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Calcium in PDB 1g4k: X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

Enzymatic activity of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin

All present enzymatic activity of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin:
3.4.24.17;

Protein crystallography data

The structure of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin, PDB code: 1g4k was solved by P.Dunten, U.Kammlott, R.Crowther, W.Levin, L.H.Foley, P.Wang, R.Palermo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.800, 103.800, 147.490, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 28.4

Other elements in 1g4k:

The structure of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin (pdb code 1g4k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin, PDB code: 1g4k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1g4k

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Calcium binding site 1 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:18.2
occ:1.00
 OE2 A:GLU184 2.1 24.9 1.0
OD1 A:ASP158 2.1 18.2 1.0
O A:VAL163 2.3 20.1 1.0
O A:GLY159 2.4 23.4 1.0
OD2 A:ASP181 2.4 19.5 1.0
O A:GLY161 2.4 24.7 1.0
CD A:GLU184 3.3 22.1 1.0
CG A:ASP158 3.4 18.9 1.0
CG A:ASP181 3.4 17.9 1.0
C A:VAL163 3.4 18.0 1.0
C A:GLY159 3.6 21.5 1.0
C A:GLY161 3.6 25.3 1.0
N A:VAL163 4.0 21.0 1.0
CB A:ASP181 4.0 15.5 1.0
OD2 A:ASP158 4.0 20.5 1.0
N A:GLY161 4.1 25.3 1.0
OE1 A:GLU184 4.1 20.4 1.0
C A:PRO160 4.1 24.5 1.0
N A:GLY159 4.2 18.1 1.0
CA A:VAL163 4.2 21.7 1.0
C A:ASN162 4.3 23.0 1.0
N A:ASP158 4.3 17.7 1.0
C A:ASP158 4.3 20.1 1.0
OD1 A:ASP181 4.4 16.4 1.0
CA A:GLY161 4.4 23.2 1.0
CG A:GLU184 4.4 14.1 1.0
N A:LEU164 4.4 15.4 1.0
O A:PRO160 4.4 23.0 1.0
N A:PRO160 4.5 23.9 1.0
CA A:GLY159 4.5 20.8 1.0
CB A:ASP158 4.5 20.4 1.0
CA A:PRO160 4.5 24.9 1.0
CA A:LEU164 4.6 16.3 1.0
N A:ASN162 4.6 20.9 1.0
CA A:ASP158 4.6 21.6 1.0
O A:ASN162 4.7 23.2 1.0
CB A:VAL163 4.7 23.2 1.0
O A:ASP158 4.8 21.2 1.0
CA A:ASN162 4.8 21.2 1.0
CB A:ASN162 4.9 23.9 1.0

Calcium binding site 2 out of 9 in 1g4k

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Calcium binding site 2 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:16.3
occ:1.00
 O A:GLY173 2.2 16.3 1.0
O A:ASN175 2.3 11.7 1.0
OD1 A:ASP177 2.3 11.4 1.0
O A:HOH321 2.4 15.7 1.0
O A:HOH312 2.4 11.3 1.0
O A:ASP141 2.4 16.2 1.0
CG A:ASP177 3.3 14.7 1.0
C A:GLY173 3.4 17.6 1.0
C A:ASN175 3.4 12.0 1.0
C A:ASP141 3.6 14.2 1.0
OD2 A:ASP177 3.7 14.5 1.0
C A:ILE174 4.0 14.3 1.0
N A:ASP177 4.1 12.5 1.0
N A:ASN175 4.1 13.2 1.0
O A:ALA140 4.1 12.7 1.0
O A:ILE174 4.1 15.3 1.0
N A:GLY173 4.3 18.5 1.0
CA A:GLY173 4.3 18.9 1.0
N A:GLY176 4.3 13.4 1.0
O A:GLY171 4.3 19.9 1.0
CA A:ASP141 4.3 15.2 1.0
CA A:GLY176 4.4 11.7 1.0
C A:GLY176 4.4 15.1 1.0
N A:ILE174 4.4 18.6 1.0
CA A:ASN175 4.4 13.1 1.0
CA A:ILE174 4.4 16.1 1.0
CB A:ASP177 4.6 11.5 1.0
N A:ILE142 4.6 11.8 1.0
C A:PRO172 4.6 19.7 1.0
OE2 A:GLU139 4.6 30.4 1.0
O A:HOH323 4.7 18.7 1.0
CA A:ASP177 4.7 11.4 1.0
CA A:ILE142 4.7 12.5 1.0
N A:MET143 4.8 13.9 1.0
O A:PRO172 4.9 19.6 1.0
O A:HOH336 4.9 21.2 1.0
CH2 A:TRP92 4.9 19.1 1.0
CG A:MET143 4.9 16.4 1.0

Calcium binding site 3 out of 9 in 1g4k

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Calcium binding site 3 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:47.4
occ:1.00
 O A:GLU184 2.6 20.6 1.0
O A:ASP182 2.7 23.3 1.0
OD1 A:ASP182 2.8 18.0 1.0
OD2 A:ASP107 2.8 26.5 1.0
OD1 A:ASP107 3.0 21.9 1.0
CG A:ASP107 3.3 25.7 1.0
C A:ASP182 3.5 20.0 1.0
C A:GLU184 3.8 22.3 1.0
CG A:ASP182 3.8 20.7 1.0
OG1 A:THR105 3.8 21.1 1.0
CA A:ASP182 4.0 18.8 1.0
CB A:ASP182 4.3 15.4 1.0
N A:GLU184 4.3 21.6 1.0
CD1 A:TRP186 4.3 24.7 1.0
N A:ASP183 4.4 19.6 1.0
CA A:GLN185 4.5 24.5 1.0
C A:ASP183 4.5 24.0 1.0
OE1 A:GLN185 4.5 54.8 1.0
CD A:PRO106 4.6 16.1 1.0
N A:GLN185 4.6 23.2 1.0
CB A:ASP107 4.6 23.0 1.0
CA A:ASP183 4.7 21.6 1.0
CA A:GLU184 4.7 20.3 1.0
N A:TRP186 4.7 25.7 1.0
OD2 A:ASP182 4.8 17.5 1.0
NE1 A:TRP186 4.8 20.8 1.0
O A:HOH369 4.9 32.5 1.0

Calcium binding site 4 out of 9 in 1g4k

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Calcium binding site 4 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:13.7
occ:1.00
 OD1 B:ASP158 2.2 13.3 1.0
OD2 B:ASP181 2.2 13.9 1.0
OE2 B:GLU184 2.3 24.8 1.0
O B:GLY159 2.3 14.4 1.0
O B:VAL163 2.4 15.1 1.0
O B:GLY161 2.4 15.6 1.0
CG B:ASP181 3.4 12.8 1.0
CG B:ASP158 3.4 17.7 1.0
C B:GLY159 3.5 17.1 1.0
CD B:GLU184 3.5 17.1 1.0
C B:VAL163 3.5 16.0 1.0
C B:GLY161 3.6 19.7 1.0
N B:GLY161 3.9 18.7 1.0
N B:VAL163 4.0 14.3 1.0
CB B:ASP181 4.0 8.6 1.0
C B:PRO160 4.1 17.8 1.0
N B:GLY159 4.1 15.0 1.0
OD2 B:ASP158 4.1 14.7 1.0
OE1 B:GLU184 4.2 18.7 1.0
C B:ASP158 4.3 15.8 1.0
CA B:VAL163 4.3 16.1 1.0
N B:ASP158 4.3 17.9 1.0
CA B:GLY161 4.3 19.3 1.0
C B:ASN162 4.3 15.3 1.0
OD1 B:ASP181 4.3 12.4 1.0
CA B:GLY159 4.4 16.4 1.0
N B:PRO160 4.4 16.6 1.0
CA B:PRO160 4.5 17.0 1.0
O B:PRO160 4.5 20.0 1.0
CG B:GLU184 4.5 15.5 1.0
N B:LEU164 4.5 13.0 1.0
CB B:ASP158 4.6 17.4 1.0
O B:ASP158 4.6 13.9 1.0
CA B:LEU164 4.6 12.9 1.0
CA B:ASP158 4.6 17.4 1.0
N B:ASN162 4.7 17.2 1.0
O B:HOH381 4.7 20.8 1.0
CB B:VAL163 4.7 18.9 1.0
O B:ASN162 4.8 17.4 1.0
CA B:ASN162 4.9 15.9 1.0

Calcium binding site 5 out of 9 in 1g4k

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Calcium binding site 5 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:17.2
occ:1.00
 O B:GLY173 2.2 18.8 1.0
O B:ASP141 2.3 19.3 1.0
O B:HOH336 2.3 17.4 1.0
O B:ASN175 2.3 15.3 1.0
O B:HOH314 2.4 16.6 1.0
OD1 B:ASP177 2.4 16.4 1.0
CG B:ASP177 3.3 20.7 1.0
C B:GLY173 3.4 17.3 1.0
C B:ASP141 3.5 15.5 1.0
C B:ASN175 3.6 14.9 1.0
OD2 B:ASP177 3.8 18.0 1.0
C B:ILE174 4.0 16.5 1.0
N B:ASP177 4.1 13.8 1.0
O B:ALA140 4.1 20.2 1.0
O B:ILE174 4.1 17.6 1.0
N B:ASN175 4.2 15.8 1.0
CA B:ASP141 4.3 16.9 1.0
N B:GLY173 4.3 22.4 1.0
CA B:GLY173 4.3 20.4 1.0
N B:ILE174 4.4 18.1 1.0
N B:GLY176 4.4 16.7 1.0
C B:GLY176 4.4 16.5 1.0
CA B:GLY176 4.4 15.8 1.0
O B:HOH333 4.4 22.8 1.0
O B:GLY171 4.4 20.0 1.0
CA B:ILE174 4.4 17.7 1.0
CA B:ASN175 4.5 14.2 1.0
N B:ILE142 4.5 15.1 1.0
CB B:ASP177 4.5 13.8 1.0
O B:HOH332 4.5 28.9 1.0
N B:MET143 4.7 15.4 1.0
C B:PRO172 4.7 23.4 1.0
CA B:ASP177 4.7 13.8 1.0
CA B:ILE142 4.7 16.6 1.0
CG B:MET143 4.8 12.9 1.0
O B:PRO172 5.0 21.6 1.0

Calcium binding site 6 out of 9 in 1g4k

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Calcium binding site 6 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:41.9
occ:1.00
 O B:GLU184 2.7 18.8 1.0
OD2 B:ASP107 2.7 19.1 1.0
OD1 B:ASP182 2.8 17.9 1.0
O B:ASP182 2.9 16.0 1.0
OD1 B:ASP107 2.9 22.6 1.0
CG B:ASP107 3.1 24.2 1.0
C B:ASP182 3.6 16.0 1.0
OG1 B:THR105 3.7 11.5 1.0
CG B:ASP182 3.8 17.8 1.0
C B:GLU184 3.9 19.1 1.0
CA B:ASP182 4.1 14.8 1.0
CD1 B:TRP186 4.2 18.1 1.0
CB B:ASP182 4.4 13.5 1.0
CD B:PRO106 4.4 13.7 1.0
N B:GLU184 4.5 14.6 1.0
N B:ASP183 4.5 16.6 1.0
CB B:ASP107 4.5 16.7 1.0
C B:ASP183 4.6 16.1 1.0
CA B:GLN185 4.8 19.0 1.0
OD2 B:ASP182 4.8 18.4 1.0
NE1 B:TRP186 4.8 15.0 1.0
CA B:ASP183 4.8 14.5 1.0
CA B:GLU184 4.8 13.6 1.0
N B:GLN185 4.8 16.4 1.0
N B:TRP186 4.9 14.2 1.0

Calcium binding site 7 out of 9 in 1g4k

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Calcium binding site 7 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:60.3
occ:1.00
 OE2 C:GLU184 2.0 56.4 1.0
O C:VAL163 2.3 47.6 1.0
O C:GLY159 2.3 58.8 1.0
O C:GLY161 2.4 53.1 1.0
OD2 C:ASP181 2.8 60.4 1.0
CD C:GLU184 3.1 52.0 1.0
OD1 C:ASP158 3.1 60.9 1.0
C C:VAL163 3.4 47.0 1.0
C C:GLY161 3.5 53.7 1.0
CG C:ASP181 3.5 53.2 1.0
C C:GLY159 3.5 58.6 1.0
OE1 C:GLU184 3.7 52.0 1.0
C C:PRO160 3.9 56.8 1.0
N C:VAL163 3.9 49.5 1.0
CB C:ASP181 4.0 45.4 1.0
N C:GLY161 4.0 56.1 1.0
O C:PRO160 4.1 57.8 1.0
CG C:GLU184 4.1 54.3 1.0
CA C:VAL163 4.2 49.1 1.0
O C:ASP158 4.2 61.3 1.0
C C:ASP158 4.2 61.9 1.0
N C:LEU164 4.2 44.9 1.0
C C:ASN162 4.3 50.0 1.0
CA C:GLY161 4.3 54.3 1.0
OD1 C:ASP181 4.3 43.9 1.0
N C:GLY159 4.3 61.4 1.0
CG C:ASP158 4.3 55.0 1.0
CA C:PRO160 4.4 57.1 1.0
N C:PRO160 4.4 57.4 1.0
CA C:LEU164 4.4 43.2 1.0
N C:ASN162 4.5 53.6 1.0
CA C:GLY159 4.5 60.0 1.0
CB C:VAL163 4.6 53.4 1.0
N C:ASP158 4.6 64.7 1.0
CA C:ASN162 4.7 52.4 1.0
CD2 C:LEU164 4.7 54.5 1.0
CB C:ASN162 4.8 53.8 1.0
CA C:ASP158 4.8 63.2 1.0
O C:ASN162 4.8 48.6 1.0

