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Calcium in PDB 3ljz: Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound

Protein crystallography data

The structure of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound, PDB code: 3ljz was solved by H.-S.Shieh, J.R.Kiefer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.604, 94.927, 120.406, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.8

Other elements in 3ljz:

The structure of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound (pdb code 3ljz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound, PDB code: 3ljz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3ljz

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:53.7
occ:1.00
 O A:ASN194 2.8 29.1 1.0
OD1 A:ASP198 2.8 15.7 1.0
O A:HOH340 2.9 27.2 1.0
O A:HOH280 3.0 10.2 1.0
O A:ASP162 3.0 18.3 1.0
O A:GLY196 3.2 19.8 1.0
O A:ALA161 3.3 17.8 1.0
O A:HOH285 3.3 16.4 1.0
CG A:ASP198 3.7 16.9 1.0
C A:ASP162 3.8 17.8 1.0
OD2 A:ASP198 3.9 17.1 1.0
C A:ASN194 3.9 30.3 1.0
CG A:MET164 4.1 17.1 1.0
C A:TYR195 4.2 24.4 1.0
C A:GLY196 4.3 20.1 1.0
N A:GLY196 4.4 23.9 1.0
CA A:TYR195 4.4 26.8 1.0
CA A:ASP162 4.4 18.9 1.0
O A:TYR195 4.5 21.9 1.0
C A:ALA161 4.5 19.1 1.0
N A:MET164 4.6 14.9 1.0
N A:TYR195 4.6 29.0 1.0
N A:ILE163 4.7 16.4 1.0
CB A:MET164 4.8 15.3 1.0
O A:HOH295 4.9 17.1 1.0
N A:ASP162 5.0 18.7 1.0
CA A:GLY196 5.0 22.6 1.0
N A:ASP198 5.0 15.5 1.0
CA A:ILE163 5.0 15.1 1.0
CA A:ASN194 5.0 33.3 1.0

Calcium binding site 2 out of 8 in 3ljz

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:27.8
occ:1.00
 OE2 A:GLU205 2.2 30.2 1.0
OD2 A:ASP202 2.3 13.5 1.0
O A:GLY180 2.3 29.9 1.0
O A:SER182 2.3 36.1 1.0
OD1 A:ASP179 2.4 25.2 1.0
O A:LEU184 2.5 28.5 1.0
CG A:ASP202 3.4 15.4 1.0
C A:SER182 3.4 37.5 1.0
CD A:GLU205 3.5 27.0 1.0
C A:GLY180 3.5 31.2 1.0
CG A:ASP179 3.6 28.0 1.0
C A:LEU184 3.6 28.5 1.0
N A:SER182 3.8 36.4 1.0
N A:LEU184 4.0 33.1 1.0
C A:PRO181 4.1 35.8 1.0
CB A:ASP202 4.1 15.7 1.0
N A:GLY180 4.1 29.1 1.0
CA A:SER182 4.1 37.8 1.0
OD2 A:ASP179 4.1 29.5 1.0
C A:GLY183 4.2 34.9 1.0
OD1 A:ASP202 4.3 17.6 1.0
OE1 A:GLU205 4.3 32.4 1.0
C A:ASP179 4.3 29.0 1.0
CG A:GLU205 4.3 24.1 1.0
N A:ASP179 4.3 24.2 1.0
CA A:LEU184 4.4 31.0 1.0
N A:GLY183 4.4 38.4 1.0
CA A:PRO181 4.4 34.4 1.0
N A:PRO181 4.5 33.4 1.0
CA A:GLY180 4.5 30.5 1.0
CA A:GLY183 4.5 37.5 1.0
O A:PRO181 4.5 36.6 1.0
O A:GLY183 4.6 34.3 1.0
N A:LEU185 4.6 25.5 1.0
CA A:ASP179 4.7 27.4 1.0
CB A:ASP179 4.7 28.3 1.0
O A:ASP179 4.8 31.2 1.0
CA A:LEU185 4.8 23.2 1.0
CB A:LEU184 4.9 30.8 1.0

