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Platinum 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:

Chlorine (Cl) 2 atoms
Calcium (Ca) 6 atoms
Zinc (Zn) 4 atoms

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 6 binding sites of Platinum where determined in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor., PDB code: 4dpe:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 4dpe

Go back to Platinum Binding Sites List in 4dpe
Platinum binding site 1 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt306

b:46.2
occ:0.64
 OE2 A:GLU139 1.7 5.2 1.0
OE1 A:GLU139 2.1 35.3 1.0
CD A:GLU139 2.2 22.0 1.0
SD A:MET143 2.3 45.5 1.0
O A:HOH460 2.3 20.7 1.0
CG A:MET143 3.2 31.6 1.0
CB A:MET143 3.6 20.0 1.0
O A:HOH459 3.7 37.2 1.0
CG A:GLU139 3.7 31.4 1.0
CE A:MET143 3.9 44.5 1.0
CA A:GLU139 4.6 30.9 1.0
O A:HOH411 4.6 21.6 1.0
O A:GLY138 4.7 32.5 1.0
CB A:GLU139 4.7 31.4 1.0
NH1 A:ARG100 4.8 33.8 1.0
N A:ALA140 4.9 27.4 1.0
CA A:MET143 4.9 18.1 1.0

Platinum binding site 2 out of 6 in 4dpe

Go back to Platinum Binding Sites List in 4dpe
Platinum binding site 2 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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
B:Pt306

b:38.0
occ:0.80
 OE1 B:GLU139 1.7 32.2 1.0
SD B:MET143 1.9 30.4 1.0
O B:HOH500 2.4 25.2 1.0
CD B:GLU139 2.6 34.6 1.0
O B:HOH501 2.7 36.1 1.0
CG B:MET143 2.8 24.6 1.0
OE2 B:GLU139 2.8 34.5 1.0
CE B:MET143 3.4 26.3 1.0
O B:HOH408 4.0 19.8 1.0
CG B:GLU139 4.0 33.9 1.0
O B:HOH473 4.1 37.9 1.0
CB B:MET143 4.3 19.8 1.0
O B:ALA140 4.4 23.2 1.0
CA B:GLU139 4.4 28.4 1.0
CB B:GLU139 4.5 31.4 1.0
N B:ALA140 4.5 24.4 1.0

Platinum binding site 3 out of 6 in 4dpe

Go back to Platinum Binding Sites List in 4dpe
Platinum binding site 3 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt307

b:30.0
occ:0.42
 CL B:CL311 1.5 28.9 0.9
O B:HOH491 1.6 24.9 1.0
CL B:CL312 2.3 55.0 1.0
ND1 B:HIS224 2.3 51.6 1.0
CE1 B:HIS224 3.2 54.7 1.0
CG B:HIS224 3.3 49.2 1.0
CA B:HIS224 3.5 45.9 1.0
CB B:HIS224 3.6 46.8 1.0
O B:TYR223 4.2 42.6 1.0
NE2 B:HIS224 4.3 54.8 1.0
C B:HIS224 4.3 46.6 1.0
N B:SER225 4.3 47.1 1.0
CD2 B:HIS224 4.3 53.2 1.0
N B:HIS224 4.5 43.4 1.0
C B:TYR223 4.7 41.9 1.0

Platinum binding site 4 out of 6 in 4dpe

Go back to Platinum Binding Sites List in 4dpe
Platinum binding site 4 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt 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:Pt308

b:51.9
occ:0.44
 O B:HOH494 1.8 36.6 1.0
O B:HOH495 2.4 40.6 1.0
O B:HOH426 4.8 27.8 1.0
O B:HOH427 4.9 25.4 1.0

Platinum binding site 5 out of 6 in 4dpe

Go back to Platinum Binding Sites List in 4dpe
Platinum binding site 5 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt309

b:49.3
occ:0.39
 NH1 B:ARG231 2.0 46.3 1.0
O B:HOH490 2.3 27.2 1.0
NH2 B:ARG231 2.3 43.0 1.0
O B:HOH401 2.4 36.2 0.8
CZ B:ARG231 2.5 49.9 1.0
O B:HOH456 2.8 41.7 1.0
NH2 B:ARG233 3.4 61.4 1.0
NE B:ARG231 3.9 50.3 1.0
CZ B:ARG233 4.6 61.5 1.0
CD B:ARG231 4.8 53.0 1.0
NH1 B:ARG233 4.9 60.6 1.0

Platinum binding site 6 out of 6 in 4dpe

Go back to Platinum Binding Sites List in 4dpe
Platinum binding site 6 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt310

b:49.7
occ:0.26
 O B:HOH403 1.6 38.2 1.0
O B:HOH402 1.8 25.2 1.0
NZ B:LYS94 2.2 45.6 1.0
O B:HOH404 2.7 38.5 1.0
CE B:LYS94 3.7 47.8 1.0
CE3 B:TRP92 4.1 30.2 1.0
CZ3 B:TRP92 4.3 30.7 1.0
CD B:LYS94 4.7 45.0 1.0
NH1 B:ARG93 4.7 62.5 1.0
CG B:LYS94 4.9 40.5 1.0
N B:ARG93 5.0 40.0 1.0
O B:HOH439 5.0 30.3 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: Thu Oct 10 11:01:11 2024

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