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Zinc in PDB 3f17: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide:
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) Biphenyl-4-Sulfonamide, PDB code: 3f17 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.59 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.636, 60.250, 54.220, 90.00, 115.44, 90.00
R / Rfree (%) 17 / 18.1

Other elements in 3f17:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide 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) Biphenyl-4-Sulfonamide (pdb code 3f17). 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) Biphenyl-4-Sulfonamide, PDB code: 3f17:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3f17

Go back to Zinc Binding Sites List in 3f17
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) Biphenyl-4-Sulfonamide


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) Biphenyl-4-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:7.5
occ:1.00
 NE2 A:HIS218 2.1 7.5 1.0
O1 A:HS40 2.1 10.6 1.0
NE2 A:HIS228 2.1 6.9 1.0
NE2 A:HIS222 2.1 6.9 1.0
O2 A:HS40 2.2 8.9 1.0
C14 A:HS40 2.8 10.9 1.0
N2 A:HS40 2.9 9.6 1.0
CD2 A:HIS218 3.0 7.5 1.0
CE1 A:HIS228 3.1 7.6 1.0
CE1 A:HIS218 3.1 7.6 1.0
CE1 A:HIS222 3.1 7.0 1.0
CD2 A:HIS228 3.1 7.6 1.0
CD2 A:HIS222 3.1 6.2 1.0
O A:HOH8 4.1 8.8 1.0
ND1 A:HIS218 4.2 6.9 1.0
CG A:HIS218 4.2 6.8 1.0
ND1 A:HIS228 4.2 7.9 1.0
ND1 A:HIS222 4.2 7.5 1.0
CG A:HIS228 4.2 7.7 1.0
CG A:HIS222 4.3 6.0 1.0
OE1 A:GLU219 4.3 9.8 1.0
C12 A:HS40 4.3 11.7 1.0
O A:HOH414 4.6 35.0 1.0
C11 A:HS40 4.8 12.4 1.0
O A:HOH96 4.8 18.5 1.0
N1 A:HS40 4.9 13.3 1.0
CE A:MET236 4.9 7.9 1.0
C8 A:HS40 4.9 12.2 1.0
CB A:PRO238 5.0 14.4 1.0
O A:HOH63 5.0 14.3 1.0

Zinc binding site 2 out of 2 in 3f17

Go back to Zinc Binding Sites List in 3f17
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) Biphenyl-4-Sulfonamide


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) Biphenyl-4-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:10.3
occ:1.00
 OD1 A:ASP170 2.0 9.2 0.7
NE2 A:HIS183 2.0 10.6 1.0
NE2 A:HIS168 2.0 9.9 1.0
ND1 A:HIS196 2.1 8.5 1.0
CE1 A:HIS183 2.8 12.7 1.0
CG A:ASP170 2.9 12.7 0.7
CD2 A:HIS168 3.0 10.1 1.0
CE1 A:HIS196 3.0 9.2 1.0
CE1 A:HIS168 3.0 10.1 1.0
CD2 A:HIS183 3.1 11.0 1.0
CG A:HIS196 3.1 7.5 1.0
OD2 A:ASP170 3.2 11.1 0.7
CB A:HIS196 3.5 6.9 1.0
O A:HIS172 3.9 15.1 1.0
ND1 A:HIS183 4.0 12.2 1.0
CG A:HIS168 4.1 11.4 1.0
ND1 A:HIS168 4.1 10.9 1.0
NE2 A:HIS196 4.1 8.2 1.0
CG A:HIS183 4.2 9.1 1.0
CD2 A:HIS196 4.2 7.7 1.0
CB A:ASP170 4.3 15.2 0.7
CE2 A:PHE185 4.4 12.6 1.0
CZ A:PHE174 4.6 9.8 1.0
CZ A:PHE185 4.6 12.4 1.0
CE1 A:PHE174 4.7 9.7 1.0
CB A:HIS172 4.9 17.6 1.0
O A:HOH30 5.0 13.6 1.0
CA A:HIS196 5.0 6.3 1.0
C A:HIS172 5.0 15.3 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 13:01:53 2024

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