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Calcium in PDB 1gkc: MMP9-Inhibitor Complex

Enzymatic activity of MMP9-Inhibitor Complex

All present enzymatic activity of MMP9-Inhibitor Complex:
3.4.24.35;

Protein crystallography data

The structure of MMP9-Inhibitor Complex, PDB code: 1gkc was solved by S.Rowsell, R.A.Pauptit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.30 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.005, 56.005, 262.655, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1gkc:

The structure of MMP9-Inhibitor Complex also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the MMP9-Inhibitor Complex (pdb code 1gkc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the MMP9-Inhibitor Complex, PDB code: 1gkc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1gkc

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Calcium binding site 1 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1444

b:25.4
occ:1.00
 O A:GLY183 2.4 32.1 1.0
O A:LEU187 2.5 23.8 1.0
OD2 A:ASP205 2.5 18.1 1.0
O A:ASP185 2.6 25.7 1.0
OD1 A:ASP182 2.7 31.0 1.0
OE2 A:GLU208 2.7 35.0 1.0
CD A:GLU208 3.3 29.7 1.0
CG A:ASP205 3.5 19.0 1.0
C A:ASP185 3.5 26.9 1.0
C A:GLY183 3.6 32.2 1.0
C A:LEU187 3.6 24.5 1.0
N A:ASP185 3.9 30.6 1.0
CG A:ASP182 3.9 30.0 1.0
CG A:GLU208 4.0 27.3 1.0
OE1 A:GLU208 4.0 36.5 1.0
CB A:ASP205 4.0 17.5 1.0
N A:LEU187 4.0 26.0 1.0
C A:LYS184 4.1 32.0 1.0
CA A:ASP185 4.1 29.0 1.0
N A:GLY183 4.2 31.9 1.0
C A:ASP182 4.3 31.8 1.0
CA A:LEU187 4.4 25.0 1.0
O A:LYS184 4.4 34.1 1.0
OD1 A:ASP205 4.4 18.9 1.0
N A:ASP182 4.4 28.5 1.0
CA A:GLY183 4.5 31.1 1.0
C A:GLY186 4.5 26.2 1.0
N A:GLY186 4.5 24.6 1.0
OD2 A:ASP182 4.5 31.9 1.0
N A:LYS184 4.5 32.1 1.0
N A:LEU188 4.6 22.4 1.0
CA A:LYS184 4.6 33.0 1.0
O A:ASP182 4.6 34.0 1.0
CA A:LEU188 4.6 20.1 1.0
CA A:ASP182 4.7 29.8 1.0
CA A:GLY186 4.8 26.4 1.0
CB A:LEU187 4.8 25.5 1.0
CB A:ASP182 4.9 28.8 1.0

Calcium binding site 2 out of 10 in 1gkc

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Calcium binding site 2 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1445

b:28.9
occ:1.00
 O A:GLY197 2.5 26.4 1.0
O A:ASP165 2.5 20.9 1.0
OD1 A:ASP201 2.6 15.2 1.0
O A:GLN199 2.6 20.6 1.0
O A:HOH2028 2.8 23.2 1.0
O A:HOH2039 2.8 22.8 1.0
CG A:ASP201 3.5 18.5 1.0
C A:ASP165 3.6 19.5 1.0
C A:GLY197 3.7 25.9 1.0
C A:GLN199 3.8 23.3 1.0
OD2 A:ASP201 3.9 19.3 1.0
O A:HOH2042 4.1 34.2 1.0
C A:ILE198 4.2 29.1 1.0
O A:ALA164 4.2 18.9 1.0
N A:ASP201 4.3 17.2 1.0
N A:GLN199 4.3 27.9 1.0
CA A:ASP165 4.3 20.0 1.0
O A:ILE198 4.4 28.3 1.0
C A:GLY200 4.4 18.7 1.0
O A:GLY195 4.5 29.2 1.0
CA A:GLY200 4.6 19.2 1.0
CA A:ILE198 4.6 27.4 1.0
N A:GLY197 4.6 28.2 1.0
N A:ILE166 4.6 18.9 1.0
N A:ILE198 4.6 24.6 1.0
CA A:GLY197 4.6 26.4 1.0
N A:GLY200 4.6 23.1 1.0
N A:VAL167 4.6 16.4 1.0
CA A:GLN199 4.7 28.1 1.0
CA A:ILE166 4.7 18.3 1.0
CG2 A:VAL167 4.7 18.1 1.0
CB A:ASP201 4.7 16.3 1.0
CA A:ASP201 4.8 19.0 1.0
C A:PRO196 4.9 29.4 1.0
O A:HOH2029 4.9 27.5 1.0
O A:GLY200 5.0 22.6 1.0

