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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

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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

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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

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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

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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

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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

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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

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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

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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

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