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Calcium in PDB 6mav: Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

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

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

Protein crystallography data

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

Resolution Low / High (Å) 52.59 / 2.37
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.703, 69.703, 321.326, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 29.8

Other elements in 6mav:

The structure of Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G 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 Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) (pdb code 6mav). 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 Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 6mav:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6mav

Go back to Calcium Binding Sites List in 6mav
Calcium binding site 1 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G 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 Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:73.8
occ:1.00
 O A:VAL163 2.2 68.8 1.0
OD2 A:ASP181 2.2 66.5 1.0
O A:GLY159 2.4 90.2 1.0
OD1 A:ASP158 2.4 75.3 1.0
O A:GLY161 2.4 68.4 1.0
OE2 A:GLU184 2.4 61.3 1.0
CG A:ASP181 3.4 70.2 1.0
C A:VAL163 3.4 65.5 1.0
C A:GLY161 3.5 66.9 1.0
C A:GLY159 3.6 74.7 1.0
CG A:ASP158 3.6 84.0 1.0
CD A:GLU184 3.6 75.8 1.0
N A:GLY161 3.7 71.5 1.0
CB A:ASP181 4.0 51.2 1.0
N A:VAL163 4.0 74.1 1.0
N A:GLY159 4.1 82.2 1.0
C A:ASP158 4.1 73.8 1.0
CA A:GLY161 4.2 53.7 1.0
CA A:VAL163 4.2 47.5 1.0
C A:PRO160 4.2 78.6 1.0
N A:ASP158 4.2 64.5 1.0
OD2 A:ASP158 4.3 89.3 1.0
OE1 A:GLU184 4.3 78.3 1.0
N A:LEU164 4.4 67.0 1.0
OD1 A:ASP181 4.4 74.8 1.0
CA A:GLY159 4.4 75.3 1.0
CB A:VAL163 4.5 48.3 1.0
O A:ASP158 4.5 76.8 1.0
CA A:LEU164 4.5 54.2 1.0
N A:PRO160 4.5 73.5 1.0
CA A:ASP158 4.5 61.6 1.0
C A:ASN162 4.5 64.2 1.0
CA A:PRO160 4.6 78.0 1.0
CG A:GLU184 4.6 72.2 1.0
N A:ASN162 4.6 73.5 1.0
CB A:ASP158 4.7 79.7 1.0
CD2 A:LEU164 4.8 59.6 1.0
O A:PRO160 4.8 83.8 1.0
CA A:ASN162 5.0 66.3 1.0

Calcium binding site 2 out of 3 in 6mav

Go back to Calcium Binding Sites List in 6mav
Calcium binding site 2 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G 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 Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:82.2
occ:1.00
 O A:ASP182 2.2 84.2 1.0
OD2 A:ASP107 2.2 91.0 1.0
OD1 A:ASP107 2.3 0.8 1.0
O A:GLU184 2.4 84.6 1.0
OD1 A:ASP182 2.4 98.3 1.0
CG A:ASP107 2.6 89.5 1.0
C A:ASP182 3.2 65.5 1.0
CG A:ASP182 3.4 78.5 1.0
C A:GLU184 3.7 77.0 1.0
CA A:ASP182 3.7 72.3 1.0
OG1 A:THR105 3.8 78.9 1.0
CB A:ASP182 4.0 73.1 1.0
CB A:ASP107 4.1 88.3 1.0
N A:GLU184 4.3 66.4 1.0
N A:ASP183 4.3 70.3 1.0
CD1 A:TRP186 4.3 69.1 1.0
OD2 A:ASP182 4.4 88.5 1.0
CA A:GLN185 4.4 60.5 1.0
OE1 A:GLN185 4.5 0.2 1.0
N A:GLN185 4.5 67.9 1.0
CA A:GLU184 4.6 64.8 1.0
CA A:ASP183 4.7 55.2 1.0
C A:ASP183 4.7 74.7 1.0
N A:TRP186 4.8 64.1 1.0
N A:ASP107 4.8 92.5 1.0
NE1 A:TRP186 4.8 66.4 1.0
CA A:ASP107 4.9 0.4 1.0
CB A:THR105 5.0 78.8 1.0

Calcium binding site 3 out of 3 in 6mav

Go back to Calcium Binding Sites List in 6mav
Calcium binding site 3 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinase-1 (Timp-1) Mutant L34G 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 Metalloproteinase-1 (Timp-1) Mutant L34G with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:68.3
occ:1.00
 O A:GLY173 2.2 71.9 1.0
O A:ASN175 2.2 64.2 1.0
O A:ASP141 2.3 70.7 1.0
O A:HOH402 2.6 67.5 1.0
OD1 A:ASP177 2.7 64.6 1.0
C A:GLY173 3.3 71.9 1.0
C A:ASN175 3.4 65.3 1.0
C A:ASP141 3.5 69.0 1.0
CG A:ASP177 3.8 69.9 1.0
N A:ASP177 3.9 53.6 1.0
C A:ILE174 4.0 73.8 1.0
N A:ASN175 4.1 67.5 1.0
O A:ALA140 4.1 65.8 1.0
N A:GLY173 4.1 87.3 1.0
CA A:GLY176 4.2 72.3 1.0
CA A:ASP141 4.2 60.2 1.0
CA A:GLY173 4.2 66.9 1.0
N A:GLY176 4.2 65.1 1.0
N A:ILE174 4.2 70.3 1.0
O A:GLY171 4.3 67.6 1.0
O A:ILE174 4.3 65.7 1.0
C A:GLY176 4.3 65.2 1.0
CA A:ILE174 4.3 78.3 1.0
CA A:ASN175 4.3 66.2 1.0
OD2 A:ASP177 4.5 70.5 1.0
N A:ILE142 4.5 72.1 1.0
C A:PRO172 4.5 77.4 1.0
CA A:ASP177 4.7 62.0 1.0
CA A:ILE142 4.7 60.8 1.0
N A:MET143 4.8 56.7 1.0
CB A:ASP177 4.8 50.8 1.0
CH2 A:TRP92 4.9 54.9 1.0
O A:PRO172 4.9 76.7 1.0
CG A:MET143 4.9 73.2 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 Jul 16 11:17:14 2024

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