Calcium binding site 3 out of 10 in 1gkc

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Calcium binding site 3 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1446

b:49.1
occ:1.00
 OD2 A:ASP131 2.6 19.1 1.0
O A:ASP206 2.7 24.0 1.0
O A:GLU208 2.7 18.2 1.0
OD1 A:ASP206 2.8 26.4 1.0
OD1 A:ASP131 3.1 23.8 1.0
CG A:ASP131 3.2 22.0 1.0
CG A:ASP206 3.4 25.2 1.0
C A:ASP206 3.5 21.6 1.0
C A:GLU208 3.9 19.6 1.0
OG A:SER129 4.0 16.5 1.0
OD2 A:ASP206 4.0 24.2 1.0
CA A:ASP206 4.0 20.8 1.0
CD1 A:TRP210 4.2 15.1 1.0
CB A:ASP206 4.3 22.4 1.0
N A:GLU208 4.4 20.4 1.0
N A:ASP207 4.4 23.3 1.0
C A:ASP207 4.5 21.4 1.0
CB A:ASP131 4.6 20.5 1.0
CA A:LEU209 4.6 17.5 1.0
CA A:ASP207 4.7 22.1 1.0
N A:LEU209 4.7 18.1 1.0
N A:TRP210 4.7 15.7 1.0
CA A:GLU208 4.8 21.0 1.0
NE1 A:TRP210 4.9 15.3 1.0
N A:ASP131 5.0 23.8 1.0

Calcium binding site 4 out of 10 in 1gkc

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Calcium binding site 4 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1447

b:56.1
occ:1.00
 O A:HOH2047 2.6 16.7 1.0
O A:LEU212 2.7 19.8 1.0
O A:HOH2050 2.7 21.1 1.0
O A:LYS214 2.7 22.1 1.0
O A:GLY213 3.1 20.3 1.0
OG A:SER211 3.2 17.5 1.0
C A:LYS214 3.2 21.4 1.0
C A:LEU212 3.5 17.0 1.0
C A:GLY213 3.5 19.7 1.0
CA A:GLY215 3.6 20.6 1.0
N A:GLY215 3.7 19.6 1.0
CB A:SER211 3.8 14.2 1.0
O A:GLN391 3.8 20.1 1.0
C A:GLY215 3.8 20.8 1.0
N A:LEU212 3.9 15.2 1.0
O A:GLY215 3.9 20.5 1.0
CD1 B:LEU212 3.9 12.5 1.0
N A:LYS214 4.0 20.8 1.0
N A:GLY213 4.1 19.3 1.0
CA A:LYS214 4.2 21.4 1.0
CA A:GLY213 4.2 20.3 1.0
CA A:LEU212 4.3 14.0 1.0
N A:GLN391 4.5 21.3 1.0
O B:HOH2015 4.7 22.0 1.0
C A:GLN391 4.7 20.9 1.0
C A:SER211 4.7 15.8 1.0
CB B:LEU212 4.9 12.6 1.0
CA A:SER211 4.9 13.2 1.0
O A:HOH2044 4.9 20.9 1.0

Calcium binding site 5 out of 10 in 1gkc

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Calcium binding site 5 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1452

b:99.9
occ:1.00
 O A:HOH2021 2.9 36.0 1.0
O A:SER149 3.0 30.5 1.0
O A:HOH2022 3.0 34.9 1.0
C A:SER149 4.1 28.6 1.0
O A:THR152 4.1 29.7 1.0
CA A:ALA150 4.4 27.5 1.0
O A:ALA150 4.6 28.8 1.0
N A:ALA150 4.7 27.5 1.0
C A:ALA150 4.7 28.6 1.0

Calcium binding site 6 out of 10 in 1gkc

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Calcium binding site 6 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1444

b:21.0
occ:1.00
 O B:LEU187 2.4 17.9 1.0
O B:GLY183 2.5 25.6 1.0
OD2 B:ASP205 2.6 22.7 1.0
OD1 B:ASP182 2.6 35.3 1.0
O B:ASP185 2.7 32.4 1.0
OE2 B:GLU208 2.7 40.0 1.0
CD B:GLU208 3.4 33.6 1.0
C B:LEU187 3.5 22.6 1.0
CG B:ASP205 3.5 17.7 1.0
C B:ASP185 3.6 31.6 1.0
C B:GLY183 3.7 29.4 1.0
CG B:ASP182 3.8 30.4 1.0
N B:LEU187 3.9 27.1 1.0
CB B:ASP205 4.0 17.0 1.0
N B:ASP185 4.0 30.0 1.0
OE1 B:GLU208 4.1 36.6 1.0
CG B:GLU208 4.1 30.0 1.0
N B:GLY183 4.2 30.9 1.0
CA B:LEU187 4.2 25.8 1.0
CA B:ASP185 4.3 30.5 1.0
C B:LYS184 4.3 28.9 1.0
C B:GLY186 4.3 27.9 1.0
C B:ASP182 4.4 30.4 1.0
N B:ASP182 4.4 28.6 1.0
OD2 B:ASP182 4.4 33.1 1.0
N B:LEU188 4.4 22.2 1.0
OD1 B:ASP205 4.4 24.2 1.0
N B:GLY186 4.5 29.4 1.0
CA B:LEU188 4.6 22.3 1.0
CA B:GLY183 4.6 29.1 1.0
N B:LYS184 4.6 29.1 1.0
CA B:GLY186 4.7 27.8 1.0
CB B:LEU187 4.7 27.9 1.0
CA B:LYS184 4.7 30.3 1.0
O B:LYS184 4.7 30.5 1.0
CA B:ASP182 4.7 30.0 1.0
O B:ASP182 4.8 30.5 1.0
CB B:ASP182 4.9 30.0 1.0
O B:GLY186 5.0 29.2 1.0

Calcium binding site 7 out of 10 in 1gkc

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Calcium binding site 7 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1445

b:25.8
occ:1.00
 O B:GLN199 2.5 25.6 1.0
O B:ASP165 2.5 19.1 1.0
O B:GLY197 2.5 21.2 1.0
O B:HOH2030 2.6 22.7 1.0
OD1 B:ASP201 2.6 14.4 1.0
O B:HOH2041 2.8 18.3 1.0
C B:GLN199 3.6 23.8 1.0
CG B:ASP201 3.6 19.4 1.0
C B:ASP165 3.6 20.9 1.0
C B:GLY197 3.7 23.1 1.0
OD2 B:ASP201 4.0 16.3 1.0
C B:ILE198 4.1 26.4 1.0
N B:ASP201 4.2 18.7 1.0
N B:GLN199 4.2 26.6 1.0
C B:GLY200 4.3 20.1 1.0
O B:HOH2044 4.3 22.2 1.0
O B:ILE198 4.3 27.1 1.0
O B:ALA164 4.3 18.6 1.0
CA B:GLY200 4.3 18.4 1.0
CA B:ASP165 4.4 19.5 1.0
N B:GLY200 4.4 23.4 1.0
O B:GLY195 4.4 27.6 1.0
CA B:GLN199 4.5 26.5 1.0
N B:ILE166 4.5 20.3 1.0
CA B:ILE198 4.6 26.3 1.0
N B:GLY197 4.6 24.1 1.0
N B:ILE198 4.6 24.4 1.0
CA B:GLY197 4.7 22.4 1.0
CA B:ILE166 4.7 17.2 1.0
N B:VAL167 4.7 13.4 1.0
CB B:ASP201 4.7 17.2 1.0
CA B:ASP201 4.8 18.7 1.0
CH2 B:TRP116 4.8 23.8 1.0
C B:PRO196 4.9 25.6 1.0
CG2 B:VAL167 4.9 12.8 1.0
O B:GLY200 4.9 21.3 1.0

