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Zinc in PDB 4h2e: Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains

Enzymatic activity of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains

All present enzymatic activity of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains, PDB code: 4h2e was solved by E.A.Stura, L.Vera, E.Cassar-Lajeunesse, E.Nuti, M.P.Catalani, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.85 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.180, 97.400, 45.690, 90.00, 111.99, 90.00
R / Rfree (%) 27.7 / 31.1

Other elements in 4h2e:

The structure of Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains also contains other interesting chemical elements:

Calcium (Ca) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains (pdb code 4h2e). 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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains, PDB code: 4h2e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4h2e

Go back to Zinc Binding Sites List in 4h2e
Zinc binding site 1 out of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:16.4
occ:1.00
NE2 A:HIS226 1.9 9.3 1.0
NE2 A:HIS236 1.9 2.8 1.0
O23 B:0Y3306 2.0 37.5 1.0
O25 B:0Y3306 2.1 36.7 1.0
NE2 A:HIS230 2.2 20.0 1.0
N22 B:0Y3306 2.7 37.4 1.0
C21 B:0Y3306 2.7 36.6 1.0
CD2 A:HIS226 2.8 9.8 1.0
CE1 A:HIS236 2.9 2.5 1.0
CE1 A:HIS226 2.9 9.0 1.0
CD2 A:HIS230 2.9 20.1 1.0
CD2 A:HIS236 2.9 3.2 1.0
CE1 A:HIS230 3.4 19.9 1.0
ND1 A:HIS226 4.0 8.8 1.0
CG A:HIS226 4.0 8.8 1.0
ND1 A:HIS236 4.0 2.9 1.0
CG A:HIS236 4.1 3.0 1.0
CG A:HIS230 4.2 20.0 1.0
C20 B:0Y3306 4.2 37.0 1.0
O36 B:0Y3306 4.3 38.5 1.0
ND1 A:HIS230 4.3 19.5 1.0
C29 B:0Y3306 4.4 38.8 1.0
N28 B:0Y3306 4.5 38.1 1.0
O17 B:0Y3306 4.6 37.3 1.0
CE A:MET244 4.6 6.5 1.0
N16 B:0Y3306 4.7 37.8 1.0
OE1 A:GLU227 4.7 18.7 1.0
C27 B:0Y3306 4.7 37.0 1.0
OE2 A:GLU227 4.8 17.9 1.0
O A:HIS226 4.9 9.4 1.0
C26 B:0Y3306 5.0 37.0 1.0

Zinc binding site 2 out of 4 in 4h2e

Go back to Zinc Binding Sites List in 4h2e
Zinc binding site 2 out of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:16.0
occ:1.00
ND1 A:HIS203 2.0 8.8 1.0
OD1 A:ASP177 2.0 5.5 1.0
NE2 A:HIS175 2.1 21.9 1.0
NE2 A:HIS190 2.3 14.9 1.0
CG A:ASP177 2.7 6.8 1.0
OD2 A:ASP177 2.8 7.0 1.0
CE1 A:HIS203 2.9 9.1 1.0
CD2 A:HIS175 2.9 23.6 1.0
CE1 A:HIS190 2.9 14.3 1.0
CG A:HIS203 3.0 8.9 1.0
CE1 A:HIS175 3.2 22.8 1.0
CB A:HIS203 3.4 9.5 1.0
CD2 A:HIS190 3.5 14.6 1.0
NE2 A:HIS203 4.0 9.5 1.0
CB A:ASP177 4.1 7.8 1.0
CD2 A:HIS203 4.1 9.7 1.0
CG A:HIS175 4.1 25.4 1.0
ND1 A:HIS190 4.2 14.9 1.0
ND1 A:HIS175 4.2 24.2 1.0
O A:TYR179 4.3 34.1 1.0
CG A:HIS190 4.5 15.3 1.0
CZ A:PHE192 4.6 14.8 1.0
N A:ASP177 4.6 9.2 1.0
CE2 A:PHE192 4.7 13.3 1.0
CE2 A:PHE181 4.8 23.1 1.0
CZ A:PHE181 4.8 21.4 1.0
CA A:HIS203 4.9 8.9 1.0
CA A:ASP177 4.9 7.8 1.0
NE2 A:GLN169 4.9 20.1 1.0

Zinc binding site 3 out of 4 in 4h2e

Go back to Zinc Binding Sites List in 4h2e
Zinc binding site 3 out of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:17.9
occ:1.00
NE2 B:HIS236 2.0 4.2 1.0
O78 B:0Y3306 2.0 39.7 1.0
O77 B:0Y3306 2.0 41.1 1.0
NE2 B:HIS226 2.1 14.8 1.0
NE2 B:HIS230 2.3 13.1 1.0
C75 B:0Y3306 2.7 39.8 1.0
N76 B:0Y3306 2.7 40.8 1.0
CD2 B:HIS226 2.9 14.9 1.0
CD2 B:HIS236 2.9 4.4 1.0
CE1 B:HIS236 3.0 3.9 1.0
CD2 B:HIS230 3.0 12.8 1.0
CE1 B:HIS226 3.2 14.4 1.0
CE1 B:HIS230 3.5 12.7 1.0
ND1 B:HIS236 4.1 4.0 1.0
CG B:HIS236 4.1 4.2 1.0
CG B:HIS226 4.1 14.2 1.0
C54 B:0Y3306 4.1 40.3 1.0
ND1 B:HIS226 4.2 14.2 1.0
CG B:HIS230 4.2 12.8 1.0
ND1 B:HIS230 4.4 12.5 1.0
OE1 B:GLU227 4.4 9.3 1.0
OE2 B:GLU227 4.4 8.6 1.0
O53 B:0Y3306 4.5 40.8 1.0
C50 B:0Y3306 4.6 42.3 1.0
CE B:MET244 4.6 10.7 1.0
N49 B:0Y3306 4.7 44.0 1.0
N55 B:0Y3306 4.8 41.5 1.0
C48 B:0Y3306 4.8 41.8 1.0
CD B:GLU227 4.9 8.9 1.0
C57 B:0Y3306 4.9 40.3 1.0
C51 B:0Y3306 4.9 40.7 1.0
C58 B:0Y3306 5.0 41.0 1.0

Zinc binding site 4 out of 4 in 4h2e

Go back to Zinc Binding Sites List in 4h2e
Zinc binding site 4 out of 4 in the Crystal Structure of An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains


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 An Mmp Twin Inhibitor Complexing Two Mmp-9 Catalytic Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:13.6
occ:1.00
OD1 B:ASP177 2.0 18.4 1.0
ND1 B:HIS203 2.2 12.4 1.0
NE2 B:HIS190 2.4 9.3 1.0
NE2 B:HIS175 2.5 20.5 1.0
CG B:ASP177 2.8 19.8 1.0
OD2 B:ASP177 3.0 19.9 1.0
CG B:HIS203 3.0 12.3 1.0
CE1 B:HIS203 3.1 12.7 1.0
CE1 B:HIS190 3.2 8.7 1.0
CB B:HIS203 3.3 12.9 1.0
CD2 B:HIS190 3.4 9.3 1.0
CD2 B:HIS175 3.4 22.1 1.0
CE1 B:HIS175 3.4 22.0 1.0
CD2 B:HIS203 4.0 13.2 1.0
NE2 B:HIS203 4.1 12.9 1.0
CB B:ASP177 4.2 20.5 1.0
CE2 B:PHE192 4.4 18.2 1.0
ND1 B:HIS190 4.4 9.2 1.0
CG B:HIS190 4.5 9.8 1.0
ND1 B:HIS175 4.5 23.4 1.0
O B:TYR179 4.5 20.8 1.0
CG B:HIS175 4.6 23.4 1.0
N B:ASP177 4.6 22.1 1.0
CE2 B:PHE181 4.6 20.9 1.0
CZ B:PHE181 4.6 19.0 1.0
CA B:HIS203 4.8 12.4 1.0
CZ B:PHE192 4.9 19.1 1.0
NE2 B:GLN169 5.0 22.6 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sat Oct 26 23:49:12 2024

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