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Chlorine 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:

Calcium (Ca) 23 atoms
Zinc (Zn) 8 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl508

b:14.9
occ:1.00
 CA A:CA507 2.9 34.1 1.0
N A:ALA385 3.5 12.4 1.0
N A:ALA337 3.5 10.8 1.0
O A:ALA337 3.5 18.1 1.0
N A:ILE293 3.6 13.5 1.0
N A:VAL434 3.6 8.6 1.0
O A:ALA385 3.6 19.8 1.0
CA A:ALA433 3.8 10.8 1.0
CA A:ALA384 3.8 8.6 1.0
CA A:ALA292 3.8 11.3 1.0
O A:VAL434 3.9 10.2 1.0
CA A:ALA336 3.9 11.6 1.0
O A:ILE293 3.9 16.2 1.0
CB A:ALA292 4.0 8.3 1.0
CB A:ALA384 4.1 11.0 1.0
CB A:ALA336 4.1 15.5 1.0
C A:ALA384 4.1 10.1 1.0
CB A:ALA433 4.2 14.1 1.0
C A:ALA433 4.2 11.6 1.0
C A:ALA292 4.2 10.9 1.0
C A:ALA336 4.2 22.1 1.0
CG1 A:VAL434 4.3 7.6 1.0
C A:ALA337 4.4 18.8 1.0
CA A:ALA337 4.4 20.0 1.0
C A:ALA385 4.5 13.7 1.0
CA A:ALA385 4.5 10.3 1.0
CA A:VAL434 4.6 11.7 1.0
CA A:ILE293 4.6 12.3 1.0
C A:VAL434 4.6 13.5 1.0
C A:ILE293 4.7 12.5 1.0
O A:ASP432 4.8 19.6 1.0
O A:ASP291 4.8 17.0 1.0
O A:ASP335 4.9 19.1 1.0
N A:ALA433 5.0 10.0 1.0
CB A:ALA337 5.0 16.2 1.0

Chlorine binding site 2 out of 8 in 4g0d

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Chlorine binding site 2 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 Chlorine with other atoms in the Cl 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
B:Cl508

b:28.6
occ:1.00
 CA B:CA507 2.8 42.1 1.0
N B:VAL434 3.4 14.8 1.0
O B:ALA337 3.5 23.2 1.0
N B:ALA337 3.5 18.4 1.0
N B:ILE293 3.5 14.1 1.0
N B:ALA385 3.7 14.6 1.0
O B:ILE293 3.7 16.7 1.0
CA B:ALA433 3.7 15.1 1.0
O B:ALA385 3.7 28.2 1.0
O B:VAL434 3.8 20.8 1.0
CA B:ALA292 3.8 16.5 1.0
CA B:ALA336 3.9 24.1 1.0
CA B:ALA384 4.0 20.1 1.0
CB B:ALA433 4.0 13.1 1.0
CB B:ALA292 4.0 20.5 1.0
CB B:ALA384 4.0 12.8 1.0
C B:ALA433 4.1 19.9 1.0
C B:ALA292 4.2 9.7 1.0
C B:ALA336 4.2 24.7 1.0
CB B:ALA336 4.3 20.1 1.0
CG1 B:VAL434 4.3 17.5 1.0
C B:ALA384 4.4 17.8 1.0
CA B:VAL434 4.4 19.7 1.0
C B:ALA337 4.4 25.8 1.0
C B:VAL434 4.5 21.3 1.0
C B:ILE293 4.5 20.1 1.0
CA B:ALA337 4.5 19.4 1.0
CA B:ILE293 4.6 22.5 1.0
C B:ALA385 4.6 15.1 1.0
O B:ASP432 4.6 21.0 1.0
CA B:ALA385 4.7 17.9 1.0
O B:ASP291 4.7 18.8 1.0
O B:ASP335 4.9 19.9 1.0
CB B:ALA337 5.0 15.1 1.0
N B:ALA433 5.0 19.4 1.0

Chlorine binding site 3 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl510

b:34.3
occ:1.00
 O B:HOH736 2.7 16.3 1.0
O B:HOH641 2.9 21.3 1.0
OG1 B:THR294 3.0 22.4 1.0
CA B:CA507 3.0 42.1 1.0
CA B:TYR338 3.5 25.6 1.0
CB B:THR294 3.5 23.1 1.0
O B:ILE293 3.6 16.7 1.0
CA B:THR294 3.6 25.7 1.0
O B:ALA337 3.7 23.2 1.0
CB B:TYR338 3.7 18.1 1.0
O B:VAL434 3.8 20.8 1.0
CB B:TYR435 4.0 10.7 1.0
O B:ALA385 4.0 28.2 1.0
N B:GLU339 4.1 30.6 1.0
CA B:TYR435 4.2 18.5 1.0
CA B:VAL386 4.2 18.1 1.0
CG2 B:VAL386 4.2 12.1 1.0
N B:SER295 4.3 26.1 1.0
C B:TYR338 4.3 23.9 1.0
O B:HOH733 4.3 32.9 1.0
CB B:VAL386 4.4 20.8 1.0
N B:TYR338 4.4 25.7 1.0
C B:ILE293 4.4 20.1 1.0
C B:ALA337 4.4 25.8 1.0
C B:THR294 4.5 20.6 1.0
N B:THR294 4.5 12.1 1.0
N B:HIS387 4.6 32.9 1.0
C B:VAL434 4.8 21.3 1.0
C B:ALA385 4.9 15.1 1.0
C B:VAL386 5.0 28.5 1.0
N B:TYR435 5.0 17.8 1.0

