Zinc in PDB 830c: Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid

Protein crystallography data

The structure of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid, PDB code: 830c was solved by B.Lovejoy, A.Welch, S.Carr, C.Luong, C.Broka, R.T.Hendricks, J.Campbell, K.Walker, R.Martin, H.Van Wart, M.F.Browner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.072, 36.098, 96.368, 90.00, 131.06, 90.00
R / Rfree (%) 20.8 / 26.6

Other elements in 830c:

The structure of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid (pdb code 830c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid, PDB code: 830c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 830c

Go back to Zinc Binding Sites List in 830c
Zinc binding site 1 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn272

b:11.1
occ:1.00
O43 A:RS11 1.8 18.4 1.0
NE2 A:HIS222 1.9 6.7 1.0
NE2 A:HIS226 2.0 11.6 1.0
O42 A:RS11 2.0 19.7 1.0
NE2 A:HIS232 2.1 13.5 1.0
HO A:RS11 2.7 0.0 1.0
N41 A:RS11 2.8 17.8 1.0
C40 A:RS11 2.8 17.5 1.0
CE1 A:HIS222 2.9 5.7 1.0
CD2 A:HIS222 2.9 7.2 1.0
CE1 A:HIS226 3.0 11.5 1.0
CD2 A:HIS232 3.0 12.6 1.0
CD2 A:HIS226 3.0 11.0 1.0
CE1 A:HIS232 3.1 13.6 1.0
HN A:RS11 3.8 0.0 1.0
OE2 A:GLU223 4.0 11.9 1.0
ND1 A:HIS222 4.0 7.0 1.0
CG A:HIS222 4.1 7.5 1.0
ND1 A:HIS226 4.1 11.3 1.0
H321 A:RS11 4.2 0.0 1.0
CG A:HIS226 4.2 11.4 1.0
CG A:HIS232 4.2 12.4 1.0
ND1 A:HIS232 4.2 12.9 1.0
H2 A:HOH289 4.2 0.0 1.0
C26 A:RS11 4.3 17.2 1.0
H332 A:RS11 4.3 0.0 1.0
O A:HOH289 4.3 13.3 1.0
C33 A:RS11 4.7 16.7 1.0
OE1 A:GLU223 4.7 11.6 1.0
O A:HOH369 4.7 24.1 1.0
CD A:GLU223 4.7 11.9 1.0
H1 A:HOH289 4.8 0.0 1.0
H252 A:RS11 4.8 0.0 1.0
C14 A:RS11 4.8 13.5 1.0
H14 A:RS11 4.8 0.0 1.0
C32 A:RS11 4.9 17.0 1.0
CE A:MET240 4.9 4.6 1.0
H302 A:RS11 4.9 0.0 1.0
HD1 A:HIS222 5.0 0.0 1.0
C13 A:RS11 5.0 14.1 1.0

Zinc binding site 2 out of 4 in 830c

Go back to Zinc Binding Sites List in 830c
Zinc binding site 2 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn273

b:11.6
occ:1.00
OD2 A:ASP174 1.7 9.8 1.0
NE2 A:HIS187 1.9 18.1 1.0
NE2 A:HIS172 1.9 8.3 1.0
ND1 A:HIS200 1.9 8.8 1.0
CE1 A:HIS187 2.7 18.4 1.0
CG A:ASP174 2.8 9.0 1.0
CD2 A:HIS172 2.9 8.8 1.0
CE1 A:HIS200 2.9 9.0 1.0
CE1 A:HIS172 3.0 8.2 1.0
CG A:HIS200 3.0 7.0 1.0
CD2 A:HIS187 3.1 16.4 1.0
OD1 A:ASP174 3.2 10.1 1.0
CB A:HIS200 3.5 7.8 1.0
ND1 A:HIS187 3.9 18.1 1.0
CG A:HIS172 4.0 9.0 1.0
NE2 A:HIS200 4.1 9.9 1.0
ND1 A:HIS172 4.1 8.2 1.0
O A:TYR176 4.1 11.0 1.0
CG A:HIS187 4.1 13.3 1.0
CD2 A:HIS200 4.1 9.6 1.0
CB A:ASP174 4.2 9.8 1.0
CE1 A:PHE189 4.5 15.4 1.0
HD1 A:HIS187 4.7 0.0 1.0
CZ A:PHE178 4.7 8.5 1.0
CE2 A:PHE178 4.8 9.9 1.0
H A:TYR176 4.8 0.0 1.0
CZ A:PHE189 4.8 14.8 1.0
CB A:TYR176 4.9 12.9 1.0
HE2 A:HIS200 4.9 0.0 1.0
C A:TYR176 5.0 9.2 1.0
CA A:HIS200 5.0 6.3 1.0
O A:HOH275 5.0 6.1 1.0
HD1 A:HIS172 5.0 0.0 1.0

Zinc binding site 3 out of 4 in 830c

Go back to Zinc Binding Sites List in 830c
Zinc binding site 3 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn272

b:11.8
occ:1.00
O42 B:RS11 1.9 20.0 1.0
O43 B:RS11 1.9 19.6 1.0
NE2 B:HIS222 1.9 8.9 1.0
NE2 B:HIS232 2.0 11.1 1.0
NE2 B:HIS226 2.1 16.1 1.0
HO B:RS11 2.7 0.0 1.0
C40 B:RS11 2.8 18.2 1.0
N41 B:RS11 2.8 18.2 1.0
CD2 B:HIS222 2.9 8.8 1.0
CE1 B:HIS232 3.0 11.5 1.0
CE1 B:HIS222 3.0 8.4 1.0
CD2 B:HIS232 3.0 10.7 1.0
CD2 B:HIS226 3.0 15.0 1.0
CE1 B:HIS226 3.1 16.0 1.0
HN B:RS11 3.8 0.0 1.0
CG B:HIS222 4.1 9.0 1.0
H321 B:RS11 4.1 0.0 1.0
ND1 B:HIS222 4.1 8.5 1.0
ND1 B:HIS232 4.1 11.4 1.0
H332 B:RS11 4.1 0.0 1.0
CG B:HIS232 4.1 11.2 1.0
OE2 B:GLU223 4.2 15.2 1.0
O B:HOH452 4.2 28.9 1.0
C26 B:RS11 4.2 16.6 1.0
CG B:HIS226 4.2 14.3 1.0
ND1 B:HIS226 4.2 15.5 1.0
O B:HOH297 4.4 13.8 1.0
C33 B:RS11 4.5 15.7 1.0
H1 B:HOH297 4.6 0.0 1.0
H14 B:RS11 4.6 0.0 1.0
H252 B:RS11 4.7 0.0 1.0
C14 B:RS11 4.7 12.4 1.0
H1 B:HOH452 4.7 0.0 1.0
OE1 B:GLU223 4.8 15.6 1.0
C32 B:RS11 4.8 15.4 1.0
CD B:GLU223 4.8 14.1 1.0
H2 B:HOH297 4.9 0.0 1.0
C13 B:RS11 4.9 10.7 1.0
H2 B:HOH452 4.9 0.0 1.0
O B:HOH329 4.9 30.3 1.0
C25 B:RS11 5.0 17.0 1.0
HD1 B:HIS232 5.0 0.0 1.0
H13 B:RS11 5.0 0.0 1.0

Zinc binding site 4 out of 4 in 830c

Go back to Zinc Binding Sites List in 830c
Zinc binding site 4 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn273

b:10.5
occ:1.00
OD2 B:ASP174 1.7 13.9 1.0
ND1 B:HIS200 1.9 7.3 1.0
NE2 B:HIS172 1.9 10.5 1.0
NE2 B:HIS187 2.0 10.3 1.0
CG B:ASP174 2.7 13.1 1.0
CE1 B:HIS187 2.8 9.6 1.0
CE1 B:HIS200 2.9 6.9 1.0
CD2 B:HIS172 2.9 8.6 1.0
CE1 B:HIS172 3.0 10.0 1.0
CG B:HIS200 3.0 6.3 1.0
OD1 B:ASP174 3.1 12.7 1.0
CD2 B:HIS187 3.1 10.0 1.0
CB B:HIS200 3.4 6.7 1.0
NE2 B:HIS200 4.0 7.7 1.0
ND1 B:HIS187 4.0 10.7 1.0
CG B:HIS172 4.1 10.2 1.0
ND1 B:HIS172 4.1 9.6 1.0
CD2 B:HIS200 4.1 6.3 1.0
CB B:ASP174 4.1 14.2 1.0
CG B:HIS187 4.2 9.6 1.0
O B:TYR176 4.3 14.8 1.0
O B:HOH412 4.3 26.6 1.0
O B:HOH436 4.5 20.8 1.0
H B:ASP174 4.6 0.0 1.0
CZ B:PHE178 4.6 8.9 1.0
CZ B:PHE189 4.7 18.0 1.0
CE1 B:PHE189 4.7 18.6 1.0
H2 B:HOH412 4.7 0.0 1.0
O B:HOH360 4.8 8.3 1.0
CE2 B:PHE178 4.8 8.5 1.0
HD1 B:HIS187 4.9 0.0 1.0
CA B:HIS200 4.9 7.0 1.0
HE2 B:HIS200 4.9 0.0 1.0
H B:TYR176 4.9 0.0 1.0
CB B:TYR176 4.9 15.6 1.0
HD1 B:HIS172 5.0 0.0 1.0

Reference:

B.Lovejoy, A.R.Welch, S.Carr, C.Luong, C.Broka, R.T.Hendricks, J.A.Campbell, K.A.Walker, R.Martin, H.Van Wart, M.F.Browner. Crystal Structures of Mmp-1 and -13 Reveal the Structural Basis For Selectivity of Collagenase Inhibitors. Nat.Struct.Biol. V. 6 217 1999.
ISSN: ISSN 1072-8368
PubMed: 10074939
DOI: 10.1038/6657
Page generated: Wed Dec 16 14:05:06 2020

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