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

Calcium in PDB 1gkd: MMP9 Active Site Mutant-Inhibitor Complex

Enzymatic activity of MMP9 Active Site Mutant-Inhibitor Complex

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

Protein crystallography data

The structure of MMP9 Active Site Mutant-Inhibitor Complex, PDB code: 1gkd 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) 36.30 / 2.1
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.523, 56.523, 263.761, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1gkd:

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

Zinc (Zn) 4 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 1 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1444

b:24.0
occ:1.00
 O A:GLY183 2.4 25.9 1.0
OE2 A:GLU208 2.5 13.9 1.0
O A:LEU187 2.6 19.0 1.0
O A:ASP185 2.6 25.2 1.0
OD2 A:ASP205 2.6 15.2 1.0
OD1 A:ASP182 2.8 25.3 1.0
CD A:GLU208 3.4 13.4 1.0
C A:ASP185 3.5 25.3 1.0
CG A:ASP205 3.6 15.7 1.0
C A:LEU187 3.6 19.9 1.0
C A:GLY183 3.6 26.5 1.0
N A:ASP185 3.8 26.1 1.0
CG A:GLU208 4.0 13.2 1.0
N A:LEU187 4.0 21.2 1.0
CG A:ASP182 4.0 25.4 1.0
C A:LYS184 4.1 26.4 1.0
CB A:ASP205 4.1 14.2 1.0
CA A:ASP185 4.2 25.9 1.0
N A:GLY183 4.3 26.0 1.0
OE1 A:GLU208 4.3 14.3 1.0
CA A:LEU187 4.3 20.6 1.0
C A:GLY186 4.3 22.2 1.0
C A:ASP182 4.3 25.7 1.0
N A:ASP182 4.4 24.6 1.0
CA A:LYS184 4.5 27.5 1.0
N A:GLY186 4.5 24.6 1.0
N A:LYS184 4.5 27.0 1.0
OD1 A:ASP205 4.5 15.0 1.0
N A:LEU188 4.5 18.3 1.0
CA A:GLY183 4.6 26.3 1.0
O A:LYS184 4.6 26.0 1.0
CA A:LEU188 4.7 17.6 1.0
O A:ASP182 4.7 26.3 1.0
CA A:GLY186 4.7 23.5 1.0
OD2 A:ASP182 4.7 25.7 1.0
CB A:LEU187 4.7 21.5 1.0
CA A:ASP182 4.8 25.1 1.0
O A:GLY186 4.8 22.2 1.0
O A:HOH2049 4.9 21.8 1.0
CB A:ASP182 5.0 25.3 1.0

Calcium binding site 2 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 2 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1445

b:24.9
occ:1.00
 O A:GLY197 2.5 19.7 1.0
O A:ASP165 2.5 16.1 1.0
OD1 A:ASP201 2.6 14.8 1.0
O A:GLN199 2.6 18.8 1.0
O A:HOH2036 2.8 21.9 1.0
O A:HOH2052 2.8 17.9 1.0
CG A:ASP201 3.4 13.9 1.0
C A:GLN199 3.7 18.9 1.0
C A:ASP165 3.7 15.9 1.0
OD2 A:ASP201 3.7 13.0 1.0
C A:GLY197 3.7 21.1 1.0
O A:HOH2054 4.0 32.4 1.0
C A:ILE198 4.0 20.1 1.0
N A:ASP201 4.1 13.4 1.0
O A:ILE198 4.1 19.6 1.0
N A:GLN199 4.2 20.1 1.0
O A:ALA164 4.4 22.2 1.0
O A:HOH2053 4.4 36.0 1.0
C A:GLY200 4.4 15.4 1.0
CA A:GLY200 4.4 15.9 1.0
CA A:ILE198 4.5 20.2 1.0
N A:GLY200 4.5 17.9 1.0
O A:GLY195 4.5 22.7 1.0
CA A:ASP165 4.5 17.7 1.0
N A:ILE198 4.6 20.4 1.0
CA A:GLN199 4.6 20.0 1.0
CB A:ASP201 4.6 12.7 1.0
N A:ILE166 4.6 14.0 1.0
N A:VAL167 4.6 12.8 1.0
N A:GLY197 4.6 21.8 1.0
CA A:ILE166 4.7 12.9 1.0
CA A:GLY197 4.7 21.4 1.0
CA A:ASP201 4.7 13.7 1.0
CG2 A:VAL167 4.8 13.0 1.0
C A:PRO196 4.9 22.2 1.0

