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Zinc in PDB 3rtt: Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide

Enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide:
3.4.24.65;

Protein crystallography data

The structure of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide, PDB code: 3rtt was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Mori, C.Nativi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.20 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.487, 60.431, 54.207, 90.00, 115.21, 90.00
R / Rfree (%) 23.4 / 31.7

Other elements in 3rtt:

The structure of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide (pdb code 3rtt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide, PDB code: 3rtt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3rtt

Go back to Zinc Binding Sites List in 3rtt
Zinc binding site 1 out of 2 in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:8.4
occ:1.00
 NE2 A:HIS222 2.0 5.1 1.0
NE2 A:HIS218 2.0 2.2 1.0
O4 A:KLH0 2.1 11.5 1.0
NE2 A:HIS228 2.2 2.0 1.0
O2 A:KLH0 2.3 5.9 1.0
CD2 A:HIS222 2.8 3.3 1.0
C13 A:KLH0 2.9 11.7 1.0
CD2 A:HIS218 3.0 2.0 1.0
N1 A:KLH0 3.0 13.2 1.0
CE1 A:HIS218 3.0 2.0 1.0
CE1 A:HIS222 3.0 4.9 1.0
CE1 A:HIS228 3.1 2.0 1.0
CD2 A:HIS228 3.2 3.6 1.0
CG A:HIS222 4.0 4.1 1.0
O A:HOH12 4.1 2.7 1.0
ND1 A:HIS222 4.1 2.3 1.0
CG A:HIS218 4.1 2.0 1.0
ND1 A:HIS218 4.1 4.2 1.0
OE1 A:GLU219 4.2 2.0 1.0
ND1 A:HIS228 4.2 2.3 1.0
CG A:HIS228 4.3 2.0 1.0
C8 A:KLH0 4.3 17.1 1.0
C1 A:KLH0 4.3 17.2 1.0
CE A:MET236 4.8 2.0 1.0
N2 A:KLH0 4.9 19.4 1.0
CD A:GLU219 4.9 2.0 1.0
OE2 A:GLU219 5.0 2.0 1.0
C3 A:KLH0 5.0 18.2 1.0

Zinc binding site 2 out of 2 in 3rtt

Go back to Zinc Binding Sites List in 3rtt
Zinc binding site 2 out of 2 in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:7.5
occ:1.00
 NE2 A:HIS183 1.9 2.0 1.0
NE2 A:HIS168 1.9 11.0 1.0
ND1 A:HIS196 2.2 4.5 1.0
CE1 A:HIS183 2.6 6.2 1.0
CD2 A:HIS168 2.7 8.5 1.0
OD1 A:ASP170 2.9 15.0 1.0
OD2 A:ASP170 3.0 15.0 1.0
CE1 A:HIS168 3.1 7.9 1.0
CD2 A:HIS183 3.1 2.9 1.0
CE1 A:HIS196 3.2 2.0 1.0
CG A:ASP170 3.2 15.0 1.0
CG A:HIS196 3.2 2.5 1.0
CB A:HIS196 3.5 3.3 1.0
ND1 A:HIS183 3.8 10.1 1.0
CG A:HIS168 3.9 6.7 1.0
ND1 A:HIS168 4.0 6.8 1.0
CG A:HIS183 4.1 2.7 1.0
NE2 A:HIS196 4.3 4.5 1.0
CD2 A:HIS196 4.3 3.4 1.0
O A:HIS172 4.4 10.3 1.0
CE2 A:PHE185 4.4 4.3 1.0
CB A:ASP170 4.5 15.0 1.0
CZ A:PHE185 4.6 4.8 1.0
CZ A:PHE174 4.6 2.0 1.0
CB A:HIS172 4.6 15.0 1.0
CE1 A:PHE174 4.9 2.1 1.0
C A:HIS172 5.0 15.0 1.0

Reference:

A.Mordini, M.Mori, A.Massaro, V.Calderone, M.Fragai, C.Luchinat. Contribution of Ligand Free Energy of Solvation to Design New Potent Mmps Inhibitors. J.Med.Chem. 2012.
ISSN: ISSN 0022-2623
Page generated: Wed Dec 16 04:48:00 2020

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