Atomistry » Zinc » PDB 1d5j-1dmy » 1d8m
Atomistry »
  Zinc »
    PDB 1d5j-1dmy »
      1d8m »

Zinc in PDB 1d8m: Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor

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

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor, PDB code: 1d8m was solved by S.Pikul, K.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, Y.O.Taiwo, L.E.Williams, B.A.Hynd, L.C.Hsieh, M.J.Janusz, F.Gu, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.960, 78.590, 105.930, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.5

Other elements in 1d8m:

The structure of Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor (pdb code 1d8m). 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 Heterocycle- Based Inhibitor, PDB code: 1d8m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1d8m

Go back to Zinc Binding Sites List in 1d8m
Zinc binding site 1 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:7.8
occ:1.00
NE2 A:HIS201 2.0 2.0 1.0
NE2 A:HIS205 2.3 2.0 1.0
NE2 A:HIS211 2.4 4.1 1.0
CD2 A:HIS201 2.8 2.0 1.0
CE1 A:HIS201 3.2 2.5 1.0
CD2 A:HIS205 3.2 2.0 1.0
CE1 A:HIS211 3.4 2.0 1.0
CD2 A:HIS211 3.4 4.4 1.0
CE1 A:HIS205 3.4 2.7 1.0
CG A:HIS201 4.1 2.0 1.0
ND1 A:HIS201 4.2 2.0 1.0
CG A:HIS205 4.4 2.0 1.0
ND1 A:HIS205 4.4 2.0 1.0
ND1 A:HIS211 4.5 2.0 1.0
OE2 A:GLU202 4.5 2.0 1.0
CG A:HIS211 4.5 2.9 1.0
OE1 A:GLU202 5.0 7.5 1.0

Zinc binding site 2 out of 4 in 1d8m

Go back to Zinc Binding Sites List in 1d8m
Zinc binding site 2 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.8
occ:1.00
NE2 A:HIS151 2.1 2.0 1.0
NE2 A:HIS166 2.1 2.0 1.0
ND1 A:HIS179 2.1 7.4 1.0
OD2 A:ASP153 2.2 15.8 1.0
CE1 A:HIS166 2.8 2.0 1.0
CG A:ASP153 3.0 9.3 1.0
CE1 A:HIS179 3.0 7.6 1.0
CD2 A:HIS151 3.0 2.0 1.0
OD1 A:ASP153 3.0 13.7 1.0
CE1 A:HIS151 3.1 2.0 1.0
CG A:HIS179 3.2 4.7 1.0
CD2 A:HIS166 3.3 2.0 1.0
CB A:HIS179 3.6 3.7 1.0
OH A:TYR168 3.9 6.1 1.0
O A:TYR155 4.0 2.7 1.0
ND1 A:HIS166 4.0 2.0 1.0
NE2 A:HIS179 4.1 2.0 1.0
CG A:HIS151 4.1 2.8 1.0
ND1 A:HIS151 4.1 2.0 1.0
CD2 A:HIS179 4.2 2.0 1.0
CG A:HIS166 4.3 2.0 1.0
CB A:ASP153 4.4 6.0 1.0
CE1 A:TYR168 4.5 2.0 1.0
CZ A:TYR168 4.7 2.0 1.0
O A:HOH12 4.7 2.0 1.0
CZ A:PHE157 4.7 2.0 1.0
C A:TYR155 4.9 5.8 1.0
CB A:TYR155 5.0 10.9 1.0
CE1 A:PHE157 5.0 2.0 1.0

Zinc binding site 3 out of 4 in 1d8m

Go back to Zinc Binding Sites List in 1d8m
Zinc binding site 3 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:6.5
occ:1.00
OA B:BBH901 1.8 20.0 1.0
OB B:BBH901 2.0 17.1 1.0
NE2 B:HIS705 2.2 2.0 1.0
NE2 B:HIS701 2.2 2.5 1.0
NE2 B:HIS711 2.6 8.2 1.0
NA B:BBH901 2.6 15.5 1.0
C B:BBH901 2.7 16.8 1.0
CD2 B:HIS701 2.9 7.4 1.0
CD2 B:HIS705 3.0 2.0 1.0
CE1 B:HIS705 3.2 5.1 1.0
CE1 B:HIS701 3.4 2.0 1.0
CE1 B:HIS711 3.5 5.2 1.0
CD2 B:HIS711 3.6 6.3 1.0
OE2 B:GLU702 3.8 2.0 1.0
C13 B:BBH901 4.2 17.6 1.0
CG B:HIS701 4.2 2.0 1.0
CG B:HIS705 4.2 2.0 1.0
ND1 B:HIS705 4.3 3.0 1.0
ND1 B:HIS701 4.4 2.0 1.0
C6 B:BBH901 4.6 8.2 1.0
ND1 B:HIS711 4.6 6.2 1.0
CD B:GLU702 4.7 2.0 1.0
CG B:HIS711 4.7 4.4 1.0
C5 B:BBH901 4.8 10.5 1.0
C14 B:BBH901 4.8 17.0 1.0
OE1 B:GLU702 4.8 2.0 1.0
N12 B:BBH901 4.8 15.3 1.0

Zinc binding site 4 out of 4 in 1d8m

Go back to Zinc Binding Sites List in 1d8m
Zinc binding site 4 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:9.7
occ:1.00
NE2 B:HIS651 2.0 2.0 1.0
NE2 B:HIS666 2.0 2.0 1.0
ND1 B:HIS679 2.1 3.7 1.0
OD2 B:ASP653 2.2 7.9 1.0
CD2 B:HIS651 2.8 3.6 1.0
CE1 B:HIS666 3.0 2.0 1.0
CG B:HIS679 3.0 2.7 1.0
CE1 B:HIS679 3.0 2.0 1.0
CD2 B:HIS666 3.1 3.6 1.0
CG B:ASP653 3.1 7.8 1.0
CE1 B:HIS651 3.1 2.0 1.0
CB B:HIS679 3.4 2.0 1.0
OD1 B:ASP653 3.5 6.8 1.0
CG B:HIS651 4.0 4.6 1.0
O B:TYR655 4.0 8.8 1.0
OH B:TYR668 4.0 2.8 1.0
NE2 B:HIS679 4.1 2.0 1.0
ND1 B:HIS666 4.1 2.3 1.0
CD2 B:HIS679 4.1 2.0 1.0
ND1 B:HIS651 4.1 2.0 1.0
CG B:HIS666 4.2 2.0 1.0
CE1 B:PHE657 4.4 2.0 1.0
CZ B:PHE657 4.4 2.0 1.0
CB B:ASP653 4.4 4.8 1.0
CE1 B:TYR668 4.8 2.0 1.0
CA B:HIS679 4.9 2.0 1.0
CZ B:TYR668 4.9 2.0 1.0

Reference:

S.Pikul, K.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, Y.O.Taiwo, L.E.Williams, B.A.Hynd, L.C.Hsieh, M.J.Janusz, F.Gu, G.E.Mieling. Heterocycle-Based Mmp Inhibitors with P2' Substituents. Bioorg.Med.Chem.Lett. V. 11 1009 2001.
ISSN: ISSN 0960-894X
PubMed: 11327577
DOI: 10.1016/S0960-894X(01)00137-8
Page generated: Mon Jan 25 16:08:18 2021

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy