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Zinc in PDB 3ma2: Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)

Enzymatic activity of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)

All present enzymatic activity of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1):
3.4.24.80;

Protein crystallography data

The structure of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1), PDB code: 3ma2 was solved by M.Grossman, D.Tworowski, O.Dym, M.-H.Lee, Y.Levy, I.Sagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.690, 63.649, 87.158, 90.00, 105.86, 90.00
R / Rfree (%) 19.6 / 24.7

Other elements in 3ma2:

The structure of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) (pdb code 3ma2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1), PDB code: 3ma2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ma2

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Zinc binding site 1 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn294

b:16.5
occ:1.00
 NE2 D:HIS239 2.0 16.6 1.0
NE2 D:HIS243 2.1 13.8 1.0
NE2 D:HIS249 2.1 18.1 1.0
O C:CYS301 2.1 17.7 1.0
N C:CYS301 2.1 13.9 1.0
C C:CYS301 2.9 15.7 1.0
CE1 D:HIS239 2.9 17.8 1.0
CD2 D:HIS243 2.9 14.7 1.0
CD2 D:HIS249 3.0 12.5 1.0
CA C:CYS301 3.0 15.1 1.0
CD2 D:HIS239 3.0 17.7 1.0
CE1 D:HIS249 3.1 15.8 1.0
CE1 D:HIS243 3.2 13.8 1.0
CB C:CYS301 3.5 14.9 1.0
OE1 D:GLU240 4.0 18.9 1.0
ND1 D:HIS239 4.1 18.3 1.0
CG D:HIS249 4.1 15.3 1.0
N C:THR302 4.1 16.1 1.0
CG D:HIS243 4.2 17.8 1.0
ND1 D:HIS249 4.2 10.4 1.0
CG D:HIS239 4.2 16.7 1.0
OE2 D:GLU240 4.2 14.7 1.0
ND1 D:HIS243 4.2 14.9 1.0
CD D:GLU240 4.4 17.4 1.0
O C:SER368 4.7 14.7 1.0
CA C:SER368 4.7 17.1 1.0
CE D:MET257 4.8 11.5 1.0
CA C:THR302 4.9 17.7 1.0
OG1 C:THR302 4.9 18.0 1.0
O C:GLU367 5.0 17.7 1.0

Zinc binding site 2 out of 4 in 3ma2

Go back to Zinc Binding Sites List in 3ma2
Zinc binding site 2 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn295

b:16.7
occ:1.00
 NE2 D:HIS186 1.9 11.0 1.0
ND1 D:HIS214 2.0 13.0 1.0
OD2 D:ASP188 2.0 18.0 1.0
NE2 D:HIS201 2.1 18.1 1.0
CD2 D:HIS186 2.9 11.8 1.0
CE1 D:HIS214 2.9 18.4 1.0
CG D:ASP188 3.0 17.9 1.0
CE1 D:HIS201 3.0 17.2 1.0
CE1 D:HIS186 3.0 10.5 1.0
CD2 D:HIS201 3.1 14.3 1.0
CG D:HIS214 3.1 14.3 1.0
OD1 D:ASP188 3.2 15.6 1.0
CB D:HIS214 3.6 13.6 1.0
CG D:HIS186 4.0 15.9 1.0
ND1 D:HIS186 4.1 13.7 1.0
NE2 D:HIS214 4.1 14.4 1.0
ND1 D:HIS201 4.1 14.1 1.0
CD2 D:HIS214 4.2 13.7 1.0
CG D:HIS201 4.2 16.9 1.0
O D:THR190 4.3 18.5 1.0
CB D:ASP188 4.4 17.6 1.0
CE2 D:TYR203 4.5 19.2 1.0
CE2 D:PHE192 4.7 14.2 1.0
CZ D:PHE192 4.7 17.5 1.0
OH D:TYR203 4.9 20.8 1.0
CA D:HIS214 4.9 14.5 1.0

Zinc binding site 3 out of 4 in 3ma2

Go back to Zinc Binding Sites List in 3ma2
Zinc binding site 3 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn294

b:20.7
occ:1.00
 NE2 A:HIS243 2.0 15.7 1.0
NE2 A:HIS249 2.0 22.3 1.0
NE2 A:HIS239 2.0 21.9 1.0
N B:CYS301 2.0 17.2 1.0
O B:CYS301 2.1 23.2 1.0
CD2 A:HIS243 2.9 17.1 1.0
C B:CYS301 2.9 19.8 1.0
CD2 A:HIS249 2.9 16.7 1.0
CE1 A:HIS239 3.0 25.4 1.0
CE1 A:HIS243 3.0 18.8 1.0
CA B:CYS301 3.0 18.9 1.0
CE1 A:HIS249 3.0 20.1 1.0
CD2 A:HIS239 3.1 22.9 1.0
CB B:CYS301 3.5 19.8 1.0
CG A:HIS243 4.1 22.9 1.0
ND1 A:HIS243 4.1 18.5 1.0
CG A:HIS249 4.1 21.9 1.0
ND1 A:HIS249 4.1 24.1 1.0
ND1 A:HIS239 4.1 24.1 1.0
N B:THR302 4.2 20.4 1.0
OE1 A:GLU240 4.2 20.3 1.0
OE2 A:GLU240 4.2 16.2 1.0
CG A:HIS239 4.2 22.0 1.0
CD A:GLU240 4.5 18.5 1.0
O B:SER368 4.6 18.7 1.0
CA B:SER368 4.7 17.7 1.0
CA B:THR302 4.9 19.8 1.0
O B:GLU367 5.0 15.4 1.0

Zinc binding site 4 out of 4 in 3ma2

Go back to Zinc Binding Sites List in 3ma2
Zinc binding site 4 out of 4 in the Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Membrane Type-1 Matrix Metalloproteinase (MT1-Mmp) with Tissue Inhibitor of Metalloproteinase-1 (Timp-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn295

b:19.8
occ:1.00
 OD2 A:ASP188 1.9 19.7 1.0
NE2 A:HIS186 1.9 11.3 1.0
NE2 A:HIS201 2.1 21.2 1.0
ND1 A:HIS214 2.1 14.2 1.0
CE1 A:HIS186 2.9 18.4 1.0
CG A:ASP188 2.9 18.5 1.0
CD2 A:HIS186 3.0 16.6 1.0
CE1 A:HIS214 3.0 19.1 1.0
CE1 A:HIS201 3.0 22.6 1.0
CG A:HIS214 3.1 13.8 1.0
CD2 A:HIS201 3.1 17.9 1.0
OD1 A:ASP188 3.2 18.6 1.0
CB A:HIS214 3.4 15.8 1.0
ND1 A:HIS186 4.0 15.2 1.0
CG A:HIS186 4.1 16.6 1.0
NE2 A:HIS214 4.1 21.8 1.0
ND1 A:HIS201 4.2 18.9 1.0
CD2 A:HIS214 4.2 13.0 1.0
CG A:HIS201 4.2 23.4 1.0
CB A:ASP188 4.2 17.2 1.0
O A:THR190 4.4 22.1 1.0
CE2 A:TYR203 4.5 22.0 1.0
CE2 A:PHE192 4.5 19.6 1.0
CZ A:PHE192 4.6 19.1 1.0
OH A:TYR203 4.8 17.8 1.0
CA A:HIS214 4.9 14.9 1.0

Reference:

M.Grossman, D.Tworowski, O.Dym, M.H.Lee, Y.Levy, G.Murphy, I.Sagi. The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor Timp-1 Controls Its Binding Interface and Affects Its Function. Biochemistry V. 49 6184 2010.
ISSN: ISSN 0006-2960
PubMed: 20545310
DOI: 10.1021/BI902141X
Page generated: Sat Oct 26 09:21:10 2024

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