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Zinc in PDB 1d8f: Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.

All present enzymatic activity of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.:
3.4.24.17;

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor., PDB code: 1d8f was solved by M.Y.Cheng, B.De, S.Pikul, N.G.Almstead, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, L.Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.270, 78.540, 106.580, 90.00, 90.00, 90.00
R / Rfree (%) 29.4 / 25.2

Other elements in 1d8f:

The structure of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor. also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor. (pdb code 1d8f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor., PDB code: 1d8f:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1d8f

Go back to Zinc Binding Sites List in 1d8f
Zinc binding site 1 out of 4 in the Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.


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 MMP3 Complexed with A Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.9
occ:1.00
NE2 A:HIS205 2.4 11.5 1.0
NE2 A:HIS201 2.4 2.0 1.0
NE2 A:HIS211 2.4 2.7 1.0
CD2 A:HIS201 3.1 3.8 1.0
CD2 A:HIS211 3.1 5.9 1.0
CD2 A:HIS205 3.2 2.6 1.0
CE1 A:HIS205 3.4 3.0 1.0
CE1 A:HIS201 3.5 3.4 1.0
CE1 A:HIS211 3.6 2.0 1.0
CG A:HIS201 4.3 2.0 1.0
CG A:HIS211 4.4 5.9 1.0
CG A:HIS205 4.4 2.0 1.0
ND1 A:HIS205 4.5 2.0 1.0
ND1 A:HIS201 4.5 2.0 1.0
ND1 A:HIS211 4.5 4.2 1.0
OE2 A:GLU202 4.6 2.4 1.0
OE1 A:GLU202 4.6 9.2 1.0
CD A:GLU202 5.0 2.0 1.0

Zinc binding site 2 out of 4 in 1d8f

Go back to Zinc Binding Sites List in 1d8f
Zinc binding site 2 out of 4 in the Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.


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 MMP3 Complexed with A Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.8
occ:1.00
OD2 A:ASP153 2.0 2.0 1.0
ND1 A:HIS179 2.2 6.1 1.0
NE2 A:HIS151 2.3 8.7 1.0
NE2 A:HIS166 2.6 2.0 1.0
CG A:ASP153 2.9 3.3 1.0
CG A:HIS179 3.0 2.1 1.0
CD2 A:HIS151 3.0 10.8 1.0
CE1 A:HIS179 3.1 3.7 1.0
OD1 A:ASP153 3.2 2.3 1.0
CB A:HIS179 3.3 9.5 1.0
CE1 A:HIS151 3.4 10.1 1.0
CD2 A:HIS166 3.4 2.0 1.0
CE1 A:HIS166 3.6 2.0 1.0
CD2 A:HIS179 4.0 3.5 1.0
NE2 A:HIS179 4.1 2.0 1.0
OH A:TYR168 4.1 8.2 1.0
O A:TYR155 4.2 9.9 1.0
CG A:HIS151 4.2 21.1 1.0
CB A:ASP153 4.4 8.6 1.0
ND1 A:HIS151 4.4 14.5 1.0
CE1 A:TYR168 4.5 7.8 1.0
CG A:HIS166 4.6 2.0 1.0
ND1 A:HIS166 4.7 5.5 1.0
CZ A:TYR168 4.8 7.8 1.0
CA A:HIS179 4.9 5.8 1.0
CE1 A:PHE157 4.9 2.0 1.0
CZ A:PHE157 5.0 3.9 1.0

Zinc binding site 3 out of 4 in 1d8f

Go back to Zinc Binding Sites List in 1d8f
Zinc binding site 3 out of 4 in the Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.4
occ:1.00
OA B:SPI901 1.8 14.2 1.0
NE2 B:HIS701 2.3 2.0 1.0
OB B:SPI901 2.3 19.5 1.0
NE2 B:HIS705 2.4 2.0 1.0
NE2 B:HIS711 2.7 2.0 1.0
CD2 B:HIS701 2.8 2.0 1.0
NA B:SPI901 2.9 10.6 1.0
C20 B:SPI901 3.0 15.9 1.0
CD2 B:HIS711 3.2 2.0 1.0
CD2 B:HIS705 3.3 2.0 1.0
CE1 B:HIS705 3.3 2.7 1.0
CE1 B:HIS701 3.5 2.0 1.0
CE1 B:HIS711 3.9 2.0 1.0
CG B:HIS701 4.1 2.0 1.0
OE2 B:GLU702 4.2 2.7 1.0
ND1 B:HIS701 4.4 2.0 1.0
ND1 B:HIS705 4.4 2.0 1.0
CG B:HIS705 4.5 2.0 1.0
C8 B:SPI901 4.5 13.5 1.0
CG B:HIS711 4.5 2.0 1.0
C6 B:SPI901 4.7 7.4 1.0
ND1 B:HIS711 4.8 6.0 1.0
OE1 B:GLU702 4.9 2.0 1.0
CD B:GLU702 4.9 2.8 1.0
C1 B:SPI901 4.9 8.1 1.0
C5 B:SPI901 5.0 4.9 1.0

Zinc binding site 4 out of 4 in 1d8f

Go back to Zinc Binding Sites List in 1d8f
Zinc binding site 4 out of 4 in the Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:9.6
occ:1.00
OD2 B:ASP653 1.9 2.0 1.0
ND1 B:HIS679 2.2 4.3 1.0
NE2 B:HIS651 2.2 2.0 1.0
NE2 B:HIS666 2.4 2.0 1.0
CG B:ASP653 2.9 5.4 1.0
CE1 B:HIS679 3.1 2.0 1.0
CD2 B:HIS651 3.2 2.1 1.0
OD1 B:ASP653 3.2 10.3 1.0
CG B:HIS679 3.2 2.5 1.0
CE1 B:HIS651 3.2 7.3 1.0
CD2 B:HIS666 3.3 2.5 1.0
CE1 B:HIS666 3.4 2.0 1.0
CB B:HIS679 3.5 5.3 1.0
OH B:TYR668 3.9 12.9 1.0
O B:TYR655 4.0 2.3 1.0
CB B:ASP653 4.2 2.0 1.0
NE2 B:HIS679 4.3 2.0 1.0
ND1 B:HIS651 4.3 6.1 1.0
CG B:HIS651 4.3 3.2 1.0
CD2 B:HIS679 4.3 3.0 1.0
CG B:HIS666 4.5 3.9 1.0
CE1 B:TYR668 4.5 2.0 1.0
ND1 B:HIS666 4.5 5.9 1.0
CZ B:TYR668 4.7 6.9 1.0
CE1 B:PHE657 4.8 2.0 1.0
CZ B:PHE657 4.9 2.0 1.0

Reference:

M.Cheng, B.De, S.Pikul, N.G.Almstead, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, L.Chen, C.M.Dunaway, F.Gu, M.E.Dowty, G.E.Mieling, M.J.Janusz, S.Wang-Weigand. Design and Synthesis of Piperazine-Based Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 43 369 2000.
ISSN: ISSN 0022-2623
PubMed: 10669564
DOI: 10.1021/JM990366Q
Page generated: Mon Jan 25 16:08:18 2021

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