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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

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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

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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

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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

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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

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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

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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: Sat Dec 12 04:47:09 2020

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