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Zinc in PDB 2oxu: Uninhibited Form of Human Mmp-12

Enzymatic activity of Uninhibited Form of Human Mmp-12

All present enzymatic activity of Uninhibited Form of Human Mmp-12:
3.4.24.65;

Protein crystallography data

The structure of Uninhibited Form of Human Mmp-12, PDB code: 2oxu was solved by V.Calderone, I.Bertini, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.64 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.545, 60.751, 54.264, 90.00, 115.64, 90.00
R / Rfree (%) 19.7 / 21.6

Other elements in 2oxu:

The structure of Uninhibited Form of Human Mmp-12 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Uninhibited Form of Human Mmp-12 (pdb code 2oxu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Uninhibited Form of Human Mmp-12, PDB code: 2oxu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2oxu

Go back to Zinc Binding Sites List in 2oxu
Zinc binding site 1 out of 2 in the Uninhibited Form of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Uninhibited Form of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:6.7
occ:1.00
NE2 A:HIS228 2.1 6.0 1.0
O A:HOH487 2.1 14.2 1.0
NE2 A:HIS222 2.1 5.3 1.0
NE2 A:HIS218 2.1 4.8 1.0
O A:HOH339 2.4 12.8 1.0
O A:HOH316 2.4 11.3 1.0
CE1 A:HIS228 3.0 7.1 1.0
CD2 A:HIS222 3.1 4.8 1.0
CE1 A:HIS218 3.1 6.1 1.0
CD2 A:HIS228 3.1 7.0 1.0
CE1 A:HIS222 3.1 5.0 1.0
CD2 A:HIS218 3.1 5.8 1.0
ND1 A:HIS228 4.2 8.2 1.0
ND1 A:HIS218 4.2 6.1 1.0
ND1 A:HIS222 4.2 6.0 1.0
CG A:HIS228 4.2 7.6 1.0
CG A:HIS222 4.2 5.0 1.0
O A:HOH384 4.3 13.6 1.0
CG A:HIS218 4.3 5.5 1.0
O A:HOH277 4.4 8.0 1.0
OE2 A:GLU219 4.5 9.6 1.0
O A:HOH347 4.5 28.8 1.0
O A:HOH393 4.5 21.9 1.0
O A:HOH435 4.6 18.9 1.0
O A:HOH269 4.6 9.0 1.0
O A:PRO238 4.8 15.1 1.0
OE1 A:GLU219 4.9 11.5 1.0
CE A:MET236 4.9 6.5 1.0

Zinc binding site 2 out of 2 in 2oxu

Go back to Zinc Binding Sites List in 2oxu
Zinc binding site 2 out of 2 in the Uninhibited Form of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Uninhibited Form of Human Mmp-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:6.0
occ:1.00
NE2 A:HIS168 2.0 6.3 1.0
OD1 A:ASP170 2.0 4.7 0.7
NE2 A:HIS183 2.0 6.0 1.0
ND1 A:HIS196 2.1 6.3 1.0
CE1 A:HIS183 2.9 7.1 1.0
CG A:ASP170 2.9 5.1 0.7
CD2 A:HIS168 2.9 7.1 1.0
CE1 A:HIS196 3.0 5.9 1.0
CE1 A:HIS168 3.0 5.5 1.0
CG A:HIS196 3.1 4.9 1.0
CD2 A:HIS183 3.1 6.3 1.0
OD2 A:ASP170 3.2 5.1 0.7
CB A:HIS196 3.5 4.6 1.0
ND1 A:HIS183 4.0 6.6 1.0
CG A:HIS168 4.1 7.3 1.0
ND1 A:HIS168 4.1 6.9 1.0
NE2 A:HIS196 4.1 5.8 1.0
CG A:HIS183 4.2 6.2 1.0
CD2 A:HIS196 4.2 5.4 1.0
O A:HIS172 4.3 9.4 1.0
CB A:ASP170 4.3 7.7 0.7
CB A:HIS172 4.3 10.2 1.0
CE2 A:PHE185 4.7 9.5 1.0
CZ A:PHE174 4.7 6.0 1.0
CE1 A:PHE174 4.8 5.7 1.0
CZ A:PHE185 4.8 9.7 1.0
C A:HIS172 4.9 9.4 1.0
CA A:HIS196 5.0 4.2 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo. Snapshots of the Reaction Mechanism of Matrix Metalloproteinases. Angew.Chem.Int.Ed.Engl. V. 45 7952 2006.
ISSN: ESSN 0570-0833
PubMed: 17096442
DOI: 10.1002/ANIE.200603100
Page generated: Wed Dec 16 03:47:22 2020

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