Calcium binding site 8 out of 10 in 1gkc

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Calcium binding site 8 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1446

b:47.8
occ:1.00
 O B:GLU208 2.5 19.1 1.0
OD2 B:ASP131 2.5 18.0 1.0
O B:ASP206 2.7 22.8 1.0
O B:HOH2011 2.8 47.8 1.0
OD1 B:ASP206 2.9 22.7 1.0
CG B:ASP131 3.2 18.4 1.0
OD1 B:ASP131 3.2 21.0 1.0
C B:ASP206 3.4 22.0 1.0
CG B:ASP206 3.6 21.6 1.0
C B:GLU208 3.7 21.0 1.0
CA B:ASP206 3.9 19.1 1.0
OG B:SER129 4.1 14.9 1.0
CD1 B:TRP210 4.2 13.9 1.0
N B:GLU208 4.2 18.7 1.0
OD2 B:ASP206 4.2 24.4 1.0
CB B:ASP206 4.3 18.6 1.0
N B:ASP207 4.3 21.7 1.0
C B:ASP207 4.4 20.8 1.0
CA B:LEU209 4.5 18.0 1.0
N B:LEU209 4.5 18.6 1.0
CB B:ASP131 4.6 22.0 1.0
CA B:ASP207 4.6 20.6 1.0
N B:TRP210 4.6 17.9 1.0
CA B:GLU208 4.6 20.1 1.0
NE1 B:TRP210 4.7 15.8 1.0
O B:ASP207 4.9 23.3 1.0

Calcium binding site 9 out of 10 in 1gkc

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Calcium binding site 9 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1447

b:57.5
occ:1.00
 O B:LEU212 2.6 16.6 1.0
O B:HOH2052 2.6 18.0 1.0
O B:LYS214 2.9 23.2 1.0
O B:GLY213 3.0 21.7 1.0
OG B:SER211 3.1 12.6 1.0
C B:LEU212 3.3 16.9 1.0
C B:LYS214 3.4 22.1 1.0
C B:GLY213 3.5 21.2 1.0
CB B:SER211 3.6 16.8 1.0
N B:LEU212 3.6 15.9 1.0
O B:GLN391 3.7 20.0 1.0
N B:GLY215 3.9 18.8 1.0
CA B:GLY215 3.9 17.8 1.0
C B:GLY215 4.0 18.9 1.0
N B:GLY213 4.0 20.6 1.0
O B:GLY215 4.0 19.6 1.0
N B:LYS214 4.1 21.0 1.0
CA B:LEU212 4.1 15.4 1.0
O B:HOH2050 4.1 23.9 1.0
CD1 A:LEU212 4.1 8.7 1.0
CA B:GLY213 4.1 20.2 1.0
CA B:LYS214 4.3 21.6 1.0
C B:SER211 4.4 17.1 1.0
N B:GLN391 4.6 19.7 1.0
CA B:SER211 4.7 16.0 1.0
C B:GLN391 4.7 22.7 1.0
O A:HOH2015 4.9 14.3 1.0
CB A:LEU212 5.0 11.0 1.0

Calcium binding site 10 out of 10 in 1gkc

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Calcium binding site 10 out of 10 in the MMP9-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of MMP9-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1448

b:99.6
occ:1.00
 O B:HOH2022 2.9 51.0 1.0
O B:HOH2021 3.0 51.1 1.0
O B:THR152 3.2 33.9 1.0
O B:SER149 3.2 38.1 1.0
C B:THR152 4.3 34.4 1.0
C B:SER149 4.4 35.4 1.0
CA B:PRO153 4.7 35.3 1.0
O B:ALA150 4.7 35.9 1.0
C B:ALA150 4.9 36.3 1.0
CA B:ALA150 4.9 35.6 1.0
N B:PRO153 5.0 35.9 1.0

Reference:

S.Rowsell, P.Hawtin, C.A.Minshull, H.Jepson, S.Brockbank, D.Barratt, A.M.Slater, W.Mcpheat, D.Waterson, A.Henney, R.A.Pauptit. Crystal Structure of MMP9 in Complex with A Reverse Hydroxamate Inhibitor J.Mol.Biol. V. 319 173 2002.
ISSN: ISSN 0022-2836
PubMed: 12051944
DOI: 10.1016/S0022-2836(02)00262-0
Page generated: Thu Jul 11 08:43:43 2024

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