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Zinc in PDB 1d7x: Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.

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

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor., PDB code: 1d7x was solved by M.Y.Cheng, M.G.Natchus, B.De, N.G.Almstead, S.Pikul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.850, 78.220, 104.740, 90.00, 90.00, 90.00
R / Rfree (%) 26.2 / 22.7

Other elements in 1d7x:

The structure of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold 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 Modified Proline Scaffold Based Inhibitor. (pdb code 1d7x). 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 Modified Proline Scaffold Based Inhibitor., PDB code: 1d7x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1d7x

Go back to Zinc Binding Sites List in 1d7x
Zinc binding site 1 out of 4 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold 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 Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.8
occ:1.00
 O33 A:SPC401 1.7 2.9 1.0
O31 A:SPC401 1.8 11.0 1.0
NE2 A:HIS205 2.2 7.1 1.0
NE2 A:HIS211 2.3 4.7 1.0
NE2 A:HIS201 2.4 2.0 1.0
N32 A:SPC401 2.4 2.0 1.0
C29 A:SPC401 2.4 6.4 1.0
CD2 A:HIS205 3.0 8.1 1.0
CE1 A:HIS211 3.2 3.0 1.0
CD2 A:HIS201 3.2 2.0 1.0
CD2 A:HIS211 3.3 5.4 1.0
CE1 A:HIS205 3.3 2.0 1.0
CE1 A:HIS201 3.5 2.9 1.0
O A:HOH488 3.7 2.1 1.0
C15 A:SPC401 4.0 7.7 1.0
O B:HOH102 4.1 13.0 1.0
OE2 A:GLU202 4.2 4.0 1.0
CG A:HIS205 4.3 3.2 1.0
ND1 A:HIS211 4.3 5.0 1.0
ND1 A:HIS205 4.4 2.0 1.0
CG A:HIS211 4.4 4.8 1.0
O B:HOH138 4.4 19.8 1.0
CG A:HIS201 4.4 2.0 1.0
C16 A:SPC401 4.5 7.8 1.0
ND1 A:HIS201 4.5 2.0 1.0
C6 A:SPC401 4.5 2.0 1.0
C17 A:SPC401 4.7 7.8 1.0
N14 A:SPC401 4.7 7.6 1.0
C18 A:SPC401 4.8 5.6 1.0
C5 A:SPC401 4.8 2.0 1.0
C1 A:SPC401 4.9 5.5 1.0
OE1 A:GLU202 4.9 8.1 1.0
CD A:GLU202 5.0 3.6 1.0

Zinc binding site 2 out of 4 in 1d7x

Go back to Zinc Binding Sites List in 1d7x
Zinc binding site 2 out of 4 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold 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 Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:10.0
occ:1.00
 ND1 A:HIS179 2.0 5.2 1.0
NE2 A:HIS151 2.0 2.0 1.0
OD2 A:ASP153 2.0 6.8 1.0
NE2 A:HIS166 2.1 6.5 1.0
CE1 A:HIS179 2.9 6.3 1.0
CE1 A:HIS166 2.9 5.7 1.0
CG A:ASP153 3.0 9.2 1.0
CE1 A:HIS151 3.0 2.0 1.0
CD2 A:HIS151 3.0 2.0 1.0
CG A:HIS179 3.0 4.4 1.0
CD2 A:HIS166 3.2 7.1 1.0
OD1 A:ASP153 3.2 6.3 1.0
CB A:HIS179 3.4 3.8 1.0
NE2 A:HIS179 4.0 3.0 1.0
ND1 A:HIS151 4.1 2.0 1.0
OH A:TYR168 4.1 3.5 1.0
ND1 A:HIS166 4.1 6.9 1.0
CD2 A:HIS179 4.1 3.1 1.0
CG A:HIS151 4.1 3.1 1.0
O A:TYR155 4.2 9.8 1.0
CG A:HIS166 4.2 5.2 1.0
CB A:ASP153 4.3 11.0 1.0
CE2 A:TYR168 4.5 2.9 1.0
CZ A:PHE157 4.6 2.0 1.0
CE2 A:PHE157 4.7 2.0 1.0
CZ A:TYR168 4.8 4.3 1.0
CA A:HIS179 4.9 2.4 1.0
O A:HOH405 5.0 5.0 1.0

Zinc binding site 3 out of 4 in 1d7x

Go back to Zinc Binding Sites List in 1d7x
Zinc binding site 3 out of 4 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold 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 Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:18.0
occ:1.00
 O31 B:SPC901 2.0 15.5 1.0
O33 B:SPC901 2.0 14.9 1.0
NE2 B:HIS701 2.2 2.6 1.0
NE2 B:HIS711 2.2 14.3 1.0
NE2 B:HIS705 2.2 9.7 1.0
C29 B:SPC901 2.7 16.3 1.0
N32 B:SPC901 2.8 13.0 1.0
CD2 B:HIS701 3.0 2.0 1.0
CD2 B:HIS711 3.1 15.0 1.0
CD2 B:HIS705 3.1 8.0 1.0
CE1 B:HIS711 3.1 15.2 1.0
CE1 B:HIS701 3.2 2.2 1.0
CE1 B:HIS705 3.3 4.9 1.0
O B:HOH48 3.8 9.1 1.0
CG B:HIS711 4.2 13.3 1.0
ND1 B:HIS711 4.2 12.6 1.0
OE2 B:GLU702 4.2 5.1 1.0
C15 B:SPC901 4.3 17.9 1.0
CG B:HIS701 4.3 2.8 1.0
CG B:HIS705 4.3 8.2 1.0
ND1 B:HIS705 4.3 5.6 1.0
ND1 B:HIS701 4.4 3.0 1.0
C6 B:SPC901 4.6 14.3 1.0
C16 B:SPC901 4.8 17.1 1.0
C5 B:SPC901 4.8 13.7 1.0
N14 B:SPC901 4.9 18.4 1.0
C1 B:SPC901 4.9 11.6 1.0
C17 B:SPC901 5.0 21.1 1.0
C18 B:SPC901 5.0 21.9 1.0
CB B:PRO721 5.0 13.6 1.0

Zinc binding site 4 out of 4 in 1d7x

Go back to Zinc Binding Sites List in 1d7x
Zinc binding site 4 out of 4 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold 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 Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:10.8
occ:1.00
 NE2 B:HIS651 2.0 4.4 1.0
ND1 B:HIS679 2.0 3.4 1.0
NE2 B:HIS666 2.1 3.6 1.0
OD2 B:ASP653 2.1 9.4 1.0
CD2 B:HIS651 2.8 6.3 1.0
CE1 B:HIS679 2.9 2.0 1.0
CG B:ASP653 2.9 9.6 1.0
CE1 B:HIS666 2.9 3.6 1.0
CE1 B:HIS651 3.1 7.6 1.0
CG B:HIS679 3.1 5.8 1.0
OD1 B:ASP653 3.2 9.2 1.0
CD2 B:HIS666 3.2 2.8 1.0
CB B:HIS679 3.5 4.9 1.0
NE2 B:HIS679 4.0 2.4 1.0
CG B:HIS651 4.0 6.7 1.0
OH B:TYR668 4.0 4.4 1.0
ND1 B:HIS666 4.1 4.1 1.0
O B:TYR655 4.1 9.7 1.0
ND1 B:HIS651 4.1 6.4 1.0
CD2 B:HIS679 4.1 5.7 1.0
CB B:ASP653 4.1 9.3 1.0
CG B:HIS666 4.3 4.2 1.0
CE2 B:PHE657 4.5 2.0 1.0
CZ B:PHE657 4.6 2.0 1.0
CE1 B:TYR668 4.6 5.0 1.0
CZ B:TYR668 4.9 6.8 1.0
O B:HOH103 4.9 6.1 1.0

Reference:

M.Cheng, B.De, N.G.Almstead, S.Pikul, M.E.Dowty, C.R.Dietsch, C.M.Dunaway, F.Gu, L.C.Hsieh, M.J.Janusz, Y.O.Taiwo, M.G.Natchus, T.Hudlicky, M.Mandel. Design, Synthesis, and Biological Evaluation of Matrix Metalloproteinase Inhibitors Derived From A Modified Proline Scaffold. J.Med.Chem. V. 42 5426 1999.
ISSN: ISSN 0022-2623
PubMed: 10639284
DOI: 10.1021/JM9904699
Page generated: Sat Oct 12 23:32:11 2024

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