Calcium 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:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6n9d

Go back to Calcium Binding Sites List in 6n9d
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca301

b:47.4
occ:1.00
 O A:VAL163 2.2 45.9 1.0
O A:GLY159 2.3 57.8 1.0
OD1 A:ASP158 2.4 44.8 1.0
O A:GLY161 2.4 62.6 1.0
OE2 A:GLU184 2.5 65.4 1.0
OD2 A:ASP181 2.5 45.6 1.0
C A:VAL163 3.4 37.3 1.0
C A:GLY159 3.5 63.5 1.0
CG A:ASP181 3.6 45.3 1.0
C A:GLY161 3.6 64.6 1.0
CG A:ASP158 3.6 54.3 1.0
CD A:GLU184 3.6 68.1 1.0
N A:GLY161 3.7 50.5 1.0
N A:VAL163 3.9 40.1 1.0
C A:PRO160 4.1 59.8 1.0
CA A:VAL163 4.1 37.3 1.0
CB A:ASP181 4.2 41.5 1.0
OE1 A:GLU184 4.2 75.1 1.0
N A:GLY159 4.2 62.8 1.0
CA A:GLY161 4.2 49.4 1.0
OD2 A:ASP158 4.3 55.9 1.0
CA A:PRO160 4.3 59.6 1.0
N A:PRO160 4.3 62.2 1.0
N A:LEU164 4.4 35.4 1.0
N A:ASP158 4.4 48.6 1.0
C A:ASP158 4.4 66.3 1.0
C A:ASN162 4.5 49.0 1.0
OD1 A:ASP181 4.5 45.6 1.0
CA A:LEU164 4.5 38.7 1.0
CA A:GLY159 4.5 62.8 1.0
CB A:VAL163 4.6 41.3 1.0
CD2 A:LEU164 4.6 45.4 1.0
N A:ASN162 4.7 60.7 1.0
CB A:ASP158 4.7 54.0 1.0
CA A:ASP158 4.7 56.5 1.0
O A:PRO160 4.7 65.9 1.0
CG A:GLU184 4.8 56.1 1.0
O A:ASP158 4.9 71.6 1.0
CA A:ASN162 5.0 51.4 1.0

Calcium binding site 2 out of 3 in 6n9d

Go back to Calcium Binding Sites List in 6n9d
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca302

b:74.9
occ:1.00
 O A:ASP182 2.4 63.6 1.0
OD2 A:ASP107 2.4 52.3 1.0
OD1 A:ASP182 2.5 59.7 1.0
OD1 A:ASP107 2.6 75.3 1.0
CG A:ASP107 2.8 63.8 1.0
O A:GLU184 3.1 58.7 1.0
CG A:ASP182 3.3 58.9 1.0
C A:ASP182 3.5 58.2 1.0
OG1 A:THR105 3.6 57.0 1.0
OD2 A:ASP182 4.0 67.5 1.0
CA A:ASP182 4.1 49.5 1.0
CB A:ASP182 4.1 54.2 1.0
C A:GLU184 4.3 62.1 1.0
CB A:ASP107 4.3 52.6 1.0
CD A:PRO106 4.6 59.2 1.0
N A:ASP183 4.6 50.7 1.0
CD1 A:TRP186 4.8 50.6 1.0
N A:ASP107 4.8 56.1 1.0
N A:GLU184 4.9 59.9 1.0
CA A:ASP183 4.9 55.4 1.0
CA A:GLN185 4.9 56.2 1.0
CB A:THR105 5.0 51.5 1.0

Calcium binding site 3 out of 3 in 6n9d

Go back to Calcium Binding Sites List in 6n9d
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca305

b:48.8
occ:1.00
 O A:ASN175 2.3 53.9 1.0
O A:ASP141 2.4 50.3 1.0
O A:GLY173 2.4 51.2 1.0
O A:HOH406 2.5 54.4 1.0
OD1 A:ASP177 2.7 42.5 1.0
C A:ASP141 3.4 48.9 1.0
C A:ASN175 3.5 44.9 1.0
C A:GLY173 3.6 41.6 1.0
O A:HOH411 3.6 42.5 1.0
O A:ALA140 3.6 62.8 1.0
CG A:ASP177 3.9 42.2 1.0
O A:GLY171 4.0 44.5 1.0
CA A:ASP141 4.0 47.2 1.0
N A:GLY173 4.2 34.5 1.0
N A:ASN175 4.2 43.5 1.0
CA A:GLY176 4.3 40.2 1.0
CA A:GLY173 4.3 34.7 1.0
N A:GLY176 4.3 34.5 1.0
C A:ILE174 4.4 39.7 1.0
OD2 A:ASP177 4.4 45.4 1.0
N A:ASP177 4.4 29.2 1.0
CA A:ASN175 4.4 40.9 1.0
N A:ILE142 4.5 46.3 1.0
C A:PRO172 4.5 41.7 1.0
C A:GLY176 4.6 39.0 1.0
N A:ILE174 4.6 44.1 1.0
C A:ALA140 4.6 53.0 1.0
O A:ILE174 4.7 47.0 1.0
CH2 A:TRP92 4.7 42.7 1.0
O A:PRO172 4.8 39.8 1.0
N A:ASP141 4.8 46.0 1.0
CA A:ILE142 4.8 46.5 1.0
CA A:ILE174 4.9 31.6 1.0
N A:MET143 4.9 40.7 1.0
CG A:MET143 5.0 48.7 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: Sat Dec 12 07:22:40 2020

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