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Zinc in PDB 3f16: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide, PDB code: 3f16 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.22 / 1.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.882, 60.366, 53.953, 90.00, 114.37, 90.00
R / Rfree (%) 16.1 / 18.2

Other elements in 3f16:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide 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)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide (pdb code 3f16). 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)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide, PDB code: 3f16:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3f16

Go back to Zinc Binding Sites List in 3f16
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide


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)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:4.0
occ:1.00
 O3 A:HS30 1.9 9.8 1.0
NE2 A:HIS218 2.1 3.6 1.0
NE2 A:HIS228 2.1 3.9 1.0
O6 A:HS30 2.1 5.6 1.0
NE2 A:HIS222 2.1 3.6 1.0
C8 A:HS30 2.7 9.8 1.0
N1 A:HS30 2.8 7.8 1.0
CD2 A:HIS218 3.0 3.6 1.0
O A:HOH74 3.1 10.7 1.0
CE1 A:HIS228 3.1 3.8 1.0
CE1 A:HIS222 3.1 3.5 1.0
CE1 A:HIS218 3.1 5.0 1.0
CD2 A:HIS228 3.1 4.1 1.0
CD2 A:HIS222 3.1 3.2 1.0
O A:HOH17 4.1 5.8 1.0
OE1 A:GLU219 4.1 4.7 1.0
ND1 A:HIS218 4.2 4.9 1.0
ND1 A:HIS228 4.2 4.3 1.0
CG A:HIS218 4.2 3.5 1.0
ND1 A:HIS222 4.2 3.7 1.0
C9 A:HS30 4.2 12.1 1.0
CG A:HIS228 4.2 4.6 1.0
CG A:HIS222 4.3 3.3 1.0
O A:HOH64 4.5 10.2 1.0
O4 A:HS30 4.6 14.9 1.0
OE2 A:GLU219 4.8 4.5 1.0
C1 A:HS30 4.8 8.8 1.0
CD A:GLU219 4.8 3.9 1.0
C7 A:HS30 4.9 13.9 1.0
CE A:MET236 5.0 5.0 1.0

Zinc binding site 2 out of 2 in 3f16

Go back to Zinc Binding Sites List in 3f16
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide


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)-N-(3-Hydroxy-1-Nitroso-1-Oxopropan-2-Yl)-4- Methoxybenzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:6.1
occ:1.00
 OD1 A:ASP170 2.0 5.4 0.7
NE2 A:HIS168 2.0 5.3 1.0
NE2 A:HIS183 2.1 5.8 1.0
ND1 A:HIS196 2.1 5.1 1.0
CD2 A:HIS168 2.9 6.0 1.0
CG A:ASP170 3.0 7.3 0.7
CE1 A:HIS196 3.0 6.1 1.0
CE1 A:HIS183 3.0 6.6 1.0
CE1 A:HIS168 3.1 5.2 1.0
CD2 A:HIS183 3.1 5.7 1.0
CG A:HIS196 3.1 4.3 1.0
OD2 A:ASP170 3.2 5.4 0.7
CB A:HIS196 3.5 4.2 1.0
CG A:HIS168 4.1 6.6 1.0
ND1 A:HIS168 4.1 5.5 1.0
NE2 A:HIS196 4.1 5.5 1.0
ND1 A:HIS183 4.1 6.5 1.0
O A:HIS172 4.2 7.7 1.0
CD2 A:HIS196 4.2 4.7 1.0
CG A:HIS183 4.2 5.2 1.0
CE2 A:PHE185 4.3 11.5 1.0
CB A:ASP170 4.4 9.5 0.7
CZ A:PHE185 4.5 11.2 1.0
CZ A:PHE174 4.6 5.7 1.0
CE1 A:PHE174 4.7 5.5 1.0
CB A:HIS172 4.7 9.5 1.0
O A:HOH29 5.0 8.2 1.0
CA A:HIS196 5.0 3.5 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, A.Giachetti, M.Loconte, C.Luchinat, M.Maletta, C.Nativi, K.J.Yeo. Exploring the Subtleties of Drug-Receptor Interactions: the Case of Matrix Metalloproteinases. J.Am.Chem.Soc. V. 129 2466 2007.
ISSN: ISSN 0002-7863
PubMed: 17269766
DOI: 10.1021/JA065156Z
Page generated: Thu Oct 24 13:01:32 2024

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