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Zinc in PDB 6n9d: Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

All present enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD):
3.4.24.17;

Protein crystallography data

The structure of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 6n9d was solved by M.Raeeszadeh-Sarmazdeh, E.S.Radisky, B.Sankaran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.99 / 2.67
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.031, 70.031, 319.512, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 25.8

Other elements in 6n9d:

The structure of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) (pdb code 6n9d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 6n9d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6n9d

Go back to Zinc Binding Sites List in 6n9d
Zinc binding site 1 out of 2 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:50.3
occ:1.00
 ND1 A:HIS179 2.0 44.1 1.0
NE2 A:HIS166 2.1 36.2 1.0
CE1 A:HIS151 2.1 43.9 1.0
NE2 A:HIS151 2.3 43.2 1.0
OD2 A:ASP153 2.4 50.5 1.0
CE1 A:HIS179 2.9 46.3 1.0
CE1 A:HIS166 3.0 42.2 1.0
CG A:ASP153 3.0 44.7 1.0
OD1 A:ASP153 3.1 37.2 1.0
CG A:HIS179 3.1 39.2 1.0
CD2 A:HIS166 3.1 36.3 1.0
ND1 A:HIS151 3.3 39.1 1.0
CD2 A:HIS151 3.5 45.4 1.0
CB A:HIS179 3.5 37.0 1.0
CG A:HIS151 4.0 44.2 1.0
O A:TYR155 4.0 41.2 1.0
NE2 A:HIS179 4.0 41.9 1.0
OH A:TYR168 4.1 49.1 1.0
ND1 A:HIS166 4.2 42.0 1.0
CD2 A:HIS179 4.2 36.4 1.0
CG A:HIS166 4.3 29.4 1.0
CB A:ASP153 4.4 38.0 1.0
CZ A:PHE157 4.6 43.2 1.0
CE1 A:TYR168 4.6 38.7 1.0
CE2 A:PHE157 4.7 43.7 1.0
CZ A:TYR168 4.8 41.9 1.0

Zinc binding site 2 out of 2 in 6n9d

Go back to Zinc Binding Sites List in 6n9d
Zinc binding site 2 out of 2 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/L133P/L151C/G154A) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:36.6
occ:1.00
 NE2 A:HIS211 2.0 35.1 1.0
NE2 A:HIS201 2.0 37.5 1.0
N B:CYS1 2.2 40.1 1.0
NE2 A:HIS205 2.2 43.6 1.0
O B:CYS1 2.4 45.1 1.0
CD2 A:HIS211 2.8 34.9 1.0
CA B:CYS1 2.9 46.1 1.0
C B:CYS1 2.9 44.8 1.0
CE1 A:HIS201 2.9 33.9 1.0
CD2 A:HIS205 3.0 43.1 1.0
CE1 A:HIS211 3.1 38.4 1.0
CD2 A:HIS201 3.1 35.8 1.0
CB B:CYS1 3.3 40.7 1.0
CE1 A:HIS205 3.3 45.4 1.0
CG A:HIS211 4.0 39.5 1.0
ND1 A:HIS201 4.1 34.5 1.0
ND1 A:HIS211 4.1 45.6 1.0
CG A:HIS201 4.2 40.1 1.0
N B:THR2 4.2 44.0 1.0
OE1 A:GLU202 4.2 37.9 1.0
CG A:HIS205 4.3 33.8 1.0
ND1 A:HIS205 4.4 38.5 1.0
O B:SER68 4.6 47.0 1.0
OE2 A:GLU202 4.7 38.5 1.0
CD A:GLU202 4.8 40.6 1.0
CB A:PRO221 4.8 37.7 1.0
CA A:PRO221 4.9 49.5 1.0
SG B:CYS1 4.9 41.1 1.0
OG1 B:THR2 5.0 48.0 1.0

Reference:

M.Raeeszadeh-Sarmazdeh, K.A.Greene, B.Sankaran, G.P.Downey, D.C.Radisky, E.S.Radisky. Directed Evolution of the Metalloproteinase Inhibitor Timp-1 Reveals That Its N- and C-Terminal Domains Cooperate in Matrix Metalloproteinase Recognition. J.Biol.Chem. V. 294 9476 2019.
ISSN: ESSN 1083-351X
PubMed: 31040180
DOI: 10.1074/JBC.RA119.008321
Page generated: Tue Oct 29 03:38:25 2024

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