Chlorine binding site 4 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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
C:Cl508

b:12.6
occ:1.00
 CA C:CA507 2.7 39.0 1.0
N C:ILE293 3.4 11.1 1.0
N C:ALA385 3.5 18.4 1.0
N C:ALA337 3.5 12.0 1.0
O C:ALA337 3.6 12.2 1.0
CA C:ALA292 3.6 9.6 1.0
CB C:ALA292 3.7 8.3 1.0
CA C:ALA384 3.7 12.1 1.0
O C:ILE293 3.8 17.0 1.0
N C:VAL434 3.8 8.1 1.0
O C:ALA385 3.9 26.2 1.0
CA C:ALA336 3.9 12.0 1.0
CA C:ALA433 3.9 9.3 1.0
CB C:ALA384 4.0 9.1 1.0
O C:VAL434 4.0 16.5 1.0
C C:ALA292 4.0 13.3 1.0
C C:ALA384 4.1 17.6 1.0
CB C:ALA336 4.1 12.5 1.0
C C:ALA336 4.2 14.5 1.0
CB C:ALA433 4.2 9.6 1.0
C C:ALA433 4.4 10.9 1.0
C C:ALA337 4.4 13.1 1.0
CA C:ALA337 4.4 15.7 1.0
C C:ILE293 4.5 19.7 1.0
CA C:ALA385 4.5 17.5 1.0
CA C:ILE293 4.5 11.3 1.0
CG1 C:VAL434 4.6 14.1 1.0
C C:ALA385 4.6 19.0 1.0
O C:ASP291 4.7 15.9 1.0
O C:SER383 4.8 18.1 1.0
O C:ASP432 4.8 22.5 1.0
CA C:VAL434 4.8 9.0 1.0
C C:VAL434 4.9 12.7 1.0
N C:ALA292 4.9 15.8 1.0
O C:ASP335 4.9 15.1 1.0
N C:ALA384 4.9 19.1 1.0
CB C:ALA385 5.0 18.4 1.0
CB C:ALA337 5.0 6.8 1.0

Chlorine binding site 5 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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
D:Cl508

b:38.6
occ:1.00
 CA D:CA507 2.9 54.1 1.0
O D:HOH676 3.1 23.5 1.0
O D:HOH657 3.3 27.0 1.0
OG1 D:THR294 3.4 27.4 1.0
CA D:THR294 3.6 30.7 1.0
CB D:THR294 3.6 29.5 1.0
O D:ILE293 3.7 20.2 1.0
CA D:TYR338 3.8 21.7 1.0
CB D:TYR435 3.8 24.1 1.0
O D:ALA337 3.9 25.3 1.0
O D:VAL434 3.9 23.2 1.0
CG2 D:VAL386 3.9 11.8 1.0
CB D:TYR338 3.9 22.2 1.0
O D:ALA385 4.0 35.0 1.0
CA D:TYR435 4.1 16.1 1.0
CA D:VAL386 4.1 27.7 1.0
CB D:VAL386 4.2 25.8 1.0
N D:GLU339 4.2 33.5 1.0
N D:SER295 4.3 28.8 1.0
C D:THR294 4.5 26.1 1.0
C D:ILE293 4.5 25.3 1.0
C D:TYR338 4.5 27.3 1.0
N D:THR294 4.5 28.7 1.0
O D:HOH607 4.5 29.0 1.0
N D:HIS387 4.7 32.9 1.0
C D:ALA337 4.7 18.1 1.0
N D:TYR338 4.7 22.6 1.0
C D:VAL434 4.8 16.6 1.0
N D:GLU436 4.9 22.6 1.0
C D:ALA385 4.9 24.1 1.0
N D:TYR435 5.0 11.2 1.0
C D:VAL386 5.0 30.3 1.0

Chlorine binding site 6 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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
D:Cl509

b:20.8
occ:1.00
 CA D:CA507 2.9 54.1 1.0
N D:VAL434 3.3 14.6 1.0
N D:ILE293 3.4 17.8 1.0
O D:ILE293 3.5 20.2 1.0
N D:ALA385 3.6 28.8 1.0
O D:ALA337 3.6 25.3 1.0
CA D:ALA433 3.6 12.6 1.0
O D:VAL434 3.7 23.2 1.0
N D:ALA337 3.7 15.2 1.0
CA D:ALA292 3.7 20.9 1.0
O D:ALA385 3.7 35.0 1.0
CB D:ALA292 3.8 14.6 1.0
CA D:ALA384 3.9 21.6 1.0
C D:ALA433 4.0 13.6 1.0
CB D:ALA384 4.0 15.2 1.0
CB D:ALA433 4.0 6.1 1.0
C D:ALA292 4.1 19.5 1.0
CA D:ALA336 4.2 19.4 1.0
C D:ALA384 4.3 30.2 1.0
CA D:VAL434 4.4 18.6 1.0
C D:ILE293 4.4 25.3 1.0
C D:VAL434 4.4 16.6 1.0
CA D:ILE293 4.4 21.6 1.0
C D:ALA336 4.5 17.3 1.0
CG1 D:VAL434 4.5 15.0 1.0
C D:ALA337 4.5 18.1 1.0
CB D:ALA336 4.5 19.8 1.0
C D:ALA385 4.6 24.1 1.0
CA D:ALA337 4.6 17.9 1.0
CA D:ALA385 4.6 24.8 1.0
O D:ASP432 4.7 17.0 1.0
N D:ALA433 4.8 13.8 1.0
O D:ASP291 4.9 16.9 1.0
N D:ALA292 5.0 23.1 1.0
CB D:ALA337 5.0 16.6 1.0

Chlorine binding site 7 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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
Y:Cl101

b:39.5
occ:1.00
 O C:HOH715 2.3 15.7 1.0
ZN C:ZN501 2.4 19.8 1.0
O Y:ARG44 2.9 30.6 1.0
C Y:SER45 2.9 22.2 1.0
N Y:TYR46 3.0 25.6 1.0
O Y:SER45 3.3 27.1 1.0
CA Y:SER45 3.4 14.9 1.0
C Y:ARG44 3.4 22.2 1.0
NE2 C:HIS222 3.4 11.1 1.0
CD2 C:HIS226 3.4 18.3 1.0
CB Y:TYR46 3.5 19.7 1.0
CA Y:TYR46 3.5 15.8 1.0
NE2 C:HIS226 3.6 13.7 1.0
N Y:SER45 3.6 26.4 1.0
CD2 C:HIS222 3.8 14.4 1.0
O C:ALA186 3.9 27.4 1.0
NE2 C:HIS232 4.2 23.7 1.0
CA C:HIS187 4.2 16.9 1.0
CB Y:ARG44 4.3 31.7 1.0
CG Y:TYR46 4.4 22.8 1.0
CA Y:ARG44 4.5 24.2 1.0
C C:ALA186 4.5 24.0 1.0
N C:ALA188 4.6 16.2 1.0
CE1 C:HIS232 4.6 18.1 1.0
CE1 C:HIS222 4.7 15.8 1.0
CG C:HIS226 4.8 22.0 1.0
N C:HIS187 4.8 20.5 1.0
C C:HIS187 4.8 20.4 1.0
CD1 Y:TYR46 4.9 17.7 1.0
CE1 C:HIS226 4.9 21.8 1.0
CB Y:SER45 4.9 24.1 1.0
C Y:TYR46 5.0 20.8 1.0

Chlorine binding site 8 out of 8 in 4g0d

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Chlorine 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 Chlorine with other atoms in the Cl 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
Z:Cl101

b:32.8
occ:1.00
 O D:HOH714 2.3 13.1 1.0
ZN D:ZN501 2.4 14.3 1.0
C Z:SER45 3.1 14.5 1.0
NE2 D:HIS226 3.2 24.1 1.0
O Z:ARG44 3.2 25.1 1.0
N Z:TYR46 3.3 10.4 1.0
O Z:SER45 3.3 20.6 1.0
CB Z:TYR46 3.3 9.7 1.0
NE2 D:HIS222 3.4 12.2 1.0
CD2 D:HIS226 3.4 18.2 1.0
CD2 D:HIS222 3.5 8.8 1.0
CA Z:SER45 3.5 14.0 1.0
C Z:ARG44 3.5 17.1 1.0
N Z:SER45 3.6 17.3 1.0
CA Z:TYR46 3.7 13.9 1.0
NE2 D:HIS232 4.1 19.4 1.0
CG Z:TYR46 4.2 18.2 1.0
O D:ALA186 4.3 21.1 1.0
CB Z:ARG44 4.4 23.8 1.0
CA D:HIS187 4.4 9.9 1.0
CE1 D:HIS226 4.4 18.7 1.0
N D:ALA188 4.6 15.4 1.0
CA Z:ARG44 4.6 16.6 1.0
CE1 D:HIS222 4.7 15.0 1.0
CD1 Z:TYR46 4.7 19.5 1.0
CG D:HIS226 4.7 18.4 1.0
C D:ALA186 4.8 20.5 1.0
CG D:HIS222 4.8 17.1 1.0
CE1 D:HIS232 4.8 15.3 1.0
C D:HIS187 4.9 18.9 1.0
N D:HIS187 5.0 13.7 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: Sun Jul 21 14:11:48 2024

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