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Chlorine in PDB 4fvl: 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: 4fvl 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) 49.11 / 2.44
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 125.780, 157.270, 105.550, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 22.3

Other elements in 4fvl:

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

Calcium (Ca) 10 atoms
Zinc (Zn) 4 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 4fvl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4fvl:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4fvl

Go back to Chlorine Binding Sites List in 4fvl
Chlorine binding site 1 out of 3 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 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:14.8
occ:1.00
 CA A:CA506 2.7 34.5 1.0
N A:ILE293 3.4 15.7 1.0
N A:ALA385 3.5 15.5 1.0
N A:VAL434 3.5 12.5 1.0
N A:ALA337 3.6 18.7 1.0
CA A:ALA292 3.7 16.7 1.0
CA A:ALA433 3.7 14.1 1.0
O A:ALA385 3.7 19.7 1.0
O A:ALA337 3.7 21.2 1.0
CA A:ALA384 3.8 17.1 1.0
O A:ILE293 3.8 22.6 1.0
CB A:ALA292 3.8 12.4 1.0
O A:VAL434 3.9 16.1 1.0
CA A:ALA336 3.9 15.7 1.0
C A:ALA292 4.1 12.9 1.0
CB A:ALA384 4.1 11.2 1.0
CB A:ALA433 4.1 16.1 1.0
C A:ALA433 4.1 15.7 1.0
C A:ALA384 4.1 21.6 1.0
CB A:ALA336 4.2 13.3 1.0
C A:ALA336 4.3 17.1 1.0
CA A:ALA385 4.5 17.7 1.0
CG1 A:VAL434 4.5 13.6 1.0
CA A:ILE293 4.5 19.3 1.0
C A:ALA385 4.5 21.1 1.0
C A:ILE293 4.5 18.6 1.0
C A:ALA337 4.6 21.3 1.0
CA A:ALA337 4.6 23.6 1.0
CA A:VAL434 4.6 14.9 1.0
C A:VAL434 4.7 14.5 1.0
O A:ASP291 4.8 19.5 1.0
N A:ALA433 4.9 13.2 1.0
O A:ASP432 4.9 17.4 1.0
N A:ALA292 4.9 18.9 1.0
O A:ASP335 4.9 16.1 1.0
CB A:ALA385 4.9 21.5 1.0
O A:SER383 5.0 18.9 1.0
N A:ALA384 5.0 18.6 1.0
CB A:ALA337 5.0 17.0 1.0

Chlorine binding site 2 out of 3 in 4fvl

Go back to Chlorine Binding Sites List in 4fvl
Chlorine binding site 2 out of 3 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 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:Cl509

b:38.0
occ:1.00
 O A:HOH647 2.6 28.3 1.0
O A:HOH621 3.1 19.4 1.0
CA A:CA506 3.1 34.5 1.0
CG2 A:THR294 3.3 27.3 1.0
O A:ILE293 3.6 22.6 1.0
O A:VAL434 3.7 16.1 1.0
O A:ALA385 3.7 19.7 1.0
CG2 A:VAL386 3.8 16.4 1.0
CA A:VAL386 3.9 19.1 1.0
CA A:THR294 3.9 20.0 1.0
O A:ALA337 3.9 21.2 1.0
CB A:TYR435 3.9 18.0 1.0
CA A:TYR435 4.0 22.4 1.0
CA A:TYR338 4.0 24.3 1.0
CB A:TYR338 4.0 22.9 1.0
CB A:VAL386 4.1 23.4 1.0
CB A:THR294 4.1 25.9 1.0
N A:HIS387 4.4 31.1 1.0
C A:ILE293 4.5 18.6 1.0
N A:GLU339 4.6 31.0 1.0
C A:ALA385 4.6 21.1 1.0
N A:THR294 4.7 18.1 1.0
C A:VAL434 4.7 14.5 1.0
C A:VAL386 4.7 26.8 1.0
OG1 A:THR294 4.7 30.3 1.0
N A:VAL386 4.8 20.0 1.0
C A:ALA337 4.8 21.3 1.0
N A:SER295 4.8 23.1 1.0
N A:GLU436 4.8 27.4 1.0
C A:TYR338 4.8 27.2 1.0
C A:THR294 4.9 22.9 1.0
N A:TYR435 4.9 17.2 1.0
N A:TYR338 4.9 22.6 1.0
C A:TYR435 5.0 24.0 1.0

Chlorine binding site 3 out of 3 in 4fvl

Go back to Chlorine Binding Sites List in 4fvl
Chlorine binding site 3 out of 3 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:Cl508

b:21.3
occ:1.00
 CA B:CA506 2.8 42.3 1.0
N B:VAL434 3.5 16.6 1.0
N B:ILE293 3.6 23.2 1.0
N B:ALA385 3.6 21.4 1.0
O B:ALA337 3.6 30.9 1.0
N B:ALA337 3.6 17.5 1.0
O B:ALA385 3.7 20.9 1.0
O B:VAL434 3.7 18.0 1.0
O B:ILE293 3.7 23.4 1.0
CA B:ALA433 3.8 19.5 1.0
CA B:ALA292 3.8 21.5 1.0
CA B:ALA384 3.8 19.4 1.0
CB B:ALA292 3.9 20.4 1.0
CA B:ALA336 4.0 25.7 1.0
CB B:ALA384 4.0 14.5 1.0
CB B:ALA433 4.1 15.5 1.0
C B:ALA433 4.1 18.1 1.0
C B:ALA292 4.2 21.7 1.0
C B:ALA384 4.2 23.9 1.0
C B:ALA336 4.3 23.1 1.0
CG1 B:VAL434 4.4 20.4 1.0
CB B:ALA336 4.4 20.9 1.0
C B:VAL434 4.5 21.3 1.0
CA B:VAL434 4.5 20.3 1.0
C B:ALA385 4.5 24.0 1.0
C B:ALA337 4.5 23.7 1.0
C B:ILE293 4.5 25.8 1.0
CA B:ALA385 4.6 24.1 1.0
CA B:ILE293 4.6 24.7 1.0
CA B:ALA337 4.6 24.3 1.0
O B:ASP291 4.8 26.6 1.0
O B:ASP432 4.8 20.2 1.0
O B:ASP335 5.0 24.4 1.0
N B:ALA433 5.0 21.9 1.0
O B:SER383 5.0 21.8 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: Sun Jul 21 14:08:54 2024

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