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Zinc in PDB 4g0d: Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain

Protein crystallography data

The structure of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4g0d 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) 49.50 / 2.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.260, 105.900, 101.180, 90.00, 102.11, 90.00
R / Rfree (%) 16.9 / 24.1

Other elements in 4g0d:

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

Chlorine (Cl) 8 atoms
Calcium (Ca) 23 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain (pdb code 4g0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4g0d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4g0d

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Zinc binding site 1 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


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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) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:17.5
occ:1.00
 NE2 A:HIS222 2.1 18.1 1.0
NE2 A:HIS232 2.1 16.2 1.0
NE2 A:HIS226 2.2 14.5 1.0
O W:HOH101 2.8 10.0 1.0
CD2 A:HIS226 2.9 18.4 1.0
CD2 A:HIS222 3.0 18.0 1.0
CD2 A:HIS232 3.0 19.4 1.0
O W:SER45 3.0 18.0 1.0
CE1 A:HIS222 3.1 17.0 1.0
CE1 A:HIS232 3.2 14.9 1.0
CE1 A:HIS226 3.4 19.4 1.0
C W:SER45 3.7 22.3 1.0
CB W:TYR46 4.0 20.2 1.0
CG A:HIS222 4.1 16.3 1.0
CA W:TYR46 4.1 18.4 1.0
CG A:HIS226 4.1 14.7 1.0
CG A:HIS232 4.1 19.4 1.0
ND1 A:HIS222 4.2 17.3 1.0
N W:TYR46 4.2 16.7 1.0
ND1 A:HIS232 4.2 19.8 1.0
CD1 W:TYR46 4.2 17.6 1.0
CB W:ARG44 4.2 22.9 1.0
ND1 A:HIS226 4.3 12.6 1.0
CG W:TYR46 4.3 20.5 1.0
CE A:MET240 4.4 8.3 1.0
O W:ARG44 4.5 21.8 1.0
C W:ARG44 4.5 19.8 1.0
N W:SER45 4.6 25.0 1.0
CA W:SER45 4.6 26.4 1.0

Zinc binding site 2 out of 8 in 4g0d

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Zinc binding site 2 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides 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) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:25.2
occ:1.00
 NE2 A:HIS172 1.9 34.0 1.0
NE2 A:HIS187 2.0 34.7 1.0
ND1 A:HIS200 2.1 19.1 1.0
OD2 A:ASP174 2.1 21.0 1.0
CE1 A:HIS172 2.8 37.0 1.0
CE1 A:HIS187 2.8 30.8 1.0
CG A:ASP174 2.8 35.8 1.0
OD1 A:ASP174 2.9 35.0 1.0
CD2 A:HIS172 3.0 31.9 1.0
CG A:HIS200 3.1 17.6 1.0
CE1 A:HIS200 3.1 29.1 1.0
CD2 A:HIS187 3.2 31.3 1.0
CB A:HIS200 3.4 28.8 1.0
ND1 A:HIS172 3.9 31.6 1.0
ND1 A:HIS187 4.0 23.9 1.0
CG A:HIS172 4.1 32.2 1.0
O A:TYR176 4.1 40.1 1.0
CG A:HIS187 4.2 24.3 1.0
NE2 A:HIS200 4.2 26.1 1.0
CD2 A:HIS200 4.3 19.4 1.0
CB A:ASP174 4.3 34.3 1.0
CZ A:PHE178 4.6 30.6 1.0
O A:HOH767 4.8 33.6 1.0
CE2 A:PHE178 4.8 28.0 1.0
CA A:HIS200 4.9 20.2 1.0

Zinc binding site 3 out of 8 in 4g0d

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Zinc binding site 3 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides 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) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:13.4
occ:1.00
 NE2 B:HIS226 2.1 8.2 1.0
NE2 B:HIS232 2.1 13.9 1.0
NE2 B:HIS222 2.1 11.6 1.0
O X:HOH107 2.8 12.9 1.0
O X:SER45 2.9 18.4 1.0
CD2 B:HIS222 2.9 8.0 1.0
CD2 B:HIS232 3.0 13.6 1.0
CD2 B:HIS226 3.0 18.2 1.0
CE1 B:HIS226 3.1 17.8 1.0
CE1 B:HIS232 3.1 12.5 1.0
CE1 B:HIS222 3.2 14.3 1.0
C X:SER45 3.6 17.5 1.0
CB X:TYR46 4.1 16.4 1.0
CG B:HIS222 4.1 9.5 1.0
ND1 B:HIS232 4.1 17.5 1.0
CG B:HIS232 4.1 19.5 1.0
ND1 B:HIS226 4.2 17.7 1.0
ND1 B:HIS222 4.2 18.0 1.0
CG B:HIS226 4.2 12.4 1.0
N X:TYR46 4.2 12.0 1.0
CA X:TYR46 4.2 20.2 1.0
N X:SER45 4.2 11.1 1.0
CB X:ARG44 4.3 15.9 1.0
CD1 X:TYR46 4.3 8.9 1.0
CG X:TYR46 4.4 15.6 1.0
CA X:SER45 4.4 17.0 1.0
C X:ARG44 4.5 15.2 1.0
CE B:MET240 4.7 16.9 1.0
O X:ARG44 4.9 15.9 1.0

Zinc binding site 4 out of 8 in 4g0d

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Zinc binding site 4 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides 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) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:18.2
occ:1.00
 NE2 B:HIS172 2.0 22.8 1.0
OD2 B:ASP174 2.0 12.6 1.0
NE2 B:HIS187 2.0 14.5 1.0
ND1 B:HIS200 2.2 14.6 1.0
CG B:ASP174 2.8 23.0 1.0
CE1 B:HIS172 2.9 17.6 1.0
CD2 B:HIS187 2.9 18.2 1.0
OD1 B:ASP174 3.0 26.0 1.0
CD2 B:HIS172 3.1 16.4 1.0
CG B:HIS200 3.1 13.6 1.0
CE1 B:HIS187 3.1 21.5 1.0
CE1 B:HIS200 3.2 20.3 1.0
CB B:HIS200 3.3 15.8 1.0
ND1 B:HIS172 4.0 26.2 1.0
CG B:HIS187 4.1 21.1 1.0
CG B:HIS172 4.1 25.5 1.0
ND1 B:HIS187 4.1 17.5 1.0
O B:TYR176 4.2 33.8 1.0
CD2 B:HIS200 4.2 20.8 1.0
CB B:ASP174 4.3 27.1 1.0
NE2 B:HIS200 4.3 16.0 1.0
CZ B:PHE178 4.6 15.5 1.0
O B:HOH723 4.6 26.1 1.0
CA B:HIS200 4.8 13.1 1.0
CE2 B:PHE178 4.8 13.6 1.0
O B:HOH602 4.9 18.1 1.0

Zinc binding site 5 out of 8 in 4g0d

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Zinc binding site 5 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:19.8
occ:1.00
 NE2 C:HIS222 2.1 11.1 1.0
NE2 C:HIS226 2.2 13.7 1.0
NE2 C:HIS232 2.2 23.7 1.0
CL Y:CL101 2.4 39.5 1.0
CE1 C:HIS222 3.0 15.8 1.0
CD2 C:HIS226 3.0 18.3 1.0
CD2 C:HIS232 3.1 22.6 1.0
CE1 C:HIS232 3.1 18.1 1.0
CD2 C:HIS222 3.2 14.4 1.0
CE1 C:HIS226 3.3 21.8 1.0
O Y:SER45 3.6 27.1 1.0
C Y:SER45 4.0 22.2 1.0
ND1 C:HIS232 4.1 20.4 1.0
ND1 C:HIS222 4.1 16.1 1.0
CG C:HIS232 4.1 16.2 1.0
O C:HOH715 4.2 15.7 1.0
CG C:HIS226 4.2 22.0 1.0
CG C:HIS222 4.2 23.6 1.0
CB Y:ARG44 4.2 31.7 1.0
CA Y:TYR46 4.2 15.8 1.0
N Y:TYR46 4.3 25.6 1.0
ND1 C:HIS226 4.3 16.9 1.0
CD1 Y:TYR46 4.4 17.7 1.0
CB Y:TYR46 4.4 19.7 1.0
O Y:ARG44 4.5 30.6 1.0
C Y:ARG44 4.5 22.2 1.0
CG Y:TYR46 4.6 22.8 1.0
CE C:MET240 4.6 12.8 1.0
N Y:SER45 4.7 26.4 1.0
CA Y:SER45 4.8 14.9 1.0

Zinc binding site 6 out of 8 in 4g0d

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Zinc binding site 6 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:29.0
occ:1.00
 OD2 C:ASP174 1.9 38.4 1.0
ND1 C:HIS200 2.0 29.9 1.0
NE2 C:HIS172 2.0 20.4 1.0
NE2 C:HIS187 2.1 26.5 1.0
CG C:ASP174 2.9 46.6 1.0
CE1 C:HIS200 2.9 32.4 1.0
CD2 C:HIS172 3.0 34.0 1.0
CE1 C:HIS187 3.0 33.2 1.0
CG C:HIS200 3.0 29.5 1.0
CE1 C:HIS172 3.0 34.4 1.0
CD2 C:HIS187 3.3 24.3 1.0
OD1 C:ASP174 3.3 33.2 1.0
CB C:HIS200 3.4 20.4 1.0
NE2 C:HIS200 4.0 34.5 1.0
CB C:ASP174 4.1 37.1 1.0
CG C:HIS172 4.1 31.8 1.0
CD2 C:HIS200 4.1 33.7 1.0
ND1 C:HIS172 4.1 29.9 1.0
ND1 C:HIS187 4.2 24.2 1.0
CG C:HIS187 4.3 26.5 1.0
O C:TYR176 4.4 41.5 1.0
CE2 C:PHE178 4.7 28.5 1.0
CZ C:PHE178 4.7 28.4 1.0
O C:HOH710 4.7 33.6 1.0
CA C:HIS200 4.9 23.8 1.0
O C:HOH780 4.9 22.0 1.0

Zinc binding site 7 out of 8 in 4g0d

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Zinc binding site 7 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:14.3
occ:1.00
 NE2 D:HIS226 2.1 24.1 1.0
NE2 D:HIS222 2.1 12.2 1.0
NE2 D:HIS232 2.2 19.4 1.0
CL Z:CL101 2.4 32.8 1.0
CD2 D:HIS232 2.8 14.3 1.0
CE1 D:HIS226 3.0 18.7 1.0
CE1 D:HIS222 3.1 15.0 1.0
CD2 D:HIS222 3.1 8.8 1.0
CD2 D:HIS226 3.2 18.2 1.0
CE1 D:HIS232 3.2 15.3 1.0
O Z:SER45 3.4 20.6 1.0
C Z:SER45 4.0 14.5 1.0
CG D:HIS232 4.0 13.8 1.0
ND1 D:HIS226 4.1 24.6 1.0
ND1 D:HIS222 4.2 16.4 1.0
ND1 D:HIS232 4.2 11.4 1.0
CB Z:ARG44 4.2 23.8 1.0
CG D:HIS222 4.2 17.1 1.0
O D:HOH714 4.2 13.1 1.0
CG D:HIS226 4.3 18.4 1.0
N Z:SER45 4.4 17.3 1.0
CB Z:TYR46 4.4 9.7 1.0
CD1 Z:TYR46 4.4 19.5 1.0
CA Z:TYR46 4.5 13.9 1.0
N Z:TYR46 4.5 10.4 1.0
C Z:ARG44 4.5 17.1 1.0
CE D:MET240 4.6 13.5 1.0
CG Z:TYR46 4.6 18.2 1.0
O Z:ARG44 4.7 25.1 1.0
CA Z:SER45 4.7 14.0 1.0

Zinc binding site 8 out of 8 in 4g0d

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Zinc binding site 8 out of 8 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:18.8
occ:1.00
 NE2 D:HIS187 2.0 17.4 1.0
NE2 D:HIS172 2.0 11.6 1.0
ND1 D:HIS200 2.1 17.3 1.0
OD2 D:ASP174 2.1 26.9 1.0
CE1 D:HIS187 2.9 12.3 1.0
CD2 D:HIS172 2.9 19.7 1.0
CG D:ASP174 2.9 23.3 1.0
CE1 D:HIS200 3.1 20.0 1.0
OD1 D:ASP174 3.1 18.4 1.0
CD2 D:HIS187 3.1 11.3 1.0
CE1 D:HIS172 3.1 21.4 1.0
CG D:HIS200 3.1 15.3 1.0
CB D:HIS200 3.4 14.1 1.0
ND1 D:HIS187 4.0 18.4 1.0
CG D:HIS172 4.1 11.1 1.0
O D:TYR176 4.2 29.6 1.0
ND1 D:HIS172 4.2 14.6 1.0
CG D:HIS187 4.2 24.6 1.0
NE2 D:HIS200 4.2 14.7 1.0
CD2 D:HIS200 4.2 13.9 1.0
CB D:ASP174 4.3 11.1 1.0
O D:HOH617 4.5 18.9 1.0
CZ D:PHE178 4.7 20.6 1.0
CE2 D:PHE178 4.8 13.4 1.0
CA D:HIS200 5.0 12.8 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: Sat Oct 26 23:04:06 2024

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