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Calcium in PDB 7s7m: Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

Enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD)

All present enzymatic activity of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) 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/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 7s7m was solved by M.Coban, M.Raeeszadeh-Sarmazdeh, B.Sankaran, A.Hockla, E.S.Radisky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.63 / 3.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.28, 69.28, 318.98, 90, 90, 120
R / Rfree (%) 20.2 / 24.8

Other elements in 7s7m:

The structure of Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) 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/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) (pdb code 7s7m). 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/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD), PDB code: 7s7m:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7s7m

Go back to Calcium Binding Sites List in 7s7m
Calcium binding site 1 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) 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/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:58.6
occ:1.00
 O A:GLY173 2.2 58.1 1.0
O A:ASN175 2.4 74.7 1.0
O A:HOH405 2.5 42.3 1.0
OD1 A:ASP177 2.5 74.8 1.0
O A:HOH401 2.5 28.0 1.0
O A:ASP141 2.5 65.3 1.0
C A:ASN175 3.3 63.7 1.0
C A:GLY173 3.4 60.1 1.0
CG A:ASP177 3.5 71.3 1.0
C A:ASP141 3.7 73.1 1.0
C A:ILE174 3.8 68.9 1.0
OD2 A:ASP177 3.9 77.3 1.0
N A:ASN175 3.9 64.1 1.0
N A:ASP177 4.1 66.6 1.0
O A:ILE174 4.1 74.8 1.0
N A:GLY176 4.1 56.2 1.0
C A:GLY176 4.1 60.8 1.0
CA A:GLY176 4.1 47.6 1.0
CA A:ASN175 4.2 59.1 1.0
CA A:ILE174 4.3 59.7 1.0
N A:ILE174 4.3 61.2 1.0
O A:ALA140 4.3 73.7 1.0
N A:GLY173 4.3 66.4 1.0
O A:GLY171 4.4 71.1 1.0
CA A:GLY173 4.4 67.3 1.0
CA A:ASP141 4.5 72.6 1.0
N A:ILE142 4.6 73.0 1.0
CB A:ASP177 4.7 71.5 1.0
CA A:ILE142 4.7 75.1 1.0
CA A:ASP177 4.7 70.4 1.0
C A:PRO172 4.7 66.9 1.0
O A:GLY176 4.8 61.0 1.0
N A:MET143 4.9 70.8 1.0
CH2 A:TRP92 5.0 67.2 1.0

Calcium binding site 2 out of 3 in 7s7m

Go back to Calcium Binding Sites List in 7s7m
Calcium binding site 2 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) 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/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:102.2
occ:1.00
 O A:GLU184 2.2 57.8 1.0
O A:ASP182 2.2 95.9 1.0
OD2 A:ASP107 2.4 101.8 1.0
O A:HOH410 2.5 64.5 1.0
OD1 A:ASP107 2.6 116.2 1.0
OD1 A:ASP182 2.7 79.6 1.0
CG A:ASP107 2.8 111.8 1.0
C A:ASP182 3.4 83.1 1.0
C A:GLU184 3.4 77.0 1.0
CG A:ASP182 3.8 71.6 1.0
CA A:ASP182 4.1 71.4 1.0
N A:GLU184 4.2 87.0 1.0
CA A:GLN185 4.2 98.2 1.0
N A:GLN185 4.2 86.8 1.0
C A:ASP183 4.2 95.7 1.0
CB A:ASP107 4.3 116.5 1.0
N A:ASP183 4.4 85.7 1.0
CA A:GLU184 4.4 82.8 1.0
OG1 A:THR105 4.4 74.0 1.0
CA A:ASP183 4.5 96.0 1.0
CB A:ASP182 4.5 66.2 1.0
CD1 A:TRP186 4.7 73.8 1.0
OD2 A:ASP182 4.7 85.1 1.0
O A:ASP183 4.7 110.1 1.0

Calcium binding site 3 out of 3 in 7s7m

Go back to Calcium Binding Sites List in 7s7m
Calcium binding site 3 out of 3 in the Complex of Tissue Inhibitor of Metalloproteinases-1 (Timp-1) Mutant (L34G/M66D/T98G/P131S/Q153N) 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/M66D/T98G/P131S/Q153N) with Matrix Metalloproteinase-3 Catalytic Domain (Mmp-3CD) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:66.6
occ:1.00
 O A:VAL163 2.2 68.1 1.0
O A:GLY159 2.2 70.8 1.0
OD2 A:ASP181 2.3 65.9 1.0
OE2 A:GLU184 2.4 88.0 1.0
O A:GLY161 2.5 71.0 1.0
OD1 A:ASP158 2.5 85.8 1.0
C A:VAL163 3.4 70.7 1.0
CG A:ASP181 3.4 67.1 1.0
C A:GLY159 3.5 78.1 1.0
C A:GLY161 3.5 80.6 1.0
CD A:GLU184 3.6 78.9 1.0
N A:GLY161 3.7 73.2 1.0
CG A:ASP158 3.7 82.8 1.0
N A:VAL163 3.9 71.1 1.0
CB A:ASP181 4.1 60.6 1.0
C A:PRO160 4.1 78.0 1.0
C A:ASP158 4.2 82.9 1.0
CA A:VAL163 4.2 70.1 1.0
CA A:GLY161 4.2 74.4 1.0
N A:GLY159 4.2 74.1 1.0
CA A:PRO160 4.2 78.7 1.0
N A:PRO160 4.3 83.4 1.0
C A:ASN162 4.3 69.2 1.0
O A:ASP158 4.3 89.7 1.0
OD2 A:ASP158 4.4 83.2 1.0
N A:ASP158 4.4 77.9 1.0
OD1 A:ASP181 4.4 69.0 1.0
OE1 A:GLU184 4.4 86.0 1.0
CA A:GLY159 4.4 83.2 1.0
N A:LEU164 4.5 78.0 1.0
N A:ASN162 4.5 83.1 1.0
CG A:GLU184 4.6 64.3 1.0
CA A:ASP158 4.6 82.9 1.0
CA A:LEU164 4.7 77.1 1.0
CB A:VAL163 4.7 54.3 1.0
CB A:ASP158 4.7 86.0 1.0
O A:ASN162 4.7 75.2 1.0
CA A:ASN162 4.8 74.8 1.0
CB A:ASN162 4.9 86.0 1.0
O A:PRO160 5.0 88.5 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 03:57:42 2024

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