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Zinc in PDB 3n2u: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) 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-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide, PDB code: 3n2u was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.22 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.394, 60.446, 54.043, 90.00, 114.67, 90.00
R / Rfree (%) 16.1 / 21.9

Other elements in 3n2u:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide 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 N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide (pdb code 3n2u). 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-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide, PDB code: 3n2u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3n2u

Go back to Zinc Binding Sites List in 3n2u
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-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) 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-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:9.0
occ:1.00
NE2 A:HIS218 2.0 5.8 1.0
O1 A:D3X0 2.0 8.8 1.0
NE2 A:HIS222 2.1 4.7 1.0
NE2 A:HIS228 2.1 7.8 1.0
O11 A:D3X0 2.3 4.7 1.0
C3 A:D3X0 2.9 10.5 1.0
CD2 A:HIS218 2.9 4.3 1.0
N1 A:D3X0 3.0 8.1 1.0
CD2 A:HIS222 3.0 4.2 1.0
CE1 A:HIS228 3.1 8.6 1.0
CE1 A:HIS218 3.1 5.6 1.0
CD2 A:HIS228 3.1 7.8 1.0
CE1 A:HIS222 3.1 6.1 1.0
O A:HOH5 4.1 5.5 1.0
CG A:HIS218 4.1 4.7 1.0
ND1 A:HIS218 4.1 6.6 1.0
ND1 A:HIS228 4.2 6.8 1.0
CG A:HIS222 4.2 5.6 1.0
ND1 A:HIS222 4.2 5.9 1.0
OE1 A:GLU219 4.2 5.7 1.0
CG A:HIS228 4.2 6.7 1.0
C10 A:D3X0 4.3 12.4 1.0
O10 A:D3X0 4.5 22.9 1.0
C14 A:D3X0 4.7 9.8 1.0
N2 A:D3X0 4.7 13.4 1.0
O A:HOH103 4.8 22.4 1.0
CE A:MET236 4.9 5.7 1.0
O A:HOH321 4.9 16.5 1.0
C11 A:D3X0 4.9 8.7 1.0

Zinc binding site 2 out of 2 in 3n2u

Go back to Zinc Binding Sites List in 3n2u
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-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) 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-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:9.2
occ:1.00
NE2 A:HIS183 2.0 7.1 1.0
NE2 A:HIS168 2.0 8.0 1.0
OD1 A:ASP170 2.0 10.2 1.0
ND1 A:HIS196 2.0 5.4 1.0
CE1 A:HIS183 2.7 9.3 1.0
CD2 A:HIS168 2.9 8.6 1.0
CG A:ASP170 3.0 13.1 1.0
CE1 A:HIS196 3.0 3.5 1.0
CE1 A:HIS168 3.1 9.0 1.0
CG A:HIS196 3.1 5.1 1.0
CD2 A:HIS183 3.1 8.8 1.0
OD2 A:ASP170 3.2 11.3 1.0
CB A:HIS196 3.4 5.2 1.0
ND1 A:HIS183 3.9 9.0 1.0
CG A:HIS168 4.1 10.1 1.0
ND1 A:HIS168 4.1 9.0 1.0
NE2 A:HIS196 4.1 4.2 1.0
CG A:HIS183 4.1 6.1 1.0
CD2 A:HIS196 4.2 6.6 1.0
CB A:ASP170 4.4 14.4 1.0
CB A:HIS172 4.4 14.4 1.0
O A:HIS172 4.4 12.2 1.0
CE2 A:PHE185 4.5 10.6 1.0
CZ A:PHE174 4.7 7.4 1.0
CZ A:PHE185 4.7 10.0 1.0
CE1 A:PHE174 4.8 8.2 1.0
CA A:HIS196 5.0 5.3 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: Wed Dec 16 04:36:37 2020

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