Zinc in PDB 5uwl: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A

Protein crystallography data

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A, PDB code: 5uwl 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) 60.07 / 2.55
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 129.962, 129.962, 142.076, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24

Other elements in 5uwl:

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A also contains other interesting chemical elements:

Calcium (Ca) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A (pdb code 5uwl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A, PDB code: 5uwl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5uwl

Go back to Zinc Binding Sites List in 5uwl
Zinc binding site 1 out of 3 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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 (S)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:36.3
occ:1.00
NE2 A:HIS232 1.9 32.6 1.0
NE2 A:HIS222 2.0 28.9 1.0
NE2 A:HIS226 2.1 28.2 1.0
CD2 A:HIS232 2.8 32.9 1.0
CD2 A:HIS226 3.0 29.7 1.0
CE1 A:HIS232 3.0 33.6 1.0
CD2 A:HIS222 3.0 35.6 1.0
CE1 A:HIS222 3.0 30.5 1.0
CE1 A:HIS226 3.3 32.4 1.0
CG A:HIS232 4.0 26.8 1.0
ND1 A:HIS232 4.0 29.6 1.0
OE2 A:GLU223 4.1 37.0 1.0
ND1 A:HIS222 4.1 30.7 1.0
CG A:HIS222 4.2 32.1 1.0
CG A:HIS226 4.2 33.6 1.0
ND1 A:HIS226 4.3 29.0 1.0
C13 A:8OJ306 4.4 31.6 1.0
OE1 A:GLU223 4.4 35.8 1.0
CD A:GLU223 4.5 36.3 1.0
C12 A:8OJ306 4.7 32.5 1.0
CE A:MET240 4.8 23.4 1.0
C14 A:8OJ306 4.8 34.5 1.0

Zinc binding site 2 out of 3 in 5uwl

Go back to Zinc Binding Sites List in 5uwl
Zinc binding site 2 out of 3 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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 (S)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:46.5
occ:1.00
NE2 A:HIS172 1.9 37.2 1.0
ND1 A:HIS200 1.9 42.2 1.0
OD2 A:ASP174 1.9 47.2 1.0
NE2 A:HIS187 2.2 45.2 1.0
CD2 A:HIS172 2.7 45.7 1.0
CG A:ASP174 2.8 56.0 1.0
CE1 A:HIS200 2.8 42.5 1.0
OD1 A:ASP174 3.0 53.0 1.0
CE1 A:HIS172 3.0 44.5 1.0
CG A:HIS200 3.1 40.8 1.0
CE1 A:HIS187 3.1 40.2 1.0
CD2 A:HIS187 3.3 41.2 1.0
CB A:HIS200 3.5 34.7 1.0
CG A:HIS172 3.9 45.9 1.0
NE2 A:HIS200 4.0 35.6 1.0
ND1 A:HIS172 4.0 43.0 1.0
CD2 A:HIS200 4.1 40.2 1.0
CB A:ASP174 4.2 58.5 1.0
ND1 A:HIS187 4.3 44.3 1.0
O A:TYR176 4.4 47.8 1.0
CG A:HIS187 4.4 43.3 1.0
CZ A:PHE178 4.4 42.0 1.0
O A:HOH414 4.8 48.4 1.0
CE2 A:PHE178 4.8 43.4 1.0
CE2 A:PHE189 4.9 42.5 1.0
CA A:HIS200 5.0 33.3 1.0
CE1 A:PHE178 5.0 40.5 1.0

Zinc binding site 3 out of 3 in 5uwl

Go back to Zinc Binding Sites List in 5uwl
Zinc binding site 3 out of 3 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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 (S)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:36.0
occ:1.00
NE2 B:HIS232 1.9 31.9 1.0
NE2 B:HIS222 2.2 34.9 1.0
NE2 B:HIS226 2.2 31.9 1.0
CE1 B:HIS232 2.8 30.5 1.0
CD2 B:HIS232 3.0 37.3 1.0
CD2 B:HIS222 3.0 32.9 1.0
CD2 B:HIS226 3.1 36.4 1.0
CE1 B:HIS222 3.2 36.3 1.0
CE1 B:HIS226 3.3 31.2 1.0
ND1 B:HIS232 3.9 27.4 1.0
CG B:HIS232 4.1 32.8 1.0
CG B:HIS222 4.2 34.8 1.0
ND1 B:HIS222 4.3 32.9 1.0
CG B:HIS226 4.3 36.1 1.0
ND1 B:HIS226 4.3 31.0 1.0
OE2 B:GLU223 4.4 40.2 1.0
C13 B:8OJ304 4.5 28.9 1.0
OE1 B:GLU223 4.6 38.7 1.0
CE B:MET240 4.8 35.3 1.0
CD B:GLU223 4.8 39.8 1.0
C12 B:8OJ304 4.9 25.8 1.0
C14 B:8OJ304 4.9 32.4 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: Wed Dec 16 11:07:07 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy