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Zinc in PDB 4fu4: Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain

Protein crystallography data

The structure of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain, PDB code: 4fu4 was solved by E.A.Stura, L.Vera, R.Visse, H.Nagase, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 2.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 127.080, 156.580, 106.140, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 24.7

Other elements in 4fu4:

The structure of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain (pdb code 4fu4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain, PDB code: 4fu4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4fu4

Go back to Zinc Binding Sites List in 4fu4
Zinc binding site 1 out of 4 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:17.2
occ:1.00
NE2 A:HIS226 2.1 16.7 1.0
NE2 A:HIS232 2.1 18.5 1.0
NE2 A:HIS222 2.2 14.8 1.0
CL C:CL101 3.0 25.6 1.0
CD2 A:HIS226 3.0 19.1 1.0
CD2 A:HIS232 3.0 18.3 1.0
CD2 A:HIS222 3.0 14.0 1.0
CE1 A:HIS226 3.1 19.5 1.0
CE1 A:HIS232 3.1 20.1 1.0
O C:ALA39 3.3 26.5 1.0
CE1 A:HIS222 3.4 15.4 1.0
C C:ALA39 3.4 21.6 1.0
N C:GLU40 3.5 21.6 1.0
CA C:GLU40 3.9 23.8 1.0
CB C:GLU40 4.0 17.8 1.0
O C:PHE38 4.1 27.0 1.0
ND1 A:HIS226 4.1 20.9 1.0
CG A:HIS226 4.2 20.4 1.0
CG A:HIS232 4.2 17.9 1.0
ND1 A:HIS232 4.2 19.6 1.0
CA C:ALA39 4.2 23.2 1.0
CG C:GLU40 4.2 15.9 1.0
N C:ALA39 4.2 25.3 1.0
C C:PHE38 4.2 24.6 1.0
CG A:HIS222 4.3 12.1 1.0
ND1 A:HIS222 4.4 11.7 1.0
CB C:PHE38 4.6 26.0 1.0

Zinc binding site 2 out of 4 in 4fu4

Go back to Zinc Binding Sites List in 4fu4
Zinc binding site 2 out of 4 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:36.3
occ:1.00
NE2 A:HIS172 2.0 37.6 1.0
OD2 A:ASP174 2.0 34.3 1.0
ND1 A:HIS200 2.2 27.1 1.0
NE2 A:HIS187 2.4 40.7 1.0
OD1 A:ASP174 2.6 39.4 1.0
CG A:ASP174 2.6 43.9 1.0
CE1 A:HIS172 2.9 42.8 1.0
CD2 A:HIS172 3.1 42.4 1.0
CG A:HIS200 3.1 31.1 1.0
CE1 A:HIS200 3.1 30.0 1.0
CD2 A:HIS187 3.4 33.3 1.0
CB A:HIS200 3.4 27.9 1.0
CE1 A:HIS187 3.4 38.7 1.0
O A:TYR176 4.0 47.8 1.0
ND1 A:HIS172 4.1 53.2 1.0
CB A:ASP174 4.1 48.0 1.0
CG A:HIS172 4.2 53.6 1.0
NE2 A:HIS200 4.2 34.4 1.0
CD2 A:HIS200 4.3 27.6 1.0
CE2 A:PHE178 4.5 37.7 1.0
ND1 A:HIS187 4.5 41.0 1.0
CG A:HIS187 4.5 40.2 1.0
CZ A:PHE178 4.6 33.9 1.0
CA A:HIS200 4.8 30.2 1.0
N A:ASP174 4.9 65.2 1.0

Zinc binding site 3 out of 4 in 4fu4

Go back to Zinc Binding Sites List in 4fu4
Zinc binding site 3 out of 4 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:12.9
occ:1.00
NE2 B:HIS232 2.0 14.4 1.0
NE2 B:HIS222 2.1 12.8 1.0
NE2 B:HIS226 2.1 9.1 1.0
CE1 B:HIS232 2.9 15.2 1.0
CD2 B:HIS232 2.9 11.3 1.0
CD2 B:HIS222 3.0 15.2 1.0
CL D:CL101 3.0 27.2 1.0
CE1 B:HIS226 3.0 9.1 1.0
CE1 B:HIS222 3.1 15.4 1.0
CD2 B:HIS226 3.1 11.1 1.0
O D:SER45 3.5 26.1 1.0
C D:SER45 3.7 20.1 1.0
ND1 B:HIS232 4.0 10.7 1.0
N D:TYR46 4.0 18.4 1.0
CG B:HIS232 4.0 10.0 1.0
CG B:HIS222 4.1 16.6 1.0
ND1 B:HIS226 4.1 9.5 1.0
ND1 B:HIS222 4.2 13.2 1.0
N D:SER45 4.2 20.0 1.0
CA D:TYR46 4.2 16.5 1.0
CG B:HIS226 4.2 10.6 1.0
CD1 D:TYR46 4.2 17.2 1.0
CB D:ARG44 4.3 12.1 1.0
CB D:TYR46 4.3 14.1 1.0
C D:ARG44 4.3 17.3 1.0
CA D:SER45 4.4 17.1 1.0
O D:ARG44 4.5 17.1 1.0
CG D:TYR46 4.6 16.9 1.0
CE B:MET240 4.6 11.5 1.0
CA D:ARG44 5.0 15.8 1.0

Zinc binding site 4 out of 4 in 4fu4

Go back to Zinc Binding Sites List in 4fu4
Zinc binding site 4 out of 4 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:14.2
occ:1.00
OD2 B:ASP174 1.9 21.1 1.0
NE2 B:HIS187 2.0 13.7 1.0
NE2 B:HIS172 2.1 21.0 1.0
ND1 B:HIS200 2.4 14.1 1.0
CG B:ASP174 2.7 31.6 1.0
CE1 B:HIS187 2.8 13.7 1.0
OD1 B:ASP174 2.9 26.8 1.0
CD2 B:HIS172 3.0 23.2 1.0
CD2 B:HIS187 3.1 12.3 1.0
CE1 B:HIS172 3.2 27.0 1.0
CG B:HIS200 3.3 15.2 1.0
CE1 B:HIS200 3.3 18.5 1.0
CB B:HIS200 3.5 11.4 1.0
ND1 B:HIS187 3.9 10.3 1.0
CG B:HIS187 4.1 13.0 1.0
CG B:HIS172 4.2 21.6 1.0
CB B:ASP174 4.2 29.4 1.0
O B:TYR176 4.2 19.3 1.0
ND1 B:HIS172 4.2 25.9 1.0
NE2 B:HIS200 4.4 17.6 1.0
CD2 B:HIS200 4.5 17.9 1.0
CE2 B:PHE178 4.6 15.0 1.0
CZ B:PHE178 4.6 15.9 1.0
O B:HOH627 4.8 23.0 1.0

Reference:

E.A.Stura, R.Visse, P.Cuniasse, V.Dive, H.Nagase. Crystal Structure of Full-Length Human Collagenase 3 (Mmp-13) with Peptides in the Active Site Defines Exosites in the Catalytic Domain. Faseb J. V. 27 4395 2013.
ISSN: ISSN 0892-6638
PubMed: 23913860
DOI: 10.1096/FJ.13-233601
Page generated: Wed Dec 16 05:18:07 2020

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