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Calcium in PDB 1cxv: Structure of Recombinant Mouse Collagenase-3 (Mmp-13)

Protein crystallography data

The structure of Structure of Recombinant Mouse Collagenase-3 (Mmp-13), PDB code: 1cxv was solved by I.Botos, E.Meyer, S.M.Swanson, V.Lemaitre, Y.Eeckhout, E.F.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.360, 48.460, 74.940, 90.00, 108.15, 90.00
R / Rfree (%) 19.6 / 23.4

Other elements in 1cxv:

The structure of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13) (pdb code 1cxv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13), PDB code: 1cxv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1cxv

Go back to Calcium Binding Sites List in 1cxv
Calcium binding site 1 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:48.9
occ:1.00
O A:GLY175 2.2 18.6 1.0
O A:GLY171 2.6 23.9 1.0
O A:HOH665 2.9 25.7 1.0
CH2 A:TRP92 2.9 25.4 1.0
O A:ASP141 3.0 19.9 1.0
C A:GLY175 3.2 19.6 1.0
CZ3 A:TRP92 3.5 25.5 1.0
O A:HOH798 3.6 38.9 1.0
O A:ASN173 3.7 24.4 1.0
CA A:GLY175 3.8 20.2 1.0
C A:GLY171 3.8 24.1 1.0
N A:GLY175 4.0 21.1 1.0
CZ2 A:TRP92 4.0 25.3 1.0
C A:ASP141 4.0 20.1 1.0
N A:GLY176 4.2 19.1 1.0
CA A:ASP141 4.3 20.7 1.0
C A:PRO172 4.4 25.3 1.0
CA A:PRO172 4.5 25.3 1.0
O A:PRO172 4.5 25.4 1.0
N A:GLY171 4.5 22.1 1.0
CA A:GLY176 4.5 18.3 1.0
N A:PRO172 4.6 25.0 1.0
C A:ASN173 4.6 24.3 1.0
C A:TYR174 4.7 22.2 1.0
N A:ASN173 4.8 25.0 1.0
CA A:GLY171 4.8 23.4 1.0
CB A:ASP141 4.9 21.0 1.0
CE3 A:TRP92 4.9 25.5 1.0
OD1 A:ASP177 5.0 17.8 1.0

Calcium binding site 2 out of 4 in 1cxv

Go back to Calcium Binding Sites List in 1cxv
Calcium binding site 2 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:27.1
occ:1.00
O A:GLY159 2.3 32.0 1.0
O A:SER161 2.3 31.6 1.0
OE2 A:GLU184 2.3 31.7 1.0
OD2 A:ASP181 2.3 24.6 1.0
O A:LEU163 2.4 26.1 1.0
OD1 A:ASP158 2.5 30.4 1.0
C A:GLY159 3.4 32.0 1.0
CG A:ASP181 3.4 23.7 1.0
C A:SER161 3.4 31.6 1.0
CD A:GLU184 3.4 31.6 1.0
C A:LEU163 3.5 26.4 1.0
CG A:ASP158 3.5 30.2 1.0
N A:LEU163 3.8 28.3 1.0
N A:SER161 3.9 32.3 1.0
N A:GLY159 3.9 31.4 1.0
C A:PRO160 4.0 32.5 1.0
OD2 A:ASP158 4.0 29.9 1.0
CB A:ASP181 4.1 23.6 1.0
C A:ASP158 4.1 31.0 1.0
CA A:LEU163 4.2 27.2 1.0
C A:GLY162 4.2 28.8 1.0
OE1 A:GLU184 4.2 31.8 1.0
CA A:SER161 4.2 32.4 1.0
CA A:GLY159 4.2 31.6 1.0
N A:ASP158 4.2 30.0 1.0
N A:PRO160 4.3 32.3 1.0
OD1 A:ASP181 4.3 23.5 1.0
CG A:GLU184 4.3 31.3 1.0
O A:PRO160 4.4 33.0 1.0
N A:GLY162 4.4 30.8 1.0
CA A:PRO160 4.5 32.5 1.0
CA A:ASP158 4.5 30.6 1.0
CB A:LEU163 4.5 27.7 1.0
CA A:GLY162 4.6 29.7 1.0
N A:LEU164 4.6 25.1 1.0
O A:ASP158 4.6 31.4 1.0
CB A:ASP158 4.6 30.3 1.0
O A:GLY162 4.7 29.2 1.0
CA A:LEU164 4.9 24.1 1.0

Calcium binding site 3 out of 4 in 1cxv

Go back to Calcium Binding Sites List in 1cxv
Calcium binding site 3 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6

b:26.6
occ:1.00
O B:GLY475 2.3 18.6 1.0
O B:ASN473 2.3 26.3 1.0
O B:HOH664 2.5 22.9 1.0
O B:ASP441 2.5 19.8 1.0
OD1 B:ASP477 2.6 17.4 1.0
C B:GLY475 3.4 19.5 1.0
C B:ASN473 3.5 26.1 1.0
CG B:ASP477 3.5 17.8 1.0
C B:ASP441 3.6 19.9 1.0
C B:TYR474 3.8 24.0 1.0
N B:GLY475 3.8 21.9 1.0
OD2 B:ASP477 3.9 17.4 1.0
O B:HOH601 4.0 24.1 1.0
O B:TYR474 4.1 23.2 1.0
N B:ASP477 4.1 18.1 1.0
O B:ALA440 4.1 21.0 1.0
CA B:GLY475 4.2 20.5 1.0
CA B:TYR474 4.2 25.5 1.0
N B:TYR474 4.3 25.6 1.0
N B:GLY476 4.4 18.6 1.0
CA B:ASP441 4.4 20.7 1.0
CA B:ASN473 4.5 26.1 1.0
CA B:GLY476 4.5 18.4 1.0
N B:ILE442 4.5 18.9 1.0
C B:GLY476 4.5 18.2 1.0
O B:GLY471 4.6 22.3 1.0
CA B:ILE442 4.6 19.2 1.0
N B:ASN473 4.6 24.8 1.0
CB B:ASP477 4.7 17.6 1.0
N B:MET443 4.7 19.3 1.0
CH2 B:TRP392 4.8 25.3 1.0
CA B:ASP477 4.8 17.8 1.0
C B:PRO472 4.9 24.2 1.0
NH1 A:ARG88 5.0 41.4 1.0

Calcium binding site 4 out of 4 in 1cxv

Go back to Calcium Binding Sites List in 1cxv
Calcium binding site 4 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8

b:22.8
occ:1.00
OE2 B:GLU484 2.2 31.6 1.0
O B:LEU463 2.2 25.7 1.0
O B:SER461 2.3 31.6 1.0
OD2 B:ASP481 2.4 24.5 1.0
O B:GLY459 2.4 31.6 1.0
OD1 B:ASP458 2.6 30.0 1.0
CD B:GLU484 3.3 31.4 1.0
C B:LEU463 3.3 26.1 1.0
CG B:ASP481 3.4 23.5 1.0
C B:SER461 3.4 31.6 1.0
C B:GLY459 3.6 31.8 1.0
CG B:ASP458 3.7 30.3 1.0
N B:LEU463 3.7 28.0 1.0
N B:SER461 3.9 32.2 1.0
CB B:ASP481 4.0 23.6 1.0
CA B:LEU463 4.0 27.0 1.0
N B:GLY459 4.1 31.2 1.0
OE1 B:GLU484 4.1 31.5 1.0
C B:PRO460 4.1 32.5 1.0
C B:GLY462 4.1 28.8 1.0
OD2 B:ASP458 4.1 30.2 1.0
CA B:SER461 4.2 32.3 1.0
CG B:GLU484 4.2 31.2 1.0
C B:ASP458 4.4 30.9 1.0
OD1 B:ASP481 4.4 23.3 1.0
N B:ASP458 4.4 30.1 1.0
N B:LEU464 4.4 24.8 1.0
N B:GLY462 4.4 30.8 1.0
CA B:GLY459 4.4 31.5 1.0
CB B:LEU463 4.4 27.5 1.0
N B:PRO460 4.5 32.2 1.0
O B:PRO460 4.5 32.6 1.0
CA B:GLY462 4.6 29.6 1.0
CA B:PRO460 4.6 32.4 1.0
CA B:LEU464 4.6 23.9 1.0
O B:GLY462 4.6 28.7 1.0
CA B:ASP458 4.7 30.5 1.0
O B:ASP458 4.8 30.9 1.0
CB B:ASP458 4.8 30.4 1.0
CD2 B:LEU464 4.9 24.2 1.0

Reference:

I.Botos, E.Meyer, S.M.Swanson, V.Lemaitre, Y.Eeckhout, E.F.Meyer. Structure of Recombinant Mouse Collagenase-3 (Mmp-13). J.Mol.Biol. V. 292 837 1999.
ISSN: ISSN 0022-2836
PubMed: 10525409
DOI: 10.1006/JMBI.1999.3068
Page generated: Sat Dec 12 02:52:16 2020

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