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Zinc in PDB 3n2v: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide, PDB code: 3n2v was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.44 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.614, 60.277, 54.186, 90.00, 115.20, 90.00
R / Rfree (%) 13.2 / 18

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide (pdb code 3n2v). 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 N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide, PDB code: 3n2v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3n2v

Go back to Zinc Binding Sites List in 3n2v
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide


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 N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:9.4
occ:1.00
O5 A:JT50 2.0 19.2 1.0
NE2 A:HIS218 2.0 7.8 1.0
NE2 A:HIS228 2.1 9.1 1.0
NE2 A:HIS222 2.1 8.9 1.0
O1 A:JT50 2.3 12.7 1.0
C3 A:JT50 2.9 20.0 1.0
CD2 A:HIS218 3.0 4.9 1.0
CD2 A:HIS228 3.0 10.0 1.0
CE1 A:HIS218 3.0 7.6 1.0
N2 A:JT50 3.0 17.3 1.0
CD2 A:HIS222 3.0 6.2 1.0
CE1 A:HIS228 3.1 11.3 1.0
CE1 A:HIS222 3.1 5.6 1.0
ND1 A:HIS218 4.1 6.8 1.0
O A:HOH5 4.1 12.4 1.0
CG A:HIS218 4.1 5.5 1.0
ND1 A:HIS228 4.1 8.8 1.0
CG A:HIS228 4.2 10.7 1.0
CG A:HIS222 4.2 4.8 1.0
ND1 A:HIS222 4.2 7.2 1.0
C4 A:JT50 4.4 23.4 1.0
OE1 A:GLU219 4.5 8.8 1.0
C18 A:JT50 4.7 15.3 1.0
O A:HOH53 4.7 19.2 1.0
CE A:MET236 4.8 9.9 1.0
N6 A:JT50 4.8 23.4 1.0
C8 A:JT50 4.8 27.2 1.0
OE2 A:GLU219 4.9 10.2 1.0
C17 A:JT50 4.9 16.1 1.0
C12 A:JT50 4.9 19.4 1.0

Zinc binding site 2 out of 2 in 3n2v

Go back to Zinc Binding Sites List in 3n2v
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide


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 N-Hydroxy-2-(N-Hydroxyethyl)Biphenyl-4- Ylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:10.8
occ:1.00
OD1 A:ASP170 1.9 8.7 0.7
NE2 A:HIS183 2.0 16.8 1.0
NE2 A:HIS168 2.0 9.5 1.0
ND1 A:HIS196 2.1 9.4 1.0
CE1 A:HIS183 2.6 15.8 1.0
CG A:ASP170 2.9 11.8 0.7
CD2 A:HIS168 2.9 9.2 1.0
CE1 A:HIS196 3.1 7.3 1.0
CE1 A:HIS168 3.1 9.9 1.0
CG A:HIS196 3.1 7.0 1.0
OD2 A:ASP170 3.2 12.0 0.7
CD2 A:HIS183 3.3 17.4 1.0
CB A:HIS196 3.5 6.7 1.0
ND1 A:HIS183 3.8 16.7 1.0
CG A:HIS168 4.1 10.3 1.0
ND1 A:HIS168 4.1 10.8 1.0
O A:HIS172 4.2 17.2 1.0
CG A:HIS183 4.2 11.2 1.0
NE2 A:HIS196 4.2 8.2 1.0
CD2 A:HIS196 4.3 5.9 1.0
CB A:ASP170 4.3 14.2 0.7
CB A:HIS172 4.4 19.1 1.0
CE2 A:PHE185 4.5 15.7 1.0
CZ A:PHE174 4.6 8.4 1.0
CZ A:PHE185 4.6 16.9 1.0
CE1 A:PHE174 4.7 8.0 1.0
O A:HOH38 4.9 14.3 1.0
C A:HIS172 4.9 16.8 1.0
CA A:HIS196 5.0 5.1 1.0

Reference:

E.Attolino, V.Calderone, E.Dragoni, M.Fragai, B.Richichi, C.Luchinat, C.Nativi. Structure-Based Approach to Nanomolar, Water Soluble Matrix Metalloproteinases Inhibitors (Mmpis). Eur.J.Med.Chem. V. 45 5919 2010.
ISSN: ISSN 0223-5234
PubMed: 20965620
DOI: 10.1016/J.EJMECH.2010.09.057
Page generated: Sat Sep 26 11:54:19 2020
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