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Calcium in PDB 2d1n: Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor

Protein crystallography data

The structure of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1n was solved by T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.98 / 2.37
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 96.470, 96.470, 67.520, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 23.9

Other elements in 2d1n:

The structure of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor (pdb code 2d1n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2d1n

Go back to Calcium Binding Sites List in 2d1n
Calcium binding site 1 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca272

b:53.2
occ:1.00
 OE2 A:GLU205 2.2 56.8 1.0
O A:SER182 2.3 57.2 1.0
O A:LEU184 2.3 57.8 1.0
O A:GLY180 2.3 60.6 1.0
OD2 A:ASP202 2.4 52.4 1.0
OD1 A:ASP179 2.6 66.3 1.0
C A:SER182 3.4 60.2 1.0
C A:LEU184 3.4 56.5 1.0
CD A:GLU205 3.5 59.0 1.0
CG A:ASP202 3.5 53.5 1.0
C A:GLY180 3.5 61.7 1.0
N A:LEU184 3.8 58.4 1.0
CG A:ASP179 3.8 67.3 1.0
N A:SER182 4.0 62.2 1.0
C A:PRO181 4.0 61.9 1.0
CA A:LEU184 4.1 57.6 1.0
C A:ASP179 4.1 64.4 1.0
CB A:ASP202 4.1 51.3 1.0
C A:GLY183 4.2 58.6 1.0
N A:GLY180 4.2 63.6 1.0
O A:ASP179 4.2 65.2 1.0
CA A:SER182 4.2 62.0 1.0
O A:PRO181 4.3 62.1 1.0
N A:ASP179 4.3 63.4 1.0
OE1 A:GLU205 4.3 60.0 1.0
CB A:LEU184 4.3 59.6 1.0
CG A:GLU205 4.4 55.1 1.0
N A:GLY183 4.4 60.2 1.0
CA A:GLY180 4.4 62.1 1.0
OD1 A:ASP202 4.4 53.1 1.0
N A:PRO181 4.4 62.2 1.0
CA A:PRO181 4.5 61.6 1.0
N A:LEU185 4.5 55.7 1.0
CA A:GLY183 4.5 59.5 1.0
CA A:ASP179 4.6 64.5 1.0
OD2 A:ASP179 4.6 71.3 1.0
O A:GLY183 4.7 58.4 1.0
CA A:LEU185 4.8 53.7 1.0
CB A:ASP179 4.8 66.0 1.0

Calcium binding site 2 out of 6 in 2d1n

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Calcium binding site 2 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca273

b:59.5
occ:1.00
 O A:GLY196 2.3 48.4 1.0
O A:ASN194 2.4 57.0 1.0
O A:ASP162 2.4 50.4 1.0
O A:HOH41 2.5 39.8 1.0
OD1 A:ASP198 2.6 45.1 1.0
O A:HOH11 2.9 51.0 1.0
CG A:ASP198 3.4 49.1 1.0
C A:GLY196 3.4 49.1 1.0
C A:ASN194 3.6 56.9 1.0
C A:ASP162 3.6 49.6 1.0
OD2 A:ASP198 3.7 46.7 1.0
C A:TYR195 3.8 54.8 1.0
N A:GLY196 3.8 53.3 1.0
O A:TYR195 4.0 55.1 1.0
N A:ASP198 4.1 47.4 1.0
CA A:GLY196 4.1 50.5 1.0
O A:ALA161 4.2 50.4 1.0
CA A:TYR195 4.3 56.8 1.0
N A:TYR195 4.3 56.9 1.0
N A:ILE163 4.4 47.9 1.0
CA A:ILE163 4.4 46.5 1.0
N A:GLY197 4.5 48.8 1.0
CA A:ASP162 4.5 51.2 1.0
N A:MET164 4.5 45.8 1.0
CB A:ASP198 4.5 48.4 1.0
O A:GLY192 4.6 53.9 1.0
CA A:ASN194 4.6 56.7 1.0
N A:ASN194 4.6 55.1 1.0
C A:GLY197 4.7 48.5 1.0
CA A:GLY197 4.7 48.3 1.0
CA A:ASP198 4.7 48.1 1.0
CG A:MET164 4.8 43.3 1.0
C A:PRO193 4.9 55.5 1.0
CH2 A:TRP113 5.0 56.0 1.0
O A:PRO193 5.0 55.2 1.0

Calcium binding site 3 out of 6 in 2d1n

Go back to Calcium Binding Sites List in 2d1n
Calcium binding site 3 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca274

b:73.4
occ:1.00
 O A:GLU205 2.3 50.2 1.0
OD2 A:ASP128 2.4 52.6 1.0
O A:ASP203 2.5 53.2 1.0
OD2 A:ASP203 2.5 48.4 1.0
CG A:ASP128 3.2 51.5 1.0
C A:ASP203 3.2 53.3 1.0
OD1 A:ASP128 3.3 54.8 1.0
CG A:ASP203 3.5 50.8 1.0
C A:GLU205 3.5 51.3 1.0
CA A:ASP203 3.6 52.1 1.0
OG1 A:THR126 3.7 49.4 1.0
CD1 A:TRP207 4.0 50.8 1.0
CB A:ASP203 4.1 51.0 1.0
N A:GLU205 4.1 55.8 1.0
CA A:THR206 4.2 52.0 1.0
N A:ASP204 4.2 55.0 1.0
N A:THR206 4.3 51.9 1.0
OD1 A:ASP203 4.4 52.4 1.0
C A:ASP204 4.4 56.0 1.0
NE1 A:TRP207 4.5 51.4 1.0
N A:TRP207 4.5 53.8 1.0
CB A:ASP128 4.5 51.4 1.0
CA A:GLU205 4.5 52.5 1.0
CA A:ASP204 4.7 55.8 1.0
O A:ASP202 4.9 50.1 1.0
C A:THR206 4.9 52.2 1.0
N A:ASP203 5.0 50.9 1.0

Calcium binding site 4 out of 6 in 2d1n

Go back to Calcium Binding Sites List in 2d1n
Calcium binding site 4 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca282

b:65.4
occ:1.00
 O B:SER182 2.2 61.5 1.0
O B:GLY180 2.4 64.2 1.0
OE2 B:GLU205 2.4 57.0 1.0
O B:LEU184 2.4 59.4 1.0
OD1 B:ASP179 2.4 65.4 1.0
OD2 B:ASP202 2.5 55.3 1.0
C B:LEU184 3.4 58.5 1.0
C B:SER182 3.4 61.8 1.0
N B:LEU184 3.5 59.0 1.0
C B:GLY180 3.6 62.4 1.0
CG B:ASP202 3.6 54.9 1.0
CD B:GLU205 3.6 59.2 1.0
CG B:ASP179 3.7 66.8 1.0
CA B:LEU184 3.9 58.6 1.0
C B:ASP179 4.0 63.1 1.0
C B:PRO181 4.0 61.7 1.0
C B:GLY183 4.1 59.8 1.0
N B:SER182 4.1 62.5 1.0
O B:ASP179 4.1 63.0 1.0
CB B:LEU184 4.2 60.5 1.0
N B:GLY180 4.2 63.6 1.0
N B:ASP179 4.2 61.5 1.0
O B:PRO181 4.2 62.5 1.0
CB B:ASP202 4.2 50.6 1.0
CA B:SER182 4.3 62.9 1.0
N B:GLY183 4.4 61.5 1.0
CA B:GLY183 4.4 59.8 1.0
OE1 B:GLU205 4.4 59.2 1.0
OD2 B:ASP179 4.4 70.0 1.0
CA B:ASP179 4.5 63.0 1.0
CA B:GLY180 4.5 62.4 1.0
N B:PRO181 4.5 61.9 1.0
CA B:PRO181 4.5 61.2 1.0
CG B:GLU205 4.6 56.7 1.0
N B:LEU185 4.6 56.7 1.0
OD1 B:ASP202 4.6 57.3 1.0
CB B:ASP179 4.6 65.2 1.0
O B:GLY183 4.8 58.5 1.0
CA B:LEU185 4.9 53.8 1.0

Calcium binding site 5 out of 6 in 2d1n

Go back to Calcium Binding Sites List in 2d1n
Calcium binding site 5 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca283

b:74.4
occ:1.00
 O B:GLY196 2.4 49.9 1.0
OD1 B:ASP198 2.4 47.2 1.0
O B:ASN194 2.4 59.1 1.0
O B:ASP162 2.4 52.6 1.0
O B:HOH19 2.5 49.4 1.0
O B:HOH18 3.1 42.0 1.0
C B:ASP162 3.4 51.4 1.0
CG B:ASP198 3.4 47.0 1.0
C B:GLY196 3.5 50.1 1.0
C B:ASN194 3.6 57.5 1.0
OD2 B:ASP198 3.9 47.9 1.0
C B:TYR195 3.9 54.9 1.0
O B:ALA161 4.0 51.4 1.0
N B:GLY196 4.0 53.5 1.0
N B:ASP198 4.0 47.6 1.0
O B:TYR195 4.1 54.4 1.0
N B:ILE163 4.2 49.7 1.0
CA B:ILE163 4.2 47.0 1.0
CA B:ASP162 4.3 51.9 1.0
CA B:GLY196 4.3 50.9 1.0
N B:MET164 4.4 47.3 1.0
CA B:TYR195 4.4 56.2 1.0
N B:TYR195 4.5 56.2 1.0
N B:GLY197 4.5 49.5 1.0
CB B:ASP198 4.6 46.3 1.0
CA B:ASN194 4.6 57.5 1.0
CG B:MET164 4.6 45.5 1.0
C B:GLY197 4.6 47.9 1.0
CA B:GLY197 4.6 48.6 1.0
CA B:ASP198 4.7 47.9 1.0
O B:GLY192 4.7 52.0 1.0
N B:ASN194 4.7 56.4 1.0
C B:ILE163 4.8 47.3 1.0
C B:ALA161 4.9 52.0 1.0
CH2 B:TRP113 5.0 54.1 1.0

Calcium binding site 6 out of 6 in 2d1n

Go back to Calcium Binding Sites List in 2d1n
Calcium binding site 6 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca284

b:77.6
occ:1.00
 O B:ASP203 2.3 53.7 1.0
OD2 B:ASP128 2.4 52.5 1.0
O B:GLU205 2.6 51.4 1.0
OD2 B:ASP203 2.7 50.2 1.0
CG B:ASP128 3.0 52.2 1.0
OD1 B:ASP128 3.1 53.9 1.0
C B:ASP203 3.3 53.0 1.0
CG B:ASP203 3.4 50.6 1.0
OG1 B:THR126 3.8 48.8 1.0
C B:GLU205 3.8 52.9 1.0
CA B:ASP203 3.9 50.9 1.0
OD1 B:ASP203 4.0 50.5 1.0
CB B:ASP203 4.1 50.7 1.0
N B:GLU205 4.3 55.1 1.0
CD1 B:TRP207 4.4 50.6 1.0
CB B:ASP128 4.4 51.7 1.0
N B:ASP204 4.4 52.9 1.0
CA B:THR206 4.5 52.4 1.0
N B:THR206 4.6 52.6 1.0
C B:ASP204 4.6 56.2 1.0
CA B:ASP204 4.8 55.1 1.0
CA B:GLU205 4.8 53.3 1.0
N B:TRP207 4.8 54.2 1.0
NE1 B:TRP207 4.9 50.6 1.0
CD B:PRO127 5.0 48.8 1.0
CG B:PRO127 5.0 49.3 1.0

Reference:

T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka. Crystal Structures of the Catalytic Domain of Human Stromelysin-1 (Mmp-3) and Collagenase-3 (Mmp-13) with A Hydroxamic Acid Inhibitor Sm-25453 Biochem.Biophys.Res.Commun. V. 344 315 2006.
ISSN: ISSN 0006-291X
PubMed: 16603129
DOI: 10.1016/J.BBRC.2006.03.098
Page generated: Fri Jul 12 09:40:06 2024

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