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Zinc in PDB 4dpe: Structure of MMP3 Complexed with A Platinum-Based Inhibitor.

Enzymatic activity of Structure of MMP3 Complexed with A Platinum-Based Inhibitor.

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

Protein crystallography data

The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor., PDB code: 4dpe was solved by B.D.Belviso, F.Arnesano, V.Calderone, R.Caliandro, G.Natile, D.Siliqi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.86 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.206, 77.714, 105.615, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.1

Other elements in 4dpe:

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

Platinum (Pt) 6 atoms
Chlorine (Cl) 2 atoms
Calcium (Ca) 6 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 4dpe

Go back to Zinc Binding Sites List in 4dpe
Zinc binding site 1 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:23.2
occ:1.00
O B:THR255 1.9 27.1 1.0
NE2 A:HIS201 1.9 18.9 1.0
NE2 A:HIS211 2.1 29.9 1.0
NE2 A:HIS205 2.1 14.3 1.0
O B:HOH483 2.6 23.2 0.7
C B:THR255 2.8 24.4 1.0
CD2 A:HIS201 2.9 17.3 1.0
CE1 A:HIS201 2.9 20.2 1.0
CE1 A:HIS205 2.9 17.8 1.0
CD2 A:HIS211 3.0 24.1 1.0
OXT B:THR255 3.1 26.1 1.0
CE1 A:HIS211 3.1 32.5 1.0
CD2 A:HIS205 3.2 12.0 1.0
ND1 A:HIS201 4.0 22.1 1.0
CG A:HIS201 4.0 15.7 1.0
ND1 A:HIS205 4.1 14.6 1.0
CG A:HIS211 4.2 25.7 1.0
CA B:THR255 4.2 23.6 1.0
ND1 A:HIS211 4.2 22.8 1.0
CG A:HIS205 4.3 15.0 1.0
N B:THR255 4.4 21.3 1.0
CG B:GLU254 4.5 34.7 1.0
O B:GLU254 4.5 17.1 1.0
C B:GLU254 4.6 22.3 1.0
OE2 A:GLU202 4.6 18.8 1.0
CE A:MET219 4.7 15.8 1.0
OG1 B:THR255 4.8 23.3 1.0
O B:HOH482 4.9 42.5 1.0
OE1 A:GLU202 4.9 19.6 1.0
CB B:GLU254 4.9 24.1 1.0

Zinc binding site 2 out of 4 in 4dpe

Go back to Zinc Binding Sites List in 4dpe
Zinc binding site 2 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:15.8
occ:1.00
NE2 A:HIS151 2.0 14.7 1.0
ND1 A:HIS179 2.0 14.1 1.0
NE2 A:HIS166 2.0 15.6 1.0
OD2 A:ASP153 2.1 19.4 1.0
CE1 A:HIS166 2.9 11.1 1.0
CE1 A:HIS179 2.9 18.3 1.0
CD2 A:HIS151 2.9 11.8 1.0
CE1 A:HIS151 3.0 19.2 1.0
CG A:ASP153 3.0 22.2 1.0
CG A:HIS179 3.1 13.7 1.0
CD2 A:HIS166 3.1 12.9 1.0
OD1 A:ASP153 3.2 16.5 1.0
CB A:HIS179 3.5 13.1 1.0
ND1 A:HIS166 4.0 11.8 1.0
ND1 A:HIS151 4.1 13.9 1.0
NE2 A:HIS179 4.1 14.0 1.0
CG A:HIS151 4.1 13.6 1.0
CG A:HIS166 4.2 13.6 1.0
CD2 A:HIS179 4.2 13.5 1.0
OH A:TYR168 4.2 18.9 1.0
O A:TYR155 4.3 20.1 1.0
CB A:ASP153 4.4 20.1 1.0
CE1 A:TYR168 4.5 16.8 1.0
CZ A:PHE157 4.6 13.9 1.0
CE2 A:PHE157 4.7 15.7 1.0
CZ A:TYR168 4.9 19.1 1.0
CA A:HIS179 5.0 12.9 1.0

