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Calcium in PDB 2pjt: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344, PDB code: 2pjt was solved by Z.Xu, A.Huang, F.Lovering, J.I.Levin, L.Mosyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.352, 35.789, 139.405, 90.00, 108.94, 90.00
R / Rfree (%) 21.2 / 27

Other elements in 2pjt:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344 (pdb code 2pjt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344, PDB code: 2pjt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 2pjt

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Calcium binding site 1 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:43.5
occ:1.00
 O A:LEU159 2.1 33.0 1.0
OE2 A:GLU180 2.2 38.8 1.0
O A:SER157 2.2 37.1 1.0
O A:GLY155 2.4 34.8 1.0
OD1 A:ASP154 2.4 43.8 1.0
OD2 A:ASP177 2.5 36.1 1.0
C A:LEU159 3.2 34.0 1.0
C A:SER157 3.2 37.7 1.0
CD A:GLU180 3.4 38.5 1.0
CG A:ASP154 3.4 43.9 1.0
N A:LEU159 3.5 34.1 1.0
C A:GLY155 3.6 36.5 1.0
CG A:ASP177 3.6 33.5 1.0
N A:SER157 3.8 38.1 1.0
CA A:LEU159 3.9 34.7 1.0
C A:GLY158 3.9 36.0 1.0
OD2 A:ASP154 3.9 44.4 1.0
C A:PRO156 4.0 38.0 1.0
CA A:SER157 4.0 38.9 1.0
N A:GLY155 4.1 39.4 1.0
OE1 A:GLU180 4.2 38.7 1.0
N A:GLY158 4.2 36.1 1.0
CB A:ASP177 4.2 32.7 1.0
C A:ASP154 4.2 40.4 1.0
N A:ASP154 4.2 41.4 1.0
CA A:GLY158 4.3 35.5 1.0
CB A:LEU159 4.3 35.5 1.0
CG A:GLU180 4.3 37.7 1.0
N A:LEU160 4.3 33.2 1.0
O A:PRO156 4.4 37.3 1.0
O A:GLY158 4.5 35.6 1.0
CA A:GLY155 4.5 37.2 1.0
N A:PRO156 4.5 37.0 1.0
CA A:PRO156 4.5 37.7 1.0
CA A:ASP154 4.6 41.1 1.0
OD1 A:ASP177 4.6 34.4 1.0
O A:ASP154 4.6 41.9 1.0
CB A:ASP154 4.6 42.8 1.0
CA A:LEU160 4.7 33.2 1.0
CB A:PHE153 5.0 39.7 1.0

Calcium binding site 2 out of 10 in 2pjt

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Calcium binding site 2 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:40.5
occ:1.00
 O A:ASN169 2.1 42.2 1.0
O A:GLY171 2.2 39.7 1.0
O A:ASP137 2.3 40.2 1.0
OD1 A:ASP173 2.6 35.0 1.0
C A:ASN169 3.3 41.5 1.0
C A:GLY171 3.4 39.1 1.0
C A:ASP137 3.5 38.8 1.0
CG A:ASP173 3.6 34.7 1.0
N A:GLY171 3.9 38.4 1.0
OD2 A:ASP173 4.0 32.9 1.0
O A:ALA136 4.0 39.6 1.0
C A:TYR170 4.0 38.6 1.0
CA A:ASP137 4.1 39.6 1.0
N A:ASP173 4.1 35.6 1.0
CA A:ASN169 4.1 43.4 1.0
N A:ASN169 4.2 42.9 1.0
O A:GLY167 4.2 42.8 1.0
CA A:GLY171 4.2 37.5 1.0
O A:TYR170 4.3 36.5 1.0
N A:TYR170 4.3 40.7 1.0
N A:GLY172 4.4 38.6 1.0
CA A:TYR170 4.4 39.3 1.0
N A:ILE138 4.5 37.7 1.0
C A:PRO168 4.5 42.4 1.0
CA A:GLY172 4.6 38.0 1.0
CH2 A:TRP88 4.6 47.5 1.0
CA A:ILE138 4.7 35.7 1.0
CB A:ASP173 4.7 35.4 1.0
C A:GLY172 4.8 36.8 1.0
N A:MET139 4.8 33.5 1.0
O A:PRO168 4.8 41.7 1.0
CA A:ASP173 4.9 36.6 1.0
C A:ALA136 5.0 39.7 1.0

Calcium binding site 3 out of 10 in 2pjt

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Calcium binding site 3 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:41.8
occ:1.00
 CD2 A:HIS106 3.4 52.1 1.0
N A:HIS106 3.9 42.2 1.0
CB A:THR105 4.0 40.3 1.0
O A:HOH412 4.1 31.6 1.0
CA A:THR105 4.1 40.7 1.0
NE2 A:HIS106 4.1 53.2 1.0
CG A:HIS106 4.3 49.8 1.0
CG2 A:THR105 4.5 38.9 1.0
C A:THR105 4.6 40.4 1.0
CB A:HIS106 4.7 45.1 1.0
CA A:HIS106 5.0 42.1 1.0

Calcium binding site 4 out of 10 in 2pjt

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Calcium binding site 4 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:37.5
occ:1.00
 O B:GLY155 2.0 31.0 1.0
OD2 B:ASP177 2.1 34.0 1.0
OE2 B:GLU180 2.4 35.8 1.0
O B:LEU159 2.4 31.3 1.0
O B:SER157 2.4 36.4 1.0
OD1 B:ASP154 2.5 36.8 1.0
CG B:ASP177 3.1 33.3 1.0
C B:GLY155 3.2 32.2 1.0
CD B:GLU180 3.4 35.7 1.0
N B:GLY155 3.6 32.7 1.0
C B:SER157 3.6 36.6 1.0
C B:LEU159 3.7 32.6 1.0
CG B:ASP154 3.7 35.2 1.0
CB B:ASP177 3.7 31.6 1.0
CA B:GLY155 3.9 32.0 1.0
C B:PRO156 3.9 32.3 1.0
O B:PRO156 4.0 33.2 1.0
OD1 B:ASP177 4.1 33.9 1.0
N B:SER157 4.1 34.3 1.0
CG B:GLU180 4.1 35.4 1.0
N B:LEU159 4.1 33.7 1.0
OE1 B:GLU180 4.2 35.5 1.0
N B:PRO156 4.2 31.3 1.0
C B:ASP154 4.2 33.0 1.0
N B:ASP154 4.3 34.5 1.0
OD2 B:ASP154 4.3 35.0 1.0
CA B:SER157 4.4 36.8 1.0
CA B:PRO156 4.4 31.6 1.0
CA B:LEU159 4.5 33.0 1.0
C B:GLY158 4.5 33.1 1.0
CA B:ASP154 4.6 33.8 1.0
N B:GLY158 4.6 35.3 1.0
N B:LEU160 4.6 33.6 1.0
CB B:ASP154 4.7 34.6 1.0
CA B:LEU160 4.8 33.2 1.0
CA B:GLY158 4.8 33.9 1.0
CB B:LEU159 4.8 32.2 1.0
CB B:ASP179 4.9 34.5 1.0
CB B:PHE153 4.9 31.4 1.0
O B:ASP154 4.9 33.8 1.0

Calcium binding site 5 out of 10 in 2pjt

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Calcium binding site 5 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:43.4
occ:1.00
 O B:ASN169 2.0 40.4 1.0
O B:ASP137 2.3 41.5 1.0
OD1 B:ASP173 2.4 36.8 1.0
O B:GLY171 2.5 35.4 1.0
CG B:ASP173 3.1 35.0 1.0
C B:ASN169 3.2 40.6 1.0
C B:ASP137 3.4 39.7 1.0
C B:GLY171 3.5 35.2 1.0
OD2 B:ASP173 3.5 35.2 1.0
O B:TYR170 3.7 36.6 1.0
C B:TYR170 3.7 36.8 1.0
N B:ASP173 3.8 29.4 1.0
N B:GLY171 4.0 35.3 1.0
O B:ALA136 4.0 39.9 1.0
N B:TYR170 4.1 38.5 1.0
CA B:ASN169 4.1 41.4 1.0
CA B:TYR170 4.2 37.9 1.0
CB B:ASP173 4.3 32.9 1.0
CA B:ASP137 4.3 40.8 1.0
C B:GLY172 4.3 31.1 1.0
N B:GLY172 4.3 34.7 1.0
CA B:GLY171 4.3 34.3 1.0
CA B:ASP173 4.4 29.9 1.0
CA B:GLY172 4.4 31.9 1.0
N B:ILE138 4.4 37.3 1.0
N B:ASN169 4.4 39.9 1.0
N B:MET139 4.5 33.0 1.0
CG B:MET139 4.5 34.6 1.0
CA B:ILE138 4.5 34.2 1.0
O B:GLY167 4.6 38.9 1.0
CH2 B:TRP88 4.9 39.3 1.0
C B:PRO168 4.9 39.3 1.0
C B:ALA136 5.0 40.2 1.0

Calcium binding site 6 out of 10 in 2pjt

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Calcium binding site 6 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:49.4
occ:1.00
 OD2 C:ASP177 2.1 47.3 1.0
O C:LEU159 2.1 32.1 1.0
O C:SER157 2.3 32.4 1.0
OE2 C:GLU180 2.4 36.1 1.0
OD1 C:ASP154 2.5 42.0 1.0
O C:GLY155 2.5 33.2 1.0
C C:LEU159 3.3 31.6 1.0
CG C:ASP177 3.3 44.6 1.0
CG C:ASP154 3.5 40.0 1.0
C C:SER157 3.5 32.7 1.0
CD C:GLU180 3.7 36.3 1.0
N C:LEU159 3.7 32.3 1.0
C C:GLY155 3.7 33.9 1.0
CB C:ASP177 3.9 42.3 1.0
N C:GLY155 3.9 34.9 1.0
N C:ASP154 3.9 38.2 1.0
CA C:LEU159 4.0 31.9 1.0
OD2 C:ASP154 4.0 42.0 1.0
C C:GLY158 4.0 32.8 1.0
C C:ASP154 4.2 36.2 1.0
N C:SER157 4.2 32.3 1.0
CB C:LEU159 4.3 32.8 1.0
C C:PRO156 4.3 31.3 1.0
OD1 C:ASP177 4.3 45.4 1.0
N C:LEU160 4.4 31.9 1.0
CA C:ASP154 4.4 37.4 1.0
CA C:SER157 4.4 33.3 1.0
N C:GLY158 4.4 32.2 1.0
CA C:GLY158 4.5 31.2 1.0
CA C:GLY155 4.5 33.5 1.0
OE1 C:GLU180 4.5 35.2 1.0
O C:PRO156 4.5 31.2 1.0
CB C:ASP154 4.5 38.1 1.0
CG C:GLU180 4.6 35.9 1.0
O C:GLY158 4.6 32.4 1.0
CB C:PHE153 4.7 38.6 1.0
CA C:LEU160 4.7 31.4 1.0
N C:PRO156 4.7 32.3 1.0
CA C:PRO156 4.8 32.5 1.0
O C:ASP154 4.9 36.0 1.0
C C:PHE153 5.0 38.4 1.0

Calcium binding site 7 out of 10 in 2pjt

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Calcium binding site 7 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:42.9
occ:1.00
 O C:HOH409 2.0 51.9 1.0
O C:GLY171 2.1 39.3 1.0
OD1 C:ASP173 2.2 36.7 1.0
O C:ASP137 2.3 37.0 1.0
O C:ASN169 2.5 40.4 1.0
CG C:ASP173 3.1 37.2 1.0
C C:GLY171 3.3 39.6 1.0
C C:ASP137 3.5 35.8 1.0
C C:ASN169 3.5 40.2 1.0
C C:TYR170 3.6 39.7 1.0
OD2 C:ASP173 3.6 37.5 1.0
N C:GLY171 3.7 38.0 1.0
N C:ASP173 3.8 38.2 1.0
O C:TYR170 3.8 39.0 1.0
CA C:TYR170 4.0 40.9 1.0
CA C:GLY171 4.1 38.3 1.0
N C:TYR170 4.1 40.8 1.0
CB C:ASP173 4.2 37.4 1.0
CA C:ASP137 4.3 37.0 1.0
C C:GLY172 4.3 38.6 1.0
N C:GLY172 4.3 39.0 1.0
CA C:ASP173 4.3 37.5 1.0
CA C:GLY172 4.5 37.8 1.0
O C:ALA136 4.5 37.2 1.0
N C:ILE138 4.5 35.1 1.0
N C:ASN169 4.5 40.7 1.0
C C:PRO168 4.6 39.2 1.0
O C:GLY167 4.6 38.0 1.0
CA C:ASN169 4.6 40.5 1.0
O C:PRO168 4.6 39.9 1.0
N C:MET139 4.6 32.2 1.0
CA C:ILE138 4.7 34.2 1.0
CG C:MET139 4.9 28.0 1.0
CH2 C:TRP88 4.9 41.2 1.0

Calcium binding site 8 out of 10 in 2pjt

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Calcium binding site 8 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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 the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca307

b:50.6
occ:1.00
 CD2 C:HIS106 3.8 46.0 1.0
N C:HIS106 3.9 41.6 1.0
CG C:HIS106 4.0 45.4 1.0
NE2 C:HIS106 4.2 46.7 1.0
CA C:THR105 4.3 41.1 1.0
CB C:THR105 4.4 40.2 1.0
CB C:HIS106 4.4 43.4 1.0
ND1 C:HIS106 4.6 46.2 1.0
C C:THR105 4.6 42.4 1.0
CE1 C:HIS106 4.7 46.7 1.0
CG2 C:THR105 4.8 40.7 1.0
CA C:HIS106 4.8 42.6 1.0

Calcium binding site 9 out of 10 in 2pjt

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Calcium binding site 9 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:43.1
occ:1.00
 O D:LEU159 2.2 42.5 1.0
OE2 D:GLU180 2.2 34.6 1.0
O D:SER157 2.2 36.2 1.0
O D:GLY155 2.4 40.7 1.0
OD2 D:ASP177 2.7 31.3 1.0
OD1 D:ASP154 2.7 48.6 1.0
CG D:ASP177 3.3 32.6 1.0
C D:LEU159 3.4 41.6 1.0
C D:SER157 3.4 37.2 1.0
CD D:GLU180 3.5 34.4 1.0
C D:GLY155 3.6 41.2 1.0
CB D:ASP177 3.8 33.7 1.0
CG D:ASP154 3.9 49.7 1.0
N D:LEU159 3.9 38.6 1.0
N D:SER157 3.9 39.4 1.0
N D:GLY155 4.1 44.9 1.0
CA D:LEU159 4.1 40.4 1.0
CA D:SER157 4.1 38.7 1.0
C D:GLY158 4.1 38.8 1.0
C D:ASP154 4.2 46.5 1.0
OD1 D:ASP177 4.2 32.1 1.0
C D:PRO156 4.3 40.1 1.0
N D:ASP154 4.3 47.9 1.0
OE1 D:GLU180 4.3 34.2 1.0
CG D:GLU180 4.4 34.5 1.0
CA D:GLY155 4.4 43.3 1.0
N D:LEU160 4.4 42.8 1.0
CB D:LEU159 4.4 40.2 1.0
N D:GLY158 4.4 36.7 1.0
O D:ASP154 4.4 47.4 1.0
OD2 D:ASP154 4.6 51.5 1.0
N D:PRO156 4.6 40.7 1.0
O D:GLY158 4.6 38.6 1.0
CA D:GLY158 4.6 37.6 1.0
CA D:LEU160 4.6 43.1 1.0
CA D:ASP154 4.6 47.8 1.0
CA D:PRO156 4.7 40.0 1.0
O D:PRO156 4.7 39.9 1.0
CB D:ASP154 4.8 49.2 1.0
CD1 D:PHE153 4.8 45.0 1.0
O D:HOH429 4.9 34.2 1.0
CD2 D:LEU160 5.0 42.4 1.0
CB D:PHE153 5.0 47.4 1.0

Calcium binding site 10 out of 10 in 2pjt

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Calcium binding site 10 out of 10 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca305

b:65.4
occ:1.00
 O D:HOH440 1.9 48.4 1.0
O D:ASN169 1.9 45.2 1.0
OD1 D:ASP173 2.2 45.0 1.0
O D:GLY171 2.3 42.8 1.0
O D:ASP137 2.6 38.1 1.0
CG D:ASP173 2.9 42.5 1.0
C D:ASN169 3.1 43.0 1.0
C D:GLY171 3.2 41.9 1.0
OD2 D:ASP173 3.4 41.7 1.0
C D:TYR170 3.4 40.8 1.0
N D:GLY171 3.5 40.5 1.0
O D:TYR170 3.6 39.5 1.0
N D:ASP173 3.7 39.6 1.0
C D:ASP137 3.7 37.8 1.0
CA D:TYR170 3.9 41.3 1.0
CA D:GLY171 3.9 40.5 1.0
N D:TYR170 3.9 42.2 1.0
CB D:ASP173 4.1 41.6 1.0
CA D:ASN169 4.2 43.0 1.0
N D:GLY172 4.2 41.6 1.0
CA D:ASP173 4.3 40.2 1.0
O D:GLY167 4.3 41.5 1.0
N D:ASN169 4.3 42.6 1.0
C D:GLY172 4.4 40.2 1.0
O D:ALA136 4.4 38.4 1.0
CA D:GLY172 4.5 41.1 1.0
CA D:ASP137 4.5 39.1 1.0
N D:ILE138 4.6 36.9 1.0
N D:MET139 4.6 36.7 1.0
CA D:ILE138 4.7 36.6 1.0
CG D:MET139 4.9 34.3 1.0
C D:PRO168 4.9 41.2 1.0

Reference:

A.Huang, D.Joseph-Mccarthy, F.Lovering, L.Sun, W.Wang, W.Xu, Y.Zhu, J.Cui, Y.Zhang, J.I.Levin. Structure-Based Design of Tace Selective Inhibitors: Manipulations in the S1'-S3' Pocket. Bioorg.Med.Chem. V. 15 6170 2007.
ISSN: ISSN 0968-0896
PubMed: 17606376
DOI: 10.1016/J.BMC.2007.06.031
Page generated: Sat Dec 12 03:50:02 2020

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