HIS200 3.1 36.6 1.0
CD2 A:HIS187 3.1 37.8 1.0
CB A:HIS200 3.5 40.0 1.0
O A:TYR176 4.0 44.2 1.0
ND1 A:HIS172 4.0 49.3 1.0
ND1 A:HIS187 4.0 43.8 1.0
NE2 A:HIS200 4.1 43.5 1.0
CG A:HIS172 4.1 41.9 1.0
CD2 A:HIS200 4.2 33.8 1.0
CB A:ASP174 4.2 39.6 1.0
CG A:HIS187 4.2 38.0 1.0
CE1 A:PHE189 4.6 48.1 1.0
CE2 A:PHE178 4.8 47.2 1.0
CZ A:PHE189 4.8 46.7 1.0
CB A:TYR176 4.9 47.1 1.0
C A:TYR176 4.9 47.1 1.0
CZ A:PHE178 4.9 46.7 1.0
CA A:HIS200 5.0 35.8 1.0

Zinc binding site 3 out of 10 in 5uwn

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Zinc binding site 3 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:35.5
occ:1.00
 NE2 B:HIS232 1.9 34.1 1.0
NE2 B:HIS222 2.2 32.9 1.0
NE2 B:HIS226 2.3 40.8 1.0
CE1 B:HIS232 2.8 36.5 1.0
CD2 B:HIS222 3.0 33.6 1.0
CD2 B:HIS232 3.1 38.5 1.0
CD2 B:HIS226 3.2 40.4 1.0
CE1 B:HIS226 3.3 41.8 1.0
CE1 B:HIS222 3.3 35.3 1.0
ND1 B:HIS232 3.9 38.3 1.0
OE2 B:GLU223 4.0 40.1 1.0
CG B:HIS232 4.1 40.0 1.0
CG B:HIS222 4.2 36.3 1.0
CG B:HIS226 4.3 43.2 1.0
ND1 B:HIS226 4.3 45.0 1.0
ND1 B:HIS222 4.3 36.5 1.0
N1 B:8O7305 4.8 56.6 1.0
C10 B:8O7305 4.8 41.1 1.0
CD B:GLU223 4.8 35.5 1.0
C9 B:8O7305 4.9 40.8 1.0

Zinc binding site 4 out of 10 in 5uwn

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Zinc binding site 4 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:34.6
occ:1.00
 OD2 B:ASP174 1.9 44.0 1.0
NE2 B:HIS172 2.0 41.4 1.0
ND1 B:HIS200 2.0 34.6 1.0
NE2 B:HIS187 2.1 34.7 1.0
CE1 B:HIS187 2.8 38.9 1.0
CG B:ASP174 2.9 46.1 1.0
CE1 B:HIS200 2.9 39.1 1.0
CD2 B:HIS172 3.0 40.9 1.0
CE1 B:HIS172 3.0 44.2 1.0
CG B:HIS200 3.1 34.4 1.0
CD2 B:HIS187 3.2 35.8 1.0
OD1 B:ASP174 3.2 49.9 1.0
CB B:HIS200 3.5 36.5 1.0
ND1 B:HIS187 4.0 37.4 1.0
NE2 B:HIS200 4.1 42.1 1.0
ND1 B:HIS172 4.1 45.2 1.0
CG B:HIS172 4.1 41.1 1.0
O B:TYR176 4.2 49.7 1.0
CD2 B:HIS200 4.2 37.0 1.0
CB B:ASP174 4.2 45.6 1.0
CG B:HIS187 4.3 35.0 1.0
CE2 B:PHE178 4.8 41.7 1.0
CE1 B:PHE189 4.8 49.0 1.0
CZ B:PHE189 4.9 48.1 1.0
CZ B:PHE178 4.9 38.6 1.0
CA B:HIS200 5.0 35.9 1.0
CB B:TYR176 5.0 45.5 1.0

Zinc binding site 5 out of 10 in 5uwn

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Zinc binding site 5 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:42.2
occ:1.00
 NE2 C:HIS232 1.9 38.2 1.0
NE2 C:HIS222 2.2 49.7 1.0
NE2 C:HIS226 2.2 40.2 1.0
CE1 C:HIS232 2.6 45.2 1.0
CD2 C:HIS232 3.0 44.3 1.0
CE1 C:HIS222 3.1 49.2 1.0
CE1 C:HIS226 3.1 43.0 1.0
CD2 C:HIS226 3.2 44.1 1.0
CD2 C:HIS222 3.2 49.3 1.0
OE2 C:GLU223 3.7 45.7 1.0
ND1 C:HIS232 3.8 47.1 1.0
CG C:HIS232 4.1 43.8 1.0
ND1 C:HIS226 4.2 42.3 1.0
ND1 C:HIS222 4.2 47.3 1.0
CG C:HIS226 4.3 42.5 1.0
CG C:HIS222 4.3 48.2 1.0
CD C:GLU223 4.6 45.3 1.0
OE1 C:GLU223 4.8 43.5 1.0
C10 C:8O7305 4.9 56.5 1.0
C11 C:8O7305 4.9 58.2 1.0

Zinc binding site 6 out of 10 in 5uwn

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Zinc binding site 6 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:43.3
occ:1.00
 NE2 C:HIS172 1.9 40.6 1.0
ND1 C:HIS200 2.0 39.1 1.0
OD2 C:ASP174 2.1 43.5 1.0
NE2 C:HIS187 2.2 45.9 1.0
CD2 C:HIS172 2.8 42.2 1.0
CE1 C:HIS200 3.0 39.1 1.0
CE1 C:HIS172 3.0 45.2 1.0
CG C:ASP174 3.0 43.2 1.0
CG C:HIS200 3.0 44.1 1.0
CE1 C:HIS187 3.1 48.4 1.0
CD2 C:HIS187 3.2 48.1 1.0
OD1 C:ASP174 3.4 46.9 1.0
CB C:HIS200 3.4 42.3 1.0
CG C:HIS172 3.9 44.3 1.0
ND1 C:HIS172 4.0 49.1 1.0
NE2 C:HIS200 4.1 38.3 1.0
CD2 C:HIS200 4.1 44.0 1.0
ND1 C:HIS187 4.3 47.2 1.0
CB C:ASP174 4.3 40.9 1.0
CG C:HIS187 4.3 43.9 1.0
O C:TYR176 4.4 50.8 1.0
CZ C:PHE189 4.6 45.1 1.0
CE2 C:PHE189 4.7 45.1 1.0
CE2 C:PHE178 4.8 44.2 1.0
CB C:TYR176 4.8 44.6 1.0
CZ C:PHE178 4.8 47.5 1.0
CA C:HIS200 4.9 41.0 1.0

Zinc binding site 7 out of 10 in 5uwn

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Zinc binding site 7 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:41.6
occ:1.00
 NE2 D:HIS232 2.0 46.2 1.0
NE2 D:HIS222 2.2 47.4 1.0
NE2 D:HIS226 2.3 46.6 1.0
CE1 D:HIS232 2.8 47.6 1.0
CD2 D:HIS222 3.0 46.3 1.0
CD2 D:HIS226 3.1 49.0 1.0
CD2 D:HIS232 3.1 48.3 1.0
CE1 D:HIS222 3.2 49.8 1.0
CE1 D:HIS226 3.4 50.2 1.0
OE2 D:GLU223 3.5 50.8 1.0
ND1 D:HIS232 4.0 44.7 1.0
CG D:HIS232 4.2 48.0 1.0
CG D:HIS222 4.2 46.3 1.0
ND1 D:HIS222 4.3 49.6 1.0
CG D:HIS226 4.3 51.1 1.0
CD D:GLU223 4.3 49.0 1.0
ND1 D:HIS226 4.4 53.7 1.0
OE1 D:GLU223 4.5 50.1 1.0
C10 D:8O7305 4.7 44.9 1.0
C9 D:8O7305 4.7 48.1 1.0
C11 D:8O7305 4.9 47.3 1.0
C8 D:8O7305 5.0 49.8 1.0

Zinc binding site 8 out of 10 in 5uwn

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Zinc binding site 8 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:39.4
occ:1.00
 NE2 D:HIS172 1.9 40.2 1.0
OD2 D:ASP174 2.0 39.9 1.0
ND1 D:HIS200 2.2 39.6 1.0
NE2 D:HIS187 2.3 45.0 1.0
CG D:ASP174 2.9 42.6 1.0
CD2 D:HIS172 2.9 43.0 1.0
CE1 D:HIS172 2.9 43.0 1.0
CD2 D:HIS187 3.1 49.2 1.0
CE1 D:HIS200 3.2 46.2 1.0
CG D:HIS200 3.2 41.4 1.0
OD1 D:ASP174 3.3 50.8 1.0
CE1 D:HIS187 3.3 48.0 1.0
CB D:HIS200 3.5 44.7 1.0
ND1 D:HIS172 4.0 46.2 1.0
CG D:HIS172 4.0 41.4 1.0
O D:TYR176 4.0 54.0 1.0
CB D:ASP174 4.1 44.6 1.0
CZ D:PHE189 4.2 50.2 1.0
CG D:HIS187 4.3 55.3 1.0
NE2 D:HIS200 4.3 51.5 1.0
CD2 D:HIS200 4.4 47.1 1.0
ND1 D:HIS187 4.4 53.9 1.0
CE2 D:PHE189 4.6 45.4 1.0
CE2 D:PHE178 4.7 47.3 1.0
CZ D:PHE178 4.7 46.1 1.0

Zinc binding site 9 out of 10 in 5uwn

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Zinc binding site 9 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:49.5
occ:1.00
 NE2 E:HIS232 2.0 59.0 1.0
NE2 E:HIS222 2.1 59.7 1.0
NE2 E:HIS226 2.3 49.3 1.0
CE1 E:HIS232 2.9 61.9 1.0
CD2 E:HIS222 3.0 60.3 1.0
CD2 E:HIS226 3.0 55.2 1.0
CD2 E:HIS232 3.0 58.9 1.0
CE1 E:HIS222 3.2 59.1 1.0
CE1 E:HIS226 3.2 54.6 1.0
OE2 E:GLU223 3.7 60.3 1.0
ND1 E:HIS232 4.0 62.9 1.0
CG E:HIS232 4.1 62.3 1.0
CG E:HIS226 4.1 55.2 1.0
CG E:HIS222 4.2 57.6 1.0
ND1 E:HIS226 4.2 55.1 1.0
ND1 E:HIS222 4.2 58.0 1.0
CD E:GLU223 4.3 57.7 1.0
OE1 E:GLU223 4.4 59.6 1.0
C2 E:8O7305 4.7 58.6 1.0
C10 E:8O7305 5.0 53.0 1.0

Zinc binding site 10 out of 10 in 5uwn

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Zinc binding site 10 out of 10 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:43.2
occ:1.00
 OD2 E:ASP174 1.8 38.3 1.0
ND1 E:HIS200 2.0 45.2 1.0
NE2 E:HIS172 2.0 40.8 1.0
NE2 E:HIS187 2.2 45.2 1.0
CG E:ASP174 2.7 42.0 1.0
CE1 E:HIS200 2.9 47.5 1.0
CD2 E:HIS172 2.9 41.0 1.0
CG E:HIS200 3.0 43.2 1.0
CE1 E:HIS172 3.0 44.4 1.0
CE1 E:HIS187 3.1 47.0 1.0
OD1 E:ASP174 3.1 39.9 1.0
CD2 E:HIS187 3.3 47.0 1.0
CB E:HIS200 3.4 41.8 1.0
CB E:ASP174 4.0 45.7 1.0
NE2 E:HIS200 4.0 46.1 1.0
CG E:HIS172 4.1 44.3 1.0
ND1 E:HIS172 4.1 46.3 1.0
O E:TYR176 4.1 40.8 1.0
CD2 E:HIS200 4.1 46.8 1.0
ND1 E:HIS187 4.3 49.1 1.0
CG E:HIS187 4.4 47.7 1.0
CE2 E:PHE189 4.4 48.5 1.0
CZ E:PHE189 4.6 49.2 1.0
CE2 E:PHE178 4.8 46.1 1.0
CB E:TYR176 4.8 44.3 1.0
CA E:HIS200 4.9 42.8 1.0
C E:TYR176 5.0 41.8 1.0

Reference:

J.Y.Choi, R.Fuerst, A.M.Knapinska, A.B.Taylor, L.Smith, X.Cao, P.J.Hart, G.B.Fields, W.R.Roush. Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J. Med. Chem. V. 60 5816 2017.
ISSN: ISSN 1520-4804
PubMed: 28653849
DOI: 10.1021/ACS.JMEDCHEM.7B00514
Page generated: Mon Oct 28 12:28:05 2024

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