Calcium binding site 3 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 3 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1446

b:36.9
occ:1.00
 O A:ASP206 2.6 14.8 1.0
O A:GLU208 2.6 14.2 1.0
OD2 A:ASP131 2.6 17.4 1.0
OD1 A:ASP206 2.7 14.5 1.0
O A:HOH2014 2.8 33.3 1.0
O A:HOH2057 2.9 30.4 1.0
OD1 A:ASP131 3.1 19.2 1.0
CG A:ASP131 3.1 17.8 1.0
CG A:ASP206 3.5 14.8 1.0
C A:ASP206 3.5 14.6 1.0
C A:GLU208 3.7 14.9 1.0
O A:HOH2058 3.9 35.6 1.0
OG A:SER129 4.0 14.9 1.0
CA A:ASP206 4.1 14.2 1.0
OD2 A:ASP206 4.1 14.2 1.0
N A:GLU208 4.3 15.2 1.0
CB A:ASP206 4.3 14.2 1.0
CD1 A:TRP210 4.4 11.3 1.0
O A:HOH2060 4.4 44.8 1.0
CA A:LEU209 4.5 14.3 1.0
C A:ASP207 4.5 16.2 1.0
N A:LEU209 4.5 14.2 1.0
CB A:ASP131 4.6 17.9 1.0
N A:ASP207 4.6 15.0 1.0
CA A:GLU208 4.7 14.7 1.0
N A:TRP210 4.7 13.5 1.0
CA A:ASP207 4.8 15.9 1.0
NE1 A:TRP210 5.0 11.2 1.0

Calcium binding site 4 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 4 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1447

b:41.2
occ:1.00
 O A:HOH2069 2.6 20.6 1.0
O A:HOH2067 2.6 11.2 1.0
O A:LEU212 2.7 12.1 1.0
O A:LYS214 2.9 20.8 1.0
O A:GLY213 3.0 15.4 1.0
C A:LYS214 3.2 19.9 1.0
C A:GLY213 3.4 16.1 1.0
OG A:SER211 3.4 10.9 1.0
C A:LEU212 3.4 12.8 1.0
N A:GLY215 3.6 20.2 1.0
CA A:GLY215 3.7 20.8 1.0
O A:GLN391 3.8 17.6 1.0
C A:GLY215 3.8 21.5 1.0
O A:GLY215 3.9 21.6 1.0
CB A:SER211 3.9 10.2 1.0
N A:LEU212 3.9 12.0 1.0
N A:LYS214 3.9 17.7 1.0
N A:GLY213 4.0 14.0 1.0
CA A:LYS214 4.1 19.7 1.0
CA A:GLY213 4.1 14.8 1.0
CD1 B:LEU212 4.1 10.7 1.0
CA A:LEU212 4.3 12.0 1.0
N A:GLN391 4.5 20.7 1.0
O B:HOH2021 4.6 16.9 1.0
C A:GLN391 4.7 18.5 1.0
C A:SER211 4.7 10.9 1.0
O A:HOH2068 4.9 31.9 1.0
NH2 B:ARG143 4.9 14.0 1.0
CA A:SER211 5.0 11.0 1.0
CB B:LEU212 5.0 11.5 1.0

Calcium binding site 5 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 5 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1444

b:18.2
occ:1.00
 O B:GLY183 2.5 26.3 1.0
O B:LEU187 2.6 19.9 1.0
OD2 B:ASP205 2.6 13.9 1.0
O B:ASP185 2.6 27.0 1.0
OD1 B:ASP182 2.6 25.0 1.0
OE2 B:GLU208 2.7 16.2 1.0
C B:ASP185 3.5 26.6 1.0
CD B:GLU208 3.6 15.3 1.0
CG B:ASP205 3.6 14.6 1.0
C B:LEU187 3.6 20.4 1.0
C B:GLY183 3.7 27.1 1.0
CG B:ASP182 3.8 25.7 1.0
N B:ASP185 4.0 27.3 1.0
N B:LEU187 4.0 22.9 1.0
C B:LYS184 4.1 28.4 1.0
CB B:ASP205 4.2 13.8 1.0
N B:GLY183 4.2 26.2 1.0
C B:ASP182 4.2 25.6 1.0
CA B:ASP185 4.2 26.6 1.0
CG B:GLU208 4.2 14.8 1.0
C B:GLY186 4.2 23.6 1.0
N B:ASP182 4.3 24.3 1.0
OE1 B:GLU208 4.3 15.3 1.0
CA B:LEU187 4.4 21.5 1.0
N B:GLY186 4.4 25.7 1.0
O B:ASP182 4.4 25.8 1.0
O B:LYS184 4.5 29.5 1.0
CA B:GLY183 4.5 26.4 1.0
OD2 B:ASP182 4.5 26.8 1.0
CA B:GLY186 4.6 24.4 1.0
N B:LYS184 4.6 27.9 1.0
N B:LEU188 4.6 19.3 1.0
OD1 B:ASP205 4.6 15.7 1.0
CA B:LYS184 4.6 28.7 1.0
CA B:ASP182 4.6 24.9 1.0
O B:HOH2048 4.6 37.2 1.0
CA B:LEU188 4.7 19.2 1.0
O B:GLY186 4.7 23.4 1.0
CB B:LEU187 4.8 21.4 1.0
CB B:ASP182 4.8 24.9 1.0