Zinc binding site 3 out of 4 in 4dpe

Go back to Zinc Binding Sites List in 4dpe
Zinc binding site 3 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:28.2
occ:1.00
NE2 B:HIS211 2.1 32.1 1.0
NE2 B:HIS205 2.1 20.6 1.0
NE2 B:HIS201 2.1 29.3 1.0
O5 B:NGH313 2.2 40.3 1.0
O4 B:NGH313 2.3 38.9 1.0
C11 B:NGH313 3.0 42.9 1.0
CD2 B:HIS201 3.0 29.9 1.0
CD2 B:HIS205 3.0 20.1 1.0
N1 B:NGH313 3.0 41.7 1.0
CD2 B:HIS211 3.0 31.9 1.0
CE1 B:HIS211 3.1 31.3 1.0
CE1 B:HIS205 3.1 23.1 1.0
CE1 B:HIS201 3.1 28.8 1.0
O B:HOH426 4.1 27.8 1.0
ND1 B:HIS211 4.2 34.0 1.0
CG B:HIS201 4.2 24.3 1.0
CG B:HIS211 4.2 31.4 1.0
CG B:HIS205 4.2 21.5 1.0
ND1 B:HIS205 4.2 22.6 1.0
OE2 B:GLU202 4.2 26.8 1.0
ND1 B:HIS201 4.2 23.2 1.0
C10 B:NGH313 4.4 41.3 1.0
C1 B:NGH313 4.7 38.0 1.0
CB B:PRO221 4.8 36.4 1.0
C2 B:NGH313 4.9 35.6 1.0
CE B:MET219 5.0 25.1 1.0

Zinc binding site 4 out of 4 in 4dpe

Go back to Zinc Binding Sites List in 4dpe
Zinc binding site 4 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:21.5
occ:1.00
OD2 B:ASP153 1.8 25.8 1.0
NE2 B:HIS166 1.9 20.2 1.0
NE2 B:HIS151 2.1 24.7 1.0
ND1 B:HIS179 2.1 20.7 1.0
CG B:ASP153 2.8 26.4 1.0
CE1 B:HIS166 2.8 26.2 1.0
CD2 B:HIS166 3.0 22.9 1.0
CD2 B:HIS151 3.0 19.9 1.0
CE1 B:HIS179 3.0 20.2 1.0
CE1 B:HIS151 3.1 20.9 1.0
OD1 B:ASP153 3.1 19.3 1.0
CG B:HIS179 3.2 17.2 1.0
CB B:HIS179 3.5 16.1 1.0
ND1 B:HIS166 4.0 23.6 1.0
OH B:TYR168 4.0 26.6 1.0
CG B:HIS166 4.1 21.9 1.0
CB B:ASP153 4.1 23.5 1.0
ND1 B:HIS151 4.2 19.8 1.0
CG B:HIS151 4.2 22.1 1.0
NE2 B:HIS179 4.2 19.0 1.0
O B:TYR155 4.3 26.6 1.0
CD2 B:HIS179 4.3 18.0 1.0
CE1 B:TYR168 4.5 24.3 1.0
CE2 B:PHE157 4.7 20.3 1.0
CZ B:PHE157 4.7 23.8 1.0
CZ B:TYR168 4.8 31.9 1.0

Reference:

B.D.Belviso, R.Caliandro, D.Siliqi, V.Calderone, F.Arnesano, G.Natile. Structure of Matrix Metalloproteinase-3 with A Platinum-Based Inhibitor. Chem.Commun.(Camb.) V. 49 5492 2013.
ISSN: ISSN 1359-7345
PubMed: 23660647
DOI: 10.1039/C3CC41278D
Page generated: Wed Dec 16 05:11:40 2020

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