Calcium binding site 8 out of 9 in 1g4k

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Calcium binding site 8 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:32.4
occ:1.00
 OD1 C:ASP177 2.2 26.6 1.0
O C:GLY173 2.2 36.8 1.0
O C:HOH322 2.3 33.1 1.0
O C:ASP141 2.3 24.2 1.0
O C:HOH313 2.5 23.0 1.0
O C:ASN175 2.5 31.4 1.0
CG C:ASP177 3.3 26.3 1.0
C C:GLY173 3.5 38.0 1.0
C C:ASP141 3.5 24.5 1.0
C C:ASN175 3.6 33.9 1.0
OD2 C:ASP177 3.9 35.3 1.0
O C:ALA140 4.0 28.9 1.0
C C:ILE174 4.1 33.2 1.0
N C:ASP177 4.1 31.5 1.0
N C:ASN175 4.1 33.4 1.0
CA C:ASP141 4.2 25.0 1.0
O C:ILE174 4.3 31.9 1.0
N C:ILE174 4.4 36.1 1.0
CA C:GLY173 4.4 38.1 1.0
C C:GLY176 4.4 31.1 1.0
O C:GLY171 4.4 40.6 1.0
CA C:GLY176 4.4 31.2 1.0
CA C:ILE174 4.5 34.6 1.0
N C:GLY173 4.5 38.7 1.0
N C:GLY176 4.5 32.3 1.0
CA C:ASN175 4.5 32.3 1.0
CB C:ASP177 4.5 31.2 1.0
N C:ILE142 4.5 23.6 1.0
OE2 C:GLU139 4.7 50.7 1.0
CA C:ASP177 4.7 32.1 1.0
C C:PRO172 4.8 40.2 1.0
CG C:MET143 4.8 34.8 1.0
N C:MET143 4.8 25.5 1.0
CA C:ILE142 4.8 24.1 1.0
O C:PRO172 4.9 40.7 1.0
CH2 C:TRP92 5.0 39.5 1.0
C C:ALA140 5.0 26.4 1.0

Calcium binding site 9 out of 9 in 1g4k

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Calcium binding site 9 out of 9 in the X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:68.0
occ:1.00
 O C:GLU184 2.3 45.3 1.0
OD2 C:ASP107 2.3 45.3 1.0
OD1 C:ASP107 2.8 50.4 1.0
OD1 C:ASP182 2.9 33.5 1.0
CG C:ASP107 2.9 45.7 1.0
O C:ASP182 3.0 40.4 1.0
C C:GLU184 3.5 44.8 1.0
C C:ASP182 3.7 41.0 1.0
OG1 C:THR105 3.8 39.4 1.0
CD1 C:TRP186 3.9 32.3 1.0
CG C:ASP182 3.9 31.4 1.0
N C:GLU184 4.1 45.1 1.0
CA C:ASP182 4.1 38.1 1.0
CA C:GLN185 4.2 44.8 1.0
N C:GLN185 4.3 44.9 1.0
CB C:ASP107 4.4 41.8 1.0
NE1 C:TRP186 4.4 36.1 1.0
CA C:GLU184 4.5 44.9 1.0
N C:ASP183 4.5 42.0 1.0
CB C:ASP182 4.5 42.7 1.0
N C:TRP186 4.5 43.8 1.0
C C:ASP183 4.6 45.9 1.0
OE1 C:GLN185 4.6 60.9 1.0
OD2 C:ASP182 4.8 43.2 1.0
CA C:ASP183 4.8 44.0 1.0
CG C:TRP186 4.9 33.5 1.0

Reference:

P.Dunten, U.Kammlott, R.Crowther, W.Levin, L.H.Foley, P.Wang, R.Palermo. X-Ray Structure of A Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin. Protein Sci. V. 10 923 2001.
ISSN: ISSN 0961-8368
PubMed: 11316871
DOI: 10.1110/PS.48401
Page generated: Thu Jul 11 08:30:01 2024

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