Atomistry » Calcium » PDB 4fsd-4gg1 » 4fu4
Atomistry »
  Calcium »
    PDB 4fsd-4gg1 »
      4fu4 »

Calcium 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
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium where determined in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain, PDB code: 4fu4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 1 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca503

b:33.5
occ:1.00
 O A:GLY180 2.3 42.3 1.0
OE2 A:GLU205 2.3 29.5 1.0
OD2 A:ASP202 2.3 43.7 1.0
O A:LEU184 2.5 34.9 1.0
O A:SER182 2.5 43.4 1.0
OD1 A:ASP179 2.7 38.0 1.0
CD A:GLU205 3.1 40.1 1.0
CG A:ASP202 3.3 46.0 1.0
OE1 A:GLU205 3.3 36.3 1.0
C A:SER182 3.4 39.7 1.0
C A:GLY180 3.5 45.9 1.0
N A:SER182 3.5 46.0 1.0
C A:LEU184 3.7 29.3 1.0
C A:PRO181 3.8 43.4 1.0
CB A:ASP202 3.8 40.7 1.0
CA A:SER182 3.9 35.6 1.0
CG A:ASP179 3.9 46.9 1.0
CA A:PRO181 4.1 39.1 1.0
N A:PRO181 4.2 49.0 1.0
O A:PRO181 4.3 41.2 1.0
OD1 A:ASP202 4.3 51.5 1.0
N A:LEU184 4.4 35.8 1.0
C A:GLY183 4.4 34.3 1.0
N A:GLY180 4.4 31.4 1.0
CG A:GLU205 4.5 41.5 1.0
N A:GLY183 4.5 36.5 1.0
OD2 A:ASP179 4.5 47.4 1.0
CA A:GLY180 4.6 36.5 1.0
CA A:LEU184 4.6 28.7 1.0
N A:LEU185 4.6 27.7 1.0
O A:GLY183 4.6 32.4 1.0
CA A:LEU185 4.6 26.4 1.0
C A:ASP179 4.6 38.0 1.0
N A:ASP179 4.7 51.3 1.0
CA A:GLY183 4.8 35.5 1.0
CD1 A:LEU185 4.9 31.3 1.0

Calcium binding site 2 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 2 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca504

b:50.8
occ:1.00
 O A:ASP162 2.3 35.0 1.0
O A:ASN194 2.4 60.0 1.0
O A:GLY196 2.4 38.0 1.0
OD1 A:ASP198 2.6 36.4 1.0
C A:ASN194 3.4 59.4 1.0
C A:ASP162 3.5 31.4 1.0
C A:GLY196 3.6 35.6 1.0
CG A:ASP198 3.8 41.2 1.0
O A:ALA161 4.0 18.1 1.0
CA A:ASN194 4.1 59.5 1.0
CA A:ASP162 4.1 29.9 1.0
N A:GLY196 4.2 38.8 1.0
C A:TYR195 4.2 48.9 1.0
N A:ASP198 4.2 35.8 1.0
N A:TYR195 4.4 47.7 1.0
CA A:GLY196 4.4 37.7 1.0
OD2 A:ASP198 4.4 43.7 1.0
N A:GLY197 4.5 32.7 1.0
O A:TYR195 4.5 47.7 1.0
N A:ILE163 4.5 17.7 1.0
O A:PRO193 4.5 70.5 1.0
N A:MET164 4.6 31.0 1.0
CA A:GLY197 4.6 30.9 1.0
CG A:MET164 4.6 44.5 1.0
O A:GLY192 4.6 44.5 1.0
N A:ASN194 4.6 44.6 1.0
CA A:TYR195 4.6 46.3 1.0
C A:GLY197 4.7 29.2 1.0
CA A:ILE163 4.7 24.5 1.0
C A:PRO193 4.8 57.9 1.0
CB A:ASP198 4.8 39.4 1.0
CA A:ASP198 4.8 35.3 1.0
C A:ALA161 4.9 24.7 1.0

Calcium binding site 3 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 3 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca505

b:15.6
occ:1.00
 O A:ASP335 2.3 11.7 1.0
O A:ASP291 2.4 13.0 1.0
O A:SER383 2.4 9.3 1.0
O A:ASP432 2.5 13.3 1.0
O A:HOH610 2.7 15.5 1.0
C A:ASP335 3.4 16.1 1.0
C A:ASP291 3.5 12.3 1.0
C A:SER383 3.5 13.4 1.0
C A:ASP432 3.6 12.8 1.0
CA A:ASP335 4.0 17.3 1.0
CA A:ASP291 4.0 13.5 1.0
CA A:SER383 4.1 13.1 1.0
CA A:ASP432 4.1 11.8 1.0
N A:ALA336 4.5 17.1 1.0
N A:ALA292 4.6 10.9 1.0
N A:ALA384 4.6 12.4 1.0
O A:ILE334 4.7 23.6 1.0
NH1 A:ARG333 4.7 38.4 1.0
CB A:SER383 4.7 9.1 1.0
N A:ALA433 4.7 11.2 1.0
CB A:ASP335 4.8 15.8 1.0
CB A:ASP291 4.8 27.7 1.0
CB A:ASP432 4.8 9.8 1.0
O A:LEU290 4.8 14.6 1.0
CA A:ALA336 4.9 18.4 1.0
O A:VAL431 4.9 8.2 1.0
CA A:ALA384 5.0 11.8 1.0
O A:ILE382 5.0 14.7 1.0

Calcium binding site 4 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 4 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca506

b:42.0
occ:1.00
 O A:VAL434 2.2 14.8 1.0
O A:ALA385 2.3 21.8 1.0
O A:ILE293 2.5 14.2 1.0
O A:ALA337 2.5 14.7 1.0
CL A:CL507 3.0 16.2 1.0
C A:VAL434 3.5 16.1 1.0
C A:ALA385 3.5 17.2 1.0
C A:ALA337 3.7 17.6 1.0
C A:ILE293 3.7 11.1 1.0
CA A:TYR435 4.2 14.3 1.0
CA A:TYR338 4.2 20.5 1.0
CA A:VAL386 4.2 20.1 1.0
CB A:TYR338 4.3 20.1 1.0
N A:TYR435 4.3 14.6 1.0
N A:VAL386 4.3 19.7 1.0
N A:VAL434 4.4 16.1 1.0
N A:ALA385 4.4 13.7 1.0
N A:TYR338 4.4 18.6 1.0
N A:ILE293 4.4 10.4 1.0
CA A:ALA385 4.5 18.0 1.0
CB A:TYR435 4.5 15.8 1.0
CA A:VAL434 4.5 14.1 1.0
CG1 A:VAL434 4.5 16.6 1.0
CB A:VAL386 4.5 13.6 1.0
CA A:ILE293 4.5 11.6 1.0
N A:THR294 4.6 9.0 1.0
CA A:THR294 4.6 12.7 1.0
O A:HOH635 4.7 27.7 1.0
CA A:ALA337 4.8 16.3 1.0
N A:ALA337 4.8 14.1 1.0
OG1 A:THR294 4.8 25.4 1.0
CB A:ILE293 5.0 12.4 1.0

Calcium binding site 5 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 5 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:17.5
occ:1.00
 O B:GLY180 2.2 20.5 1.0
O B:SER182 2.3 17.1 1.0
OE2 B:GLU205 2.3 20.1 1.0
OD1 B:ASP179 2.3 19.9 1.0
O B:LEU184 2.4 18.0 1.0
OD2 B:ASP202 2.5 18.7 1.0
CG B:ASP202 3.3 18.7 1.0
C B:SER182 3.3 19.1 1.0
C B:GLY180 3.4 19.4 1.0
CG B:ASP179 3.5 20.2 1.0
CD B:GLU205 3.5 17.6 1.0
C B:LEU184 3.5 15.8 1.0
N B:SER182 3.7 21.6 1.0
N B:LEU184 3.8 13.0 1.0
CB B:ASP202 3.9 14.1 1.0
C B:PRO181 3.9 19.9 1.0
CA B:SER182 4.0 17.7 1.0
N B:GLY180 4.1 14.5 1.0
OD2 B:ASP179 4.1 24.6 1.0
OD1 B:ASP202 4.1 17.6 1.0
CA B:LEU184 4.1 14.1 1.0
C B:ASP179 4.1 18.0 1.0
N B:ASP179 4.2 17.8 1.0
CG B:GLU205 4.2 19.3 1.0
N B:GLY183 4.3 24.3 1.0
N B:PRO181 4.3 20.4 1.0
CA B:PRO181 4.3 15.5 1.0
C B:GLY183 4.3 15.4 1.0
CA B:GLY180 4.4 13.3 1.0
CB B:LEU184 4.4 15.9 1.0
O B:PRO181 4.4 14.2 1.0
OE1 B:GLU205 4.5 17.1 1.0
CA B:ASP179 4.5 14.9 1.0
O B:ASP179 4.5 19.3 1.0
CB B:ASP179 4.6 14.6 1.0
CA B:GLY183 4.6 16.2 1.0
N B:LEU185 4.7 12.9 1.0
CD1 B:LEU185 4.9 16.0 1.0
CA B:LEU185 4.9 12.7 1.0

Calcium binding site 6 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 6 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:32.0
occ:1.00
 O B:ASN194 2.3 29.6 1.0
O B:GLY196 2.3 26.3 1.0
OD1 B:ASP198 2.5 16.4 1.0
O B:ASP162 2.6 19.1 1.0
C B:ASN194 3.3 25.4 1.0
CG B:ASP198 3.4 21.0 1.0
C B:GLY196 3.5 23.1 1.0
C B:ASP162 3.7 15.5 1.0
OD2 B:ASP198 3.7 22.9 1.0
C B:TYR195 3.9 22.0 1.0
N B:GLY196 4.0 16.6 1.0
O B:ALA161 4.0 20.4 1.0
O B:TYR195 4.0 29.3 1.0
CA B:ASN194 4.2 23.8 1.0
N B:ASN194 4.2 28.5 1.0
N B:TYR195 4.2 24.8 1.0
O B:GLY192 4.2 25.8 1.0
N B:ASP198 4.3 18.0 1.0
CA B:TYR195 4.3 20.9 1.0
CA B:GLY196 4.3 15.8 1.0
N B:MET164 4.4 20.0 1.0
N B:GLY197 4.5 17.6 1.0
N B:ILE163 4.5 12.4 1.0
CA B:ILE163 4.5 14.5 1.0
CA B:GLY197 4.5 15.2 1.0
CA B:ASP162 4.5 22.0 1.0
O B:HOH650 4.6 19.8 1.0
CB B:ASP198 4.6 19.4 1.0
C B:PRO193 4.7 27.9 1.0
C B:GLY197 4.7 16.2 1.0
CG B:MET164 4.7 29.5 1.0
CA B:ASP198 4.9 18.0 1.0
O B:PRO193 4.9 29.6 1.0

Calcium binding site 7 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 7 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:16.3
occ:1.00
 O B:ASP335 2.3 21.0 1.0
O B:SER383 2.4 13.5 1.0
O B:ASP432 2.5 19.3 1.0
O B:ASP291 2.5 16.3 1.0
O B:HOH653 2.7 18.6 1.0
O B:HOH636 2.7 18.1 1.0
C B:ASP335 3.4 21.1 1.0
C B:SER383 3.5 15.9 1.0
C B:ASP291 3.6 21.2 1.0
C B:ASP432 3.6 18.1 1.0
CA B:ASP335 4.0 21.1 1.0
CA B:SER383 4.1 17.9 1.0
CA B:ASP291 4.1 18.3 1.0
CA B:ASP432 4.2 17.5 1.0
O B:ILE334 4.4 15.4 1.0
N B:ALA336 4.6 15.9 1.0
N B:ALA384 4.7 20.3 1.0
N B:ALA433 4.7 12.6 1.0
N B:ALA292 4.7 14.5 1.0
O B:LEU290 4.8 14.3 1.0
O B:ILE382 4.8 31.6 1.0
CB B:SER383 4.8 23.2 1.0
CB B:ASP291 4.9 18.0 1.0
CB B:ASP432 4.9 17.2 1.0
CA B:ALA336 4.9 16.4 1.0
NZ B:LYS381 4.9 42.9 1.0
O B:VAL431 4.9 12.8 1.0
CB B:ASP335 5.0 23.2 1.0

Calcium binding site 8 out of 8 in 4fu4

Go back to Calcium Binding Sites List in 4fu4
Calcium binding site 8 out of 8 in the Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Collagenase 3 (Mmp-13) with Peptide From Pro-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca506

b:41.6
occ:1.00
 O B:ILE293 2.4 18.2 1.0
O B:VAL434 2.5 25.3 1.0
O B:ALA385 2.5 26.6 1.0
O B:ALA337 2.5 26.3 1.0
O B:HOH635 2.8 20.4 1.0
C B:ILE293 3.6 18.9 1.0
C B:ALA337 3.6 20.1 1.0
CL B:CL507 3.6 19.4 1.0
C B:VAL434 3.7 20.7 1.0
C B:ALA385 3.7 22.0 1.0
CG2 B:THR294 3.8 20.6 1.0
CA B:TYR338 3.9 26.1 1.0
CB B:TYR338 3.9 22.5 1.0
OG1 B:THR294 4.0 32.9 1.0
CB B:TYR435 4.0 15.1 1.0
CA B:VAL386 4.1 20.7 1.0
CA B:THR294 4.1 18.1 1.0
CA B:TYR435 4.1 16.4 1.0
CB B:VAL386 4.2 14.3 1.0
N B:TYR338 4.2 24.5 1.0
CB B:THR294 4.2 22.1 1.0
N B:THR294 4.3 17.3 1.0
N B:VAL386 4.3 22.6 1.0
N B:TYR435 4.4 16.4 1.0
CG2 B:VAL386 4.6 15.4 1.0
CA B:ILE293 4.6 19.5 1.0
CG1 B:VAL434 4.6 19.2 1.0
N B:ILE293 4.6 15.8 1.0
CA B:VAL434 4.8 22.1 1.0
CA B:ALA337 4.8 17.0 1.0
N B:VAL434 4.8 16.8 1.0
CA B:ALA385 4.8 16.8 1.0
N B:ALA385 4.9 23.0 1.0
N B:ALA337 4.9 14.9 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: Tue Jul 8 20:08:51 2025

Last articles

Mg in 9AYP
Mg in 9AW3
Mg in 9AYN
Mg in 9AYI
Mg in 9AXL
Mg in 9AXJ
Mg in 9AVJ
Mg in 9AX5
Mg in 9AUB
Mg in 9ASI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy