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Zinc in PDB 3f1a: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide, PDB code: 3f1a was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.69 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.834, 60.282, 54.178, 90.00, 115.17, 90.00
R / Rfree (%) 16.7 / 18.9

Other elements in 3f1a:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide 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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide (pdb code 3f1a). 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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide, PDB code: 3f1a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3f1a

Go back to Zinc Binding Sites List in 3f1a
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide


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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:6.9
occ:1.00
 O3 A:HS70 2.0 9.7 1.0
NE2 A:HIS218 2.1 6.0 1.0
NE2 A:HIS228 2.1 7.3 1.0
NE2 A:HIS222 2.2 5.8 1.0
O4 A:HS70 2.2 8.0 1.0
C7 A:HS70 2.8 10.8 1.0
N2 A:HS70 2.9 9.7 1.0
O A:HOH360 2.9 21.9 1.0
CD2 A:HIS218 3.0 5.9 1.0
CE1 A:HIS228 3.0 7.2 1.0
CD2 A:HIS228 3.1 6.9 1.0
CE1 A:HIS218 3.1 7.2 1.0
CD2 A:HIS222 3.1 5.6 1.0
CE1 A:HIS222 3.2 6.1 1.0
O A:HOH18 4.1 8.8 1.0
ND1 A:HIS228 4.2 7.8 1.0
CG A:HIS218 4.2 5.7 1.0
ND1 A:HIS218 4.2 7.3 1.0
CG A:HIS228 4.2 7.6 1.0
OE1 A:GLU219 4.2 8.1 1.0
C8 A:HS70 4.3 13.1 1.0
ND1 A:HIS222 4.3 6.2 1.0
CG A:HIS222 4.3 5.9 1.0
O A:HOH309 4.7 38.5 1.0
O A:HOH103 4.7 17.3 1.0
N1 A:HS70 4.8 13.7 1.0
C1 A:HS70 4.9 13.1 1.0
CE A:MET236 4.9 7.8 1.0
C3 A:HS70 4.9 13.0 1.0
O A:HOH298 5.0 27.1 1.0
C2 A:HS70 5.0 13.3 1.0
CD A:GLU219 5.0 7.2 1.0

Zinc binding site 2 out of 2 in 3f1a

Go back to Zinc Binding Sites List in 3f1a
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide


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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:8.9
occ:1.00
 OD1 A:ASP170 1.9 9.5 0.7
NE2 A:HIS183 1.9 14.0 1.0
NE2 A:HIS168 2.0 9.1 1.0
ND1 A:HIS196 2.1 8.0 1.0
CE1 A:HIS183 2.7 15.4 1.0
CG A:ASP170 2.9 11.9 0.7
CD2 A:HIS168 2.9 9.8 1.0
CE1 A:HIS196 3.0 8.9 1.0
CE1 A:HIS168 3.1 9.2 1.0
CD2 A:HIS183 3.1 16.1 1.0
CG A:HIS196 3.1 7.0 1.0
OD2 A:ASP170 3.2 10.1 0.7
CB A:HIS196 3.5 6.7 1.0
ND1 A:HIS183 3.9 15.5 1.0
CG A:HIS183 4.1 12.2 1.0
CG A:HIS168 4.1 10.7 1.0
ND1 A:HIS168 4.1 9.6 1.0
NE2 A:HIS196 4.1 7.9 1.0
CB A:ASP170 4.2 14.1 0.7
O A:HIS172 4.2 13.9 1.0
CD2 A:HIS196 4.2 7.2 1.0
CE2 A:PHE185 4.5 14.2 1.0
CB A:HIS172 4.5 15.4 1.0
CZ A:PHE174 4.6 8.7 1.0
CZ A:PHE185 4.6 14.2 1.0
CE1 A:PHE174 4.7 9.0 1.0
C A:HIS172 5.0 13.8 1.0
O A:HOH28 5.0 11.9 1.0
CA A:HIS196 5.0 6.2 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 13:02:34 2024

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