Atomistry » Calcium » PDB 1gk9-1gxo » 1gkc
Atomistry »
  Calcium »
    PDB 1gk9-1gxo »
      1gkc »

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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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

Go back to Calcium Binding Sites List in 1gkc
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: Mon Jul 7 15:15:47 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy