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Calcium in PDB 1q3a: Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10:
3.4.24.22;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10, PDB code: 1q3a was solved by V.Calderone, I.Bertini, M.Fragai, C.Luchinat, S.Mangani, B.Terni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.30 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.152, 61.141, 68.588, 90.00, 108.68, 90.00
R / Rfree (%) 27.6 / 29.8

Other elements in 1q3a:

The structure of Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10 (pdb code 1q3a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10, PDB code: 1q3a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1q3a

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Calcium binding site 1 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca466

b:31.9
occ:1.00
 O A:GLY175 2.1 31.1 1.0
OE2 A:GLU200 2.2 22.4 1.0
OD2 A:ASP197 2.2 19.7 1.0
O A:SER179 2.3 30.7 1.0
O A:GLY177 2.4 34.9 1.0
OD2 A:ASP174 2.5 28.9 1.0
C A:GLY175 3.2 31.9 1.0
CG A:ASP197 3.4 21.2 1.0
C A:SER179 3.4 30.6 1.0
CD A:GLU200 3.4 24.4 1.0
CG A:ASP174 3.6 30.7 1.0
C A:GLY177 3.6 34.7 1.0
N A:SER179 3.7 33.2 1.0
CA A:SER179 4.0 31.8 1.0
N A:GLY177 4.0 33.8 1.0
N A:GLY175 4.1 31.6 1.0
OD1 A:ASP174 4.1 30.6 1.0
OE1 A:GLU200 4.1 23.5 1.0
CA A:GLY175 4.1 31.8 1.0
CB A:ASP197 4.1 21.3 1.0
N A:PRO176 4.2 32.7 1.0
C A:PRO176 4.3 33.6 1.0
OD1 A:ASP197 4.3 21.6 1.0
C A:ASP174 4.4 31.7 1.0
C A:HIS178 4.4 34.0 1.0
CA A:GLY177 4.4 34.2 1.0
CA A:PRO176 4.5 33.2 1.0
N A:LEU180 4.5 28.8 1.0
N A:ASP174 4.5 32.0 1.0
CG A:GLU200 4.5 25.4 1.0
CB A:SER179 4.7 31.8 1.0
N A:HIS178 4.7 34.9 1.0
CA A:LEU180 4.8 27.1 1.0
O A:ASP174 4.8 32.3 1.0
CB A:ASP174 4.8 31.2 1.0
O A:PRO176 4.9 33.6 1.0
CA A:ASP174 4.9 31.7 1.0
CA A:HIS178 5.0 34.4 1.0

Calcium binding site 2 out of 9 in 1q3a

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Calcium binding site 2 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca467

b:31.2
occ:1.00
 O A:TYR191 2.2 30.1 1.0
OD1 A:ASP193 2.3 22.2 1.0
O A:GLY189 2.4 33.7 1.0
O A:ASP157 2.6 33.5 1.0
CG A:ASP193 3.3 26.1 1.0
C A:TYR191 3.4 30.1 1.0
OD2 A:ASP193 3.6 26.2 1.0
C A:GLY189 3.6 33.6 1.0
C A:ASP157 3.7 33.4 1.0
C A:LEU190 4.1 32.3 1.0
N A:ASP193 4.1 26.8 1.0
O A:ALA156 4.1 35.6 1.0
O A:LEU190 4.1 32.5 1.0
N A:TYR191 4.2 31.5 1.0
O A:GLY187 4.2 32.4 1.0
N A:GLY189 4.4 33.1 1.0
N A:GLY192 4.4 29.0 1.0
CA A:TYR191 4.4 31.0 1.0
CA A:ASP157 4.4 34.2 1.0
CA A:GLY192 4.5 27.9 1.0
O A:HOH585 4.5 64.9 1.0
C A:GLY192 4.5 27.1 1.0
CB A:ASP193 4.5 25.6 1.0
CA A:GLY189 4.5 33.2 1.0
N A:LEU190 4.6 33.2 1.0
N A:ILE158 4.7 32.3 1.0
CA A:LEU190 4.7 33.2 1.0
CH2 A:TRP108 4.7 35.7 1.0
CG A:MET159 4.7 28.3 1.0
CA A:ASP193 4.7 25.8 1.0
C A:PRO188 4.8 32.8 1.0
CA A:ILE158 4.9 31.2 1.0
N A:MET159 4.9 28.6 1.0

Calcium binding site 3 out of 9 in 1q3a

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Calcium binding site 3 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca468

b:25.3
occ:1.00
 O A:HOH564 2.3 74.5 1.0
OD1 A:ASP198 2.3 32.4 1.0
O A:GLU200 2.4 26.5 1.0
O A:ASP198 2.5 28.3 1.0
OD2 A:ASP123 2.6 32.4 1.0
OD1 A:ASP123 2.8 30.2 1.0
O A:HOH597 2.9 62.9 1.0
CG A:ASP123 3.1 31.5 1.0
CG A:ASP198 3.3 29.5 1.0
C A:ASP198 3.3 28.0 1.0
C A:GLU200 3.6 27.2 1.0
CA A:ASP198 3.8 27.3 1.0
OD2 A:ASP198 4.1 30.3 1.0
CD1 A:TRP202 4.1 28.5 1.0
CB A:ASP198 4.1 27.6 1.0
N A:GLU200 4.1 27.7 1.0
CA A:LYS201 4.3 28.6 1.0
N A:ASP199 4.3 28.1 1.0
N A:LYS201 4.3 27.6 1.0
OG1 A:THR121 4.4 26.9 1.0
C A:ASP199 4.5 28.2 1.0
CA A:GLU200 4.6 26.9 1.0
NE1 A:TRP202 4.6 28.5 1.0
CB A:ASP123 4.6 30.4 1.0
CA A:ASP199 4.6 28.5 1.0
N A:TRP202 4.7 28.9 1.0
O A:HOH506 4.7 36.9 1.0
O A:HOH589 4.8 57.4 1.0

Calcium binding site 4 out of 9 in 1q3a

Go back to Calcium Binding Sites List in 1q3a
Calcium binding site 4 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca471

b:26.0
occ:1.00
 O B:GLY177 2.1 29.0 1.0
OD2 B:ASP197 2.2 25.1 1.0
OE2 B:GLU200 2.3 22.8 1.0
O B:GLY175 2.4 33.0 1.0
O B:SER179 2.5 28.2 1.0
OD1 B:ASP174 2.6 30.1 1.0
CG B:ASP197 3.3 26.4 1.0
C B:GLY177 3.4 30.0 1.0
CD B:GLU200 3.6 24.2 1.0
C B:SER179 3.6 28.4 1.0
C B:GLY175 3.6 32.9 1.0
CG B:ASP174 3.9 32.9 1.0
N B:SER179 4.0 29.3 1.0
C B:HIS178 4.0 29.9 1.0
N B:GLY177 4.1 31.6 1.0
N B:GLY175 4.1 33.5 1.0
CB B:ASP197 4.1 26.1 1.0
OD1 B:ASP197 4.1 28.3 1.0
C B:ASP174 4.1 33.0 1.0
N B:ASP174 4.1 32.5 1.0
CA B:GLY177 4.3 30.8 1.0
O B:HIS178 4.3 30.4 1.0
C B:PRO176 4.3 31.7 1.0
OE1 B:GLU200 4.3 23.9 1.0
CB B:HIS178 4.3 30.1 1.0
CA B:SER179 4.3 28.9 1.0
N B:HIS178 4.4 29.9 1.0
O B:ASP174 4.4 33.6 1.0
CA B:GLY175 4.4 33.0 1.0
CA B:HIS178 4.5 30.1 1.0
CA B:ASP174 4.5 32.7 1.0
OD2 B:ASP174 4.6 34.5 1.0
N B:PRO176 4.6 32.4 1.0
N B:LEU180 4.6 27.1 1.0
O B:PRO176 4.7 31.1 1.0
CA B:PRO176 4.7 32.1 1.0
CG B:GLU200 4.7 26.4 1.0
O B:HOH496 4.7 31.1 1.0
CB B:ASP174 4.8 32.2 1.0
CA B:LEU180 4.8 26.3 1.0
CB B:SER179 4.9 28.9 1.0

Calcium binding site 5 out of 9 in 1q3a

Go back to Calcium Binding Sites List in 1q3a
Calcium binding site 5 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca472

b:30.8
occ:1.00
 O B:ASP157 2.3 27.9 1.0
O B:GLY189 2.4 32.9 1.0
OD1 B:ASP193 2.4 26.6 1.0
O B:TYR191 2.6 29.5 1.0
O B:HOH513 2.9 36.8 1.0
CG B:ASP193 3.4 26.5 1.0
C B:ASP157 3.5 28.8 1.0
C B:GLY189 3.6 32.5 1.0
C B:TYR191 3.7 29.3 1.0
OD2 B:ASP193 3.8 26.9 1.0
O B:ALA156 3.8 30.6 1.0
O B:LEU190 4.0 29.8 1.0
C B:LEU190 4.1 30.3 1.0
N B:ASP193 4.1 26.4 1.0
O B:HOH568 4.3 69.7 1.0
CA B:ASP157 4.3 29.6 1.0
C B:GLY192 4.3 27.1 1.0
N B:MET159 4.3 27.6 1.0
N B:GLY189 4.4 33.3 1.0
N B:ILE158 4.4 27.9 1.0
CG B:MET159 4.4 30.9 1.0
N B:TYR191 4.4 29.9 1.0
CA B:GLY192 4.4 27.9 1.0
CA B:GLY189 4.5 33.0 1.0
O B:GLY187 4.5 33.6 1.0
N B:LEU190 4.5 31.8 1.0
N B:GLY192 4.5 28.8 1.0
CA B:LEU190 4.6 31.0 1.0
CB B:ASP193 4.6 25.7 1.0
CA B:ILE158 4.6 27.7 1.0
CA B:ASP193 4.7 25.9 1.0
CA B:TYR191 4.7 30.3 1.0
O B:GLY192 4.9 26.9 1.0
C B:ALA156 4.9 30.5 1.0
CB B:MET159 4.9 28.5 1.0
CH2 B:TRP108 5.0 29.3 1.0
C B:ILE158 5.0 27.4 1.0
OE1 B:GLU155 5.0 31.5 1.0

Calcium binding site 6 out of 9 in 1q3a

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Calcium binding site 6 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca473

b:34.1
occ:1.00
 O B:ASP198 2.1 29.6 1.0
OD1 B:ASP198 2.2 29.7 1.0
O B:GLU200 2.3 29.2 1.0
OD2 B:ASP123 2.5 28.4 1.0
O B:HOH482 2.6 18.4 1.0
O B:HOH500 2.8 28.0 1.0
OD1 B:ASP123 2.8 29.1 1.0
CG B:ASP123 3.0 30.1 1.0
C B:ASP198 3.1 29.5 1.0
CG B:ASP198 3.3 29.6 1.0
C B:GLU200 3.4 29.4 1.0
CA B:ASP198 3.7 28.8 1.0
CB B:ASP198 3.9 29.1 1.0
OD2 B:ASP198 4.2 32.3 1.0
N B:GLU200 4.2 29.5 1.0
N B:ASP199 4.2 30.4 1.0
CD1 B:TRP202 4.3 26.4 1.0
N B:LYS201 4.3 29.9 1.0
OG1 B:THR121 4.3 24.9 1.0
CA B:LYS201 4.3 30.4 1.0
C B:ASP199 4.4 30.4 1.0
CA B:GLU200 4.4 28.8 1.0
CA B:ASP199 4.5 30.6 1.0
CB B:ASP123 4.5 29.5 1.0
N B:TRP202 4.7 29.8 1.0
NE1 B:TRP202 4.8 27.0 1.0
O B:ASP199 5.0 30.1 1.0

Calcium binding site 7 out of 9 in 1q3a

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Calcium binding site 7 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca476

b:36.4
occ:1.00
 OE1 C:GLU200 2.3 36.3 1.0
OD1 C:ASP174 2.4 24.5 1.0
O C:SER179 2.4 28.0 1.0
O C:GLY175 2.4 30.2 1.0
O C:GLY177 2.4 30.9 1.0
OD2 C:ASP197 2.6 29.2 1.0
CD C:GLU200 3.4 35.8 1.0
C C:SER179 3.5 28.5 1.0
C C:GLY177 3.5 30.8 1.0
C C:GLY175 3.6 30.4 1.0
CG C:ASP174 3.6 26.2 1.0
CG C:ASP197 3.6 28.7 1.0
N C:SER179 3.6 29.3 1.0
N C:GLY175 3.9 28.1 1.0
C C:HIS178 3.9 29.6 1.0
OE2 C:GLU200 4.1 33.5 1.0
C C:ASP174 4.1 27.3 1.0
CA C:SER179 4.1 28.7 1.0
N C:ASP174 4.2 26.8 1.0
N C:GLY177 4.2 31.0 1.0
CB C:ASP197 4.2 28.5 1.0
CB C:HIS178 4.2 29.9 1.0
OD2 C:ASP174 4.3 25.1 1.0
CA C:GLY175 4.3 29.3 1.0
N C:HIS178 4.4 30.6 1.0
CA C:HIS178 4.4 30.0 1.0
O C:HIS178 4.4 29.6 1.0
CG C:GLU200 4.5 35.4 1.0
C C:PRO176 4.5 30.9 1.0
CA C:GLY177 4.5 31.1 1.0
N C:LEU180 4.5 28.6 1.0
CA C:ASP174 4.5 26.9 1.0
O C:ASP174 4.6 27.2 1.0
CB C:ASP174 4.6 26.5 1.0
OD1 C:ASP197 4.6 30.0 1.0
N C:PRO176 4.6 31.0 1.0
CA C:LEU180 4.8 28.5 1.0
CA C:PRO176 4.8 31.2 1.0
O C:PRO176 4.9 31.0 1.0
CB C:SER179 5.0 29.1 1.0

Calcium binding site 8 out of 9 in 1q3a

Go back to Calcium Binding Sites List in 1q3a
Calcium binding site 8 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca477

b:40.5
occ:1.00
 O C:ASP157 2.0 25.9 1.0
O C:HOH498 2.3 30.0 1.0
O C:TYR191 2.4 29.1 1.0
OD2 C:ASP193 2.4 24.2 1.0
O C:GLY189 2.8 31.8 1.0
C C:ASP157 3.2 27.1 1.0
CG C:ASP193 3.4 23.3 1.0
C C:TYR191 3.4 29.0 1.0
OD1 C:ASP193 3.8 23.5 1.0
C C:GLY189 3.9 31.4 1.0
N C:ASP193 4.0 25.0 1.0
O C:ALA156 4.0 29.1 1.0
CA C:GLY192 4.1 26.5 1.0
N C:ILE158 4.1 25.9 1.0
CA C:ASP157 4.2 28.2 1.0
N C:GLY192 4.2 27.8 1.0
CA C:ILE158 4.2 25.3 1.0
C C:GLY192 4.2 25.8 1.0
C C:LEU190 4.3 30.3 1.0
O C:LEU190 4.3 29.6 1.0
N C:TYR191 4.3 30.3 1.0
N C:GLY189 4.4 31.6 1.0
CA C:TYR191 4.5 30.4 1.0
N C:MET159 4.5 24.5 1.0
CB C:ASP193 4.5 24.8 1.0
CA C:ASP193 4.6 25.0 1.0
CA C:GLY189 4.7 31.5 1.0
CH2 C:TRP108 4.8 38.9 1.0
O C:GLY187 4.8 31.7 1.0
N C:LEU190 4.8 30.8 1.0
C C:ILE158 4.8 24.9 1.0
OE2 C:GLU155 4.8 42.2 1.0
CA C:LEU190 4.8 30.6 1.0
C C:ALA156 4.9 29.8 1.0

Calcium binding site 9 out of 9 in 1q3a

Go back to Calcium Binding Sites List in 1q3a
Calcium binding site 9 out of 9 in the Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10


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 Human Matrix Metalloproteinase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca478

b:44.6
occ:1.00
 OD1 C:ASP123 2.0 38.4 1.0
O C:GLU200 2.5 33.9 1.0
O C:ASP198 2.7 36.2 1.0
CG C:ASP123 2.7 37.0 1.0
OD2 C:ASP123 2.7 38.6 1.0
OD1 C:ASP198 2.8 38.2 1.0
C C:GLU200 3.5 34.9 1.0
C C:ASP198 3.6 35.2 1.0
CG C:ASP198 3.7 36.7 1.0
CA C:LYS201 4.0 35.0 1.0
CD1 C:TRP202 4.0 35.2 1.0
CA C:ASP198 4.1 34.5 1.0
CB C:ASP123 4.1 35.3 1.0
N C:LYS201 4.1 34.6 1.0
CB C:ASP198 4.4 35.2 1.0
OD2 C:ASP198 4.5 36.6 1.0
N C:GLU200 4.6 35.9 1.0
NE1 C:TRP202 4.6 33.9 1.0
C C:ASP199 4.6 36.3 1.0
N C:TRP202 4.6 35.2 1.0
N C:ASP199 4.6 35.9 1.0
CA C:GLU200 4.7 35.2 1.0
OG1 C:THR121 4.7 30.6 1.0
CB C:LYS201 4.8 34.4 1.0
CA C:ASP199 4.9 36.5 1.0
C C:LYS201 4.9 34.9 1.0
O C:ASP199 5.0 36.4 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, S.Mangani, B.Terni. Crystal Structure of the Catalytic Domain of Human Matrix Metalloproteinase 10. J.Mol.Biol. V. 336 707 2004.
ISSN: ISSN 0022-2836
PubMed: 15095982
DOI: 10.1016/J.JMB.2003.12.033
Page generated: Thu Jul 11 13:58:30 2024

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