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Calcium in PDB 7s7l: Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

All present enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) 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/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 7s7l was solved by M.Coban, M.Raeeszadeh-Sarmazdeh, A.Hockla, B.Sankaran, E.S.Radisky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.60 / 2.34
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.332, 69.332, 312.215, 90, 90, 120
R / Rfree (%) 20.6 / 23.9

Other elements in 7s7l:

The structure of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
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/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) (pdb code 7s7l). 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/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 7s7l:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7s7l

Go back to Calcium Binding Sites List in 7s7l
Calcium binding site 1 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) 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/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:39.1
occ:1.00
 O A:HOH404 2.4 25.4 0.9
OD1 A:ASP177 2.4 54.9 1.0
O A:ASN175 2.4 41.9 1.0
O A:ASP141 2.4 45.7 1.0
O A:GLY173 2.5 53.9 1.0
CG A:ASP177 3.4 57.5 1.0
C A:ASN175 3.5 48.4 1.0
C A:ASP141 3.5 49.4 1.0
C A:GLY173 3.7 62.4 1.0
O A:ALA140 3.8 50.2 1.0
OD2 A:ASP177 3.9 61.1 1.0
N A:ASP177 4.0 33.1 1.0
C A:ILE174 4.1 53.7 1.0
N A:ASN175 4.2 49.3 1.0
CA A:GLY176 4.2 46.6 1.0
C A:GLY176 4.2 40.6 1.0
O A:GLY171 4.3 46.1 1.0
CA A:ASP141 4.3 51.9 1.0
N A:GLY176 4.3 50.6 1.0
O A:ILE174 4.3 54.1 1.0
N A:ILE142 4.4 47.2 1.0
CA A:ASN175 4.5 48.1 1.0
N A:GLY173 4.5 53.5 1.0
CA A:ILE174 4.5 41.4 1.0
N A:ILE174 4.5 53.7 1.0
CG A:MET143 4.6 45.3 1.0
CA A:GLY173 4.6 54.7 1.0
N A:MET143 4.6 36.0 1.0
CB A:ASP177 4.6 48.2 1.0
CA A:ILE142 4.7 36.8 1.0
CA A:ASP177 4.7 45.2 1.0
CH2 A:TRP92 4.7 49.8 1.0
C A:ALA140 4.8 51.9 1.0
C A:PRO172 4.9 54.5 1.0
O A:GLY176 5.0 45.5 1.0

Calcium binding site 2 out of 3 in 7s7l

Go back to Calcium Binding Sites List in 7s7l
Calcium binding site 2 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) 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/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:39.0
occ:1.00
 O A:VAL163 2.2 34.9 1.0
O A:GLY159 2.2 42.4 1.0
OE2 A:GLU184 2.3 53.7 1.0
OD2 A:ASP181 2.3 34.7 1.0
OD1 A:ASP158 2.4 34.7 1.0
O A:GLY161 2.5 63.7 1.0
C A:VAL163 3.3 23.4 1.0
CG A:ASP181 3.4 40.9 1.0
C A:GLY159 3.5 53.8 1.0
CD A:GLU184 3.6 63.0 1.0
CG A:ASP158 3.6 54.9 1.0
C A:GLY161 3.6 54.8 1.0
N A:VAL163 3.8 39.2 1.0
N A:GLY161 4.0 40.5 1.0
CB A:ASP181 4.0 43.4 1.0
CA A:VAL163 4.1 26.2 1.0
N A:GLY159 4.1 48.5 1.0
C A:PRO160 4.1 50.0 1.0
C A:ASP158 4.1 61.3 1.0
N A:ASP158 4.2 54.5 1.0
OE1 A:GLU184 4.2 69.5 1.0
OD2 A:ASP158 4.3 56.1 1.0
CA A:GLY159 4.4 42.5 1.0
N A:PRO160 4.4 67.2 1.0
OD1 A:ASP181 4.4 43.3 1.0
CA A:PRO160 4.4 51.1 1.0
N A:LEU164 4.4 33.8 1.0
C A:ASN162 4.4 53.9 1.0
CA A:GLY161 4.4 37.7 1.0
O A:ASP158 4.4 56.7 1.0
CB A:VAL163 4.4 44.1 1.0
O A:PRO160 4.5 63.5 1.0
CA A:ASP158 4.5 54.9 1.0
CB A:ASP158 4.6 57.7 1.0
N A:ASN162 4.6 52.0 1.0
CG A:GLU184 4.6 61.3 1.0
CA A:LEU164 4.6 37.2 1.0
CA A:ASN162 4.8 37.9 1.0
CB A:ASN162 4.9 52.7 1.0

Calcium binding site 3 out of 3 in 7s7l

Go back to Calcium Binding Sites List in 7s7l
Calcium binding site 3 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66S/E67Y/L133N/S155L) 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/M66S/E67Y/L133N/S155L) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:67.6
occ:1.00
 OD2 A:ASP107 2.3 71.8 1.0
O A:ASP182 2.4 64.5 1.0
O A:GLU184 2.4 70.4 1.0
OD1 A:ASP107 2.4 89.1 1.0
OD1 A:ASP182 2.5 57.9 1.0
CG A:ASP107 2.7 78.3 1.0
C A:GLU184 3.5 54.9 1.0
C A:ASP182 3.5 45.4 1.0
CG A:ASP182 3.7 61.8 1.0
CA A:GLN185 3.9 60.0 1.0
NE2 A:GLN185 3.9 103.1 1.0
CD A:GLN185 4.1 105.7 1.0
N A:GLN185 4.1 54.3 1.0
CG A:GLN185 4.1 94.6 1.0
CA A:ASP182 4.2 47.2 1.0
CB A:ASP107 4.2 74.9 1.0
OG1 A:THR105 4.2 56.7 1.0
CB A:ASP182 4.4 43.8 1.0
C A:ASP183 4.6 39.8 1.0
OD2 A:ASP182 4.6 57.5 1.0
N A:GLU184 4.6 58.3 1.0
N A:ASP183 4.6 48.6 1.0
CB A:GLN185 4.6 72.6 1.0
OE1 A:GLN185 4.7 105.3 1.0
CA A:GLU184 4.7 61.2 1.0
CA A:ASP183 4.8 51.7 1.0
CD1 A:TRP186 4.8 42.8 1.0
N A:TRP186 4.8 53.9 1.0
O A:HOH410 4.9 54.9 1.0
O A:ASP183 4.9 63.1 1.0
C A:GLN185 4.9 50.5 1.0

Reference:

M.Raeeszadeh-Sarmazdeh, M.Coban, S.Mahajan, A.Hockla, B.Sankaran, G.P.Downey, D.C.Radisky, E.S.Radisky. Engineering of Tissue Inhibitor of Metalloproteinases Timp-1 For Fine Discrimination Between Closely Related Stromelysins Mmp-3 and Mmp-10. J.Biol.Chem. V. 298 01654 2022.
ISSN: ESSN 1083-351X
PubMed: 35101440
DOI: 10.1016/J.JBC.2022.101654
Page generated: Fri Jul 19 03:57:06 2024

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