Calcium binding site 6 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 6 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1445

b:25.9
occ:1.00
 O B:GLY197 2.5 16.8 1.0
O B:ASP165 2.5 13.3 1.0
O B:GLN199 2.6 17.4 1.0
OD1 B:ASP201 2.7 12.8 1.0
O B:HOH2039 2.7 18.4 1.0
O B:HOH2050 2.7 15.8 1.0
CG B:ASP201 3.5 13.2 1.0
C B:GLN199 3.6 17.6 1.0
C B:GLY197 3.7 18.3 1.0
C B:ASP165 3.7 14.4 1.0
O B:HOH2051 3.8 20.1 1.0
OD2 B:ASP201 3.9 11.0 1.0
O B:HOH2055 3.9 29.4 1.0
C B:ILE198 4.1 18.3 1.0
N B:GLN199 4.2 18.8 1.0
N B:ASP201 4.2 13.3 1.0
O B:ILE198 4.2 17.5 1.0
O B:GLY195 4.3 21.1 1.0
O B:ALA164 4.4 19.3 1.0
N B:GLY197 4.5 20.8 1.0
CA B:ILE198 4.5 18.6 1.0
N B:GLY200 4.5 17.1 1.0
C B:GLY200 4.5 15.2 1.0
CA B:ASP165 4.5 15.4 1.0
CA B:GLY200 4.5 16.1 1.0
CA B:GLN199 4.5 18.7 1.0
N B:ILE198 4.5 18.2 1.0
CA B:GLY197 4.6 19.3 1.0
N B:ILE166 4.6 13.3 1.0
CB B:ASP201 4.7 11.7 1.0
C B:PRO196 4.8 21.4 1.0
CA B:ILE166 4.8 12.9 1.0
N B:VAL167 4.8 12.9 1.0
CA B:ASP201 4.9 12.8 1.0
O B:HOH2035 4.9 33.9 1.0
CH2 B:TRP116 5.0 19.9 1.0
CG2 B:VAL167 5.0 14.0 1.0

Calcium binding site 7 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 7 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1446

b:37.2
occ:1.00
 O B:GLU208 2.4 16.1 1.0
O B:ASP206 2.5 14.1 1.0
OD2 B:ASP131 2.6 13.5 1.0
OD1 B:ASP206 2.8 14.5 1.0
O B:HOH2061 2.8 34.7 1.0
O B:HOH2015 2.9 27.4 1.0
CG B:ASP131 3.3 15.2 1.0
OD1 B:ASP131 3.3 15.6 1.0
C B:ASP206 3.4 14.3 1.0
CG B:ASP206 3.5 15.2 1.0
C B:GLU208 3.6 15.6 1.0
CA B:ASP206 3.9 13.3 1.0
OG B:SER129 4.1 11.7 1.0
OD2 B:ASP206 4.1 16.7 1.0
N B:GLU208 4.2 15.1 1.0
CD1 B:TRP210 4.3 12.0 1.0
CB B:ASP206 4.3 13.9 1.0
O B:HOH2059 4.3 33.9 1.0
C B:ASP207 4.3 15.3 1.0
CA B:LEU209 4.4 14.1 1.0
N B:ASP207 4.4 14.4 1.0
N B:LEU209 4.4 15.1 1.0
CA B:GLU208 4.5 15.1 1.0
N B:TRP210 4.6 14.3 1.0
CA B:ASP207 4.6 15.5 1.0
CB B:ASP131 4.6 15.9 1.0
O B:ASP207 4.8 16.1 1.0
NE1 B:TRP210 4.8 12.1 1.0
O B:HOH2057 4.9 38.8 1.0

Calcium binding site 8 out of 8 in 1gkd

Go back to Calcium Binding Sites List in 1gkd
Calcium binding site 8 out of 8 in the MMP9 Active Site Mutant-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 Active Site Mutant-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1447

b:36.1
occ:1.00
 O B:HOH2068 2.7 6.7 1.0
O B:LEU212 2.7 13.1 1.0
O B:HOH2070 2.7 19.7 1.0
O B:LYS214 2.8 22.1 1.0
O B:GLY213 3.0 16.9 1.0
C B:LYS214 3.2 21.1 1.0
C B:GLY213 3.3 16.9 1.0
C B:LEU212 3.3 13.6 1.0
OG B:SER211 3.4 13.6 1.0
N B:GLY215 3.7 21.3 1.0
CA B:GLY215 3.7 21.0 1.0
N B:LYS214 3.8 18.3 1.0
N B:LEU212 3.9 12.7 1.0
N B:GLY213 3.9 14.8 1.0
O B:GLN391 3.9 18.3 1.0
C B:GLY215 4.0 20.8 1.0
CD1 A:LEU212 4.0 9.4 1.0
CB B:SER211 4.0 14.2 1.0
CA B:GLY213 4.0 15.7 1.0
O B:GLY215 4.1 21.5 1.0
CA B:LYS214 4.1 20.0 1.0
O B:HOH2067 4.1 22.2 1.0
CA B:LEU212 4.2 13.0 1.0
O B:HOH2069 4.6 9.3 1.0
N B:GLN391 4.6 20.0 1.0
C B:SER211 4.7 13.5 1.0
CB A:LEU212 4.8 11.0 1.0
C B:GLN391 4.9 18.5 1.0
O B:HOH2065 4.9 19.8 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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy