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Zinc in PDB 3ehx: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid, PDB code: 3ehx was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.27 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.181, 60.554, 54.428, 90.00, 115.90, 90.00
R / Rfree (%) 16.3 / 20.1

Other elements in 3ehx:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid (pdb code 3ehx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid, PDB code: 3ehx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ehx

Go back to Zinc Binding Sites List in 3ehx
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid


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 Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:8.1
occ:1.00
NE2 A:HIS228 1.9 6.8 1.0
O3 A:BDL0 2.0 11.5 1.0
NE2 A:HIS222 2.0 3.6 1.0
NE2 A:HIS218 2.1 2.3 1.0
O4 A:BDL0 2.7 10.1 1.0
C15 A:BDL0 2.7 13.0 1.0
CE1 A:HIS228 2.9 8.9 1.0
CD2 A:HIS228 3.0 7.1 1.0
CD2 A:HIS222 3.0 2.0 1.0
CD2 A:HIS218 3.0 3.2 1.0
CE1 A:HIS222 3.1 2.5 1.0
CE1 A:HIS218 3.1 2.0 1.0
ND1 A:HIS228 4.0 6.5 1.0
CG A:HIS228 4.1 5.0 1.0
ND1 A:HIS222 4.1 4.7 1.0
CG A:HIS222 4.2 4.0 1.0
C17 A:BDL0 4.2 16.2 1.0
ND1 A:HIS218 4.2 2.5 1.0
CG A:HIS218 4.2 2.5 1.0
O A:HOH342 4.3 10.1 1.0
O A:HOH299 4.6 5.9 1.0
C6 A:BDL0 4.6 11.4 1.0
C16 A:BDL0 4.7 19.2 1.0
CE A:MET236 4.7 2.1 1.0
C4 A:BDL0 4.7 10.8 1.0
OE1 A:GLU219 4.8 2.5 1.0
N1 A:BDL0 4.9 17.1 1.0
C7 A:BDL0 4.9 11.8 1.0

Zinc binding site 2 out of 2 in 3ehx

Go back to Zinc Binding Sites List in 3ehx
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid


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 Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:8.7
occ:1.00
OD1 A:ASP170 1.9 3.9 0.7
NE2 A:HIS183 2.0 12.8 1.0
NE2 A:HIS168 2.0 7.2 1.0
ND1 A:HIS196 2.1 3.5 1.0
CE1 A:HIS183 2.5 12.4 1.0
CD2 A:HIS168 2.8 6.9 1.0
CG A:ASP170 2.8 7.4 0.7
CE1 A:HIS196 3.0 2.5 1.0
OD2 A:ASP170 3.0 2.8 0.7
CG A:HIS196 3.1 3.8 1.0
CE1 A:HIS168 3.2 8.8 1.0
CD2 A:HIS183 3.3 10.8 1.0
CB A:HIS196 3.5 3.9 1.0
ND1 A:HIS183 3.8 12.0 1.0
CG A:HIS168 4.0 8.9 1.0
NE2 A:HIS196 4.1 2.0 1.0
CG A:HIS183 4.1 5.8 1.0
ND1 A:HIS168 4.1 9.5 1.0
O A:HIS172 4.2 13.5 1.0
CD2 A:HIS196 4.2 3.3 1.0
CB A:ASP170 4.2 10.7 0.7
CB A:HIS172 4.5 15.4 1.0
CE2 A:PHE185 4.6 10.9 1.0
O A:HOH408 4.7 30.6 1.0
CZ A:PHE185 4.7 12.7 1.0
CZ A:PHE174 4.7 2.3 1.0
CE1 A:PHE174 4.8 2.7 1.0
C A:HIS172 4.9 13.2 1.0

Reference:

E.Dragoni, V.Calderone, M.Fragai, R.Jaiswal, C.Luchinat, C.Nativi. Biotin-Tagged Probes For Mmp Expression and Activation: Design, Synthesis, and Binding Properties Bioconjug.Chem. V. 20 719 2009.
ISSN: ISSN 1043-1802
PubMed: 19275207
DOI: 10.1021/BC8003827
Page generated: Wed Dec 16 04:16:14 2020

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