Calcium binding site 3 out of 8 in 3ljz

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Calcium binding site 3 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca996

b:42.9
occ:1.00
 O B:ASN194 2.7 22.6 1.0
OD1 B:ASP198 2.7 15.0 1.0
O B:HOH270 3.2 7.4 1.0
O B:ASP162 3.2 16.5 1.0
O B:GLY196 3.3 16.3 1.0
O B:HOH51 3.5 11.2 1.0
CG B:ASP198 3.5 15.8 1.0
O B:ALA161 3.7 19.0 1.0
OD2 B:ASP198 3.7 15.9 1.0
C B:ASN194 3.8 23.6 1.0
C B:TYR195 3.9 19.2 1.0
C B:ASP162 4.0 16.4 1.0
CG B:MET164 4.0 16.9 1.0
CA B:TYR195 4.1 21.1 1.0
O B:TYR195 4.1 17.5 1.0
N B:GLY196 4.2 18.9 1.0
C B:GLY196 4.3 15.8 1.0
N B:TYR195 4.4 22.4 1.0
N B:MET164 4.6 14.4 1.0
CA B:ASP162 4.7 18.2 1.0
CB B:MET164 4.7 15.5 1.0
N B:ASP198 4.8 13.1 1.0
C B:ALA161 4.8 19.3 1.0
N B:ILE163 4.8 14.7 1.0
CB B:ASP198 4.9 13.1 1.0
CA B:GLY196 4.9 17.8 1.0
CA B:ASN194 5.0 26.0 1.0

Calcium binding site 4 out of 8 in 3ljz

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Calcium binding site 4 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca997

b:15.6
occ:1.00
 O B:SER182 2.2 21.5 1.0
OE2 B:GLU205 2.3 20.9 1.0
OD2 B:ASP202 2.3 12.7 1.0
OD1 B:ASP179 2.3 13.8 1.0
O B:LEU184 2.4 17.4 1.0
O B:GLY180 2.4 16.1 1.0
C B:SER182 3.4 22.7 1.0
CG B:ASP202 3.4 14.0 1.0
CD B:GLU205 3.5 19.6 1.0
C B:LEU184 3.5 17.2 1.0
CG B:ASP179 3.5 16.0 1.0
C B:GLY180 3.6 18.0 1.0
N B:SER182 3.9 22.2 1.0
N B:LEU184 4.1 20.4 1.0
CB B:ASP202 4.1 12.8 1.0
C B:PRO181 4.1 21.3 1.0
N B:GLY180 4.1 16.6 1.0
OD2 B:ASP179 4.1 17.5 1.0
C B:GLY183 4.1 21.0 1.0
CA B:SER182 4.1 23.5 1.0
N B:ASP179 4.2 14.8 1.0
CA B:LEU184 4.2 19.1 1.0
C B:ASP179 4.3 16.8 1.0
OE1 B:GLU205 4.3 20.3 1.0
OD1 B:ASP202 4.3 15.3 1.0
CG B:GLU205 4.4 17.2 1.0
CB B:LEU184 4.4 20.3 1.0
O B:GLY183 4.4 20.4 1.0
N B:GLY183 4.4 23.1 1.0
CA B:GLY180 4.5 17.5 1.0
CA B:PRO181 4.5 20.5 1.0
N B:LEU185 4.5 15.0 1.0
N B:PRO181 4.5 19.6 1.0
O B:PRO181 4.5 22.0 1.0
CA B:ASP179 4.6 16.3 1.0
CA B:GLY183 4.6 22.6 1.0
CB B:ASP179 4.6 16.6 1.0
CA B:LEU185 4.7 12.9 1.0
O B:ASP179 4.8 17.7 1.0

Calcium binding site 5 out of 8 in 3ljz

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Calcium binding site 5 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca996

b:60.7
occ:1.00
 O C:ASN194 2.7 33.2 1.0
OD1 C:ASP198 2.7 19.8 1.0
O C:ASP162 3.0 20.5 1.0
O C:HOH293 3.2 14.4 1.0
O C:GLY196 3.3 22.3 1.0
O C:HOH302 3.4 24.7 1.0
O C:ALA161 3.5 20.9 1.0
CG C:ASP198 3.6 19.3 1.0
O C:HOH85 3.6 13.6 1.0
OD2 C:ASP198 3.8 20.6 1.0
C C:ASP162 3.8 20.2 1.0
C C:ASN194 3.9 33.7 1.0
CG C:MET164 3.9 17.7 1.0
C C:TYR195 4.2 27.2 1.0
C C:GLY196 4.3 23.1 1.0
O C:TYR195 4.4 24.6 1.0
CA C:TYR195 4.4 29.8 1.0
N C:GLY196 4.5 27.0 1.0
CA C:ASP162 4.5 21.7 1.0
N C:TYR195 4.6 32.2 1.0
N C:MET164 4.6 15.8 1.0
C C:ALA161 4.6 21.2 1.0
N C:ILE163 4.7 18.5 1.0
CB C:MET164 4.7 15.9 1.0
N C:ASP198 4.9 18.3 1.0
CA C:ASN194 4.9 37.1 1.0
CA C:ILE163 4.9 17.1 1.0
CA C:GLY196 5.0 25.8 1.0
CB C:ASP198 5.0 17.4 1.0

Calcium binding site 6 out of 8 in 3ljz

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Calcium binding site 6 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca997

b:24.4
occ:1.00
 OE2 C:GLU205 2.1 29.5 1.0
O C:LEU184 2.3 25.4 1.0
O C:GLY180 2.3 30.1 1.0
OD2 C:ASP202 2.3 15.9 1.0
OD1 C:ASP179 2.4 25.1 1.0
O C:SER182 2.4 33.2 1.0
CD C:GLU205 3.3 25.6 1.0
C C:LEU184 3.4 25.9 1.0
CG C:ASP202 3.4 17.4 1.0
C C:GLY180 3.5 30.7 1.0
CG C:ASP179 3.5 28.8 1.0
C C:SER182 3.6 34.8 1.0
N C:LEU184 4.0 30.5 1.0
N C:GLY180 4.0 28.4 1.0
N C:SER182 4.0 34.5 1.0
CB C:ASP202 4.1 16.7 1.0
C C:PRO181 4.1 34.4 1.0
OE1 C:GLU205 4.1 28.4 1.0
OD2 C:ASP179 4.1 31.5 1.0
C C:GLY183 4.2 32.5 1.0
CA C:LEU184 4.2 28.3 1.0
CG C:GLU205 4.2 21.9 1.0
N C:ASP179 4.3 24.6 1.0
C C:ASP179 4.3 28.9 1.0
OD1 C:ASP202 4.3 16.4 1.0
CA C:SER182 4.4 35.7 1.0
CA C:GLY180 4.4 29.9 1.0
N C:LEU185 4.4 23.8 1.0
N C:PRO181 4.5 32.5 1.0
CA C:PRO181 4.5 33.3 1.0
O C:PRO181 4.5 35.1 1.0
N C:GLY183 4.5 35.7 1.0
O C:GLY183 4.6 32.2 1.0
CA C:LEU185 4.6 22.0 1.0
CA C:GLY183 4.6 35.0 1.0
O C:HOH295 4.6 19.2 1.0
CA C:ASP179 4.6 27.3 1.0
CB C:ASP179 4.7 28.7 1.0
CB C:LEU184 4.7 28.5 1.0
O C:ASP179 4.8 30.4 1.0

Calcium binding site 7 out of 8 in 3ljz

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Calcium binding site 7 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca996

b:52.1
occ:1.00
 OD1 D:ASP198 2.6 15.8 1.0
O D:ASN194 2.8 31.3 1.0
O D:HOH57 2.8 11.8 1.0
O D:ASP162 3.0 18.0 1.0
O D:HOH86 3.2 8.0 1.0
O D:GLY196 3.2 20.5 1.0
O D:HOH277 3.4 17.3 1.0
CG D:ASP198 3.4 16.5 1.0
OD2 D:ASP198 3.6 16.7 1.0
O D:ALA161 3.7 19.1 1.0
C D:ASN194 3.9 31.9 1.0
C D:ASP162 3.9 17.6 1.0
C D:TYR195 3.9 26.1 1.0
CG D:MET164 4.0 17.2 1.0
O D:TYR195 4.1 23.6 1.0
C D:GLY196 4.2 20.8 1.0
N D:GLY196 4.2 25.3 1.0
CA D:TYR195 4.2 28.9 1.0
N D:TYR195 4.4 30.8 1.0
N D:MET164 4.5 14.8 1.0
CA D:ASP162 4.6 18.7 1.0
N D:ILE163 4.7 16.5 1.0
CB D:MET164 4.7 15.4 1.0
N D:ASP198 4.7 15.0 1.0
CB D:ASP198 4.8 14.9 1.0
CA D:GLY196 4.8 23.2 1.0
C D:ALA161 4.8 18.9 1.0
CA D:ILE163 4.8 14.8 1.0
CA D:ASN194 5.0 34.6 1.0

Calcium binding site 8 out of 8 in 3ljz

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Calcium binding site 8 out of 8 in the Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Mmp-13 Complexed with An Amino-2-Indanol Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca997

b:13.7
occ:1.00
 OE2 D:GLU205 2.2 15.8 1.0
OD2 D:ASP202 2.3 10.3 1.0
OD1 D:ASP179 2.3 9.7 1.0
O D:LEU184 2.3 14.6 1.0
O D:GLY180 2.3 17.4 1.0
O D:SER182 2.4 16.4 1.0
CD D:GLU205 3.4 17.6 1.0
CG D:ASP202 3.4 11.6 1.0
CG D:ASP179 3.5 15.1 1.0
C D:LEU184 3.5 15.0 1.0
C D:GLY180 3.5 17.4 1.0
C D:SER182 3.6 17.4 1.0
N D:LEU184 3.9 16.6 1.0
N D:SER182 4.0 17.3 1.0
OD2 D:ASP179 4.0 14.0 1.0
N D:GLY180 4.1 16.4 1.0
C D:PRO181 4.1 18.0 1.0
CB D:ASP202 4.1 11.7 1.0
OE1 D:GLU205 4.1 19.0 1.0
C D:GLY183 4.2 17.2 1.0
CA D:LEU184 4.2 16.2 1.0
C D:ASP179 4.3 17.2 1.0
OD1 D:ASP202 4.3 11.2 1.0
N D:ASP179 4.3 15.2 1.0
CA D:SER182 4.4 18.2 1.0
CG D:GLU205 4.4 16.9 1.0
CA D:GLY180 4.4 17.4 1.0
CA D:PRO181 4.4 18.3 1.0
N D:PRO181 4.5 18.1 1.0
N D:GLY183 4.5 18.4 1.0
N D:LEU185 4.5 13.8 1.0
O D:PRO181 4.5 18.3 1.0
O D:GLY183 4.6 17.0 1.0
CA D:ASP179 4.6 16.0 1.0
CB D:ASP179 4.6 16.6 1.0
CA D:GLY183 4.7 18.1 1.0
CB D:LEU184 4.7 16.5 1.0
CA D:LEU185 4.7 13.2 1.0
O D:ASP179 4.8 17.9 1.0

Reference:

H.S.Shieh, A.G.Tomasselli, K.J.Mathis, M.E.Schnute, S.S.Woodard, N.Caspers, J.M.Williams, J.R.Kiefer, G.Munie, A.Wittwer, A.M.Malfait, M.D.Tortorella. Structure Analysis Reveals the Flexibility of the Adamts-5 Active Site. Protein Sci. V. 20 735 2011.
ISSN: ISSN 0961-8368
PubMed: 21370305
DOI: 10.1002/PRO.606
Page generated: Sat Jul 13 13:08:58 2024

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