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Calcium in PDB 1eak: Catalytic Domain of Prommp-2 E404Q Mutant

Enzymatic activity of Catalytic Domain of Prommp-2 E404Q Mutant

All present enzymatic activity of Catalytic Domain of Prommp-2 E404Q Mutant:
3.4.24.24;

Protein crystallography data

The structure of Catalytic Domain of Prommp-2 E404Q Mutant, PDB code: 1eak was solved by U.Bergmann, A.Tuuttila, K.Tryggvason, E.Morgunova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.58 / 2.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.670, 166.150, 170.130, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 30.3

Other elements in 1eak:

The structure of Catalytic Domain of Prommp-2 E404Q Mutant also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catalytic Domain of Prommp-2 E404Q Mutant (pdb code 1eak). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Catalytic Domain of Prommp-2 E404Q Mutant, PDB code: 1eak:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1eak

Go back to Calcium Binding Sites List in 1eak
Calcium binding site 1 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca998

b:20.6
occ:1.00
OD2 A:ASP208 2.3 25.4 1.0
O A:LEU190 2.4 21.4 1.0
O A:GLY186 2.4 30.9 1.0
OD1 A:ASP185 2.6 28.9 1.0
O A:ASP188 2.7 28.7 1.0
OE2 A:GLU211 2.7 23.8 1.0
CG A:ASP208 3.4 25.8 1.0
C A:LEU190 3.5 22.1 1.0
C A:GLY186 3.6 29.8 1.0
CG A:ASP185 3.6 30.9 1.0
C A:ASP188 3.7 27.1 1.0
N A:GLY186 3.8 27.6 1.0
N A:LEU190 3.8 22.7 1.0
CD A:GLU211 3.9 25.9 1.0
N A:ASP188 4.0 27.7 1.0
CB A:ASP208 4.0 23.3 1.0
N A:ASP185 4.1 25.1 1.0
OD2 A:ASP185 4.2 31.1 1.0
CA A:LEU190 4.2 22.7 1.0
OD1 A:ASP208 4.3 28.1 1.0
C A:ASP185 4.3 28.1 1.0
C A:LYS187 4.3 28.2 1.0
CA A:ASP188 4.4 27.8 1.0
C A:GLY189 4.4 23.0 1.0
CA A:GLY186 4.4 28.9 1.0
CA A:ASP185 4.5 27.7 1.0
CG A:GLU211 4.5 26.0 1.0
N A:LYS187 4.6 29.4 1.0
N A:LEU191 4.6 20.6 1.0
CA A:LYS187 4.6 28.9 1.0
CB A:LEU190 4.7 25.2 1.0
CB A:ASP185 4.7 29.0 1.0
CA A:GLY189 4.7 24.1 1.0
N A:GLY189 4.7 26.3 1.0
CA A:LEU191 4.8 19.2 1.0
CB A:PHE184 4.8 20.0 1.0
CD2 A:LEU191 4.8 16.1 1.0
OE1 A:GLU211 4.9 26.7 1.0
O A:HOH2006 4.9 15.0 1.0
O A:LYS187 5.0 26.8 1.0

Calcium binding site 2 out of 8 in 1eak

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Calcium binding site 2 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca999

b:76.7
occ:1.00
O A:GLY202 2.9 31.2 1.0
O A:ASP168 3.0 28.1 1.0
O A:GLY200 3.2 39.3 1.0
O A:GLY198 3.5 38.0 1.0
O A:ALA167 3.7 32.4 1.0
C A:GLY202 3.9 28.2 1.0
C A:ASP168 3.9 27.2 1.0
N A:GLY202 4.0 28.9 1.0
C A:GLY200 4.1 36.5 1.0
CA A:ASP168 4.2 26.4 1.0
OE2 A:GLU166 4.3 40.4 1.0
OD1 A:ASP204 4.3 31.0 1.0
N A:GLY200 4.3 36.2 1.0
C A:THR199 4.3 37.9 1.0
CA A:GLY202 4.3 28.3 1.0
C A:VAL201 4.4 30.6 1.0
CA A:THR199 4.4 39.0 1.0
C A:GLY198 4.6 35.7 1.0
C A:ALA167 4.7 31.4 1.0
CA A:VAL201 4.8 31.5 1.0
O A:THR199 4.8 39.3 1.0
N A:VAL201 4.8 34.0 1.0
CA A:GLY200 4.8 36.5 1.0
CH2 A:TRP119 4.9 40.1 1.0
O A:VAL201 5.0 30.7 1.0

Calcium binding site 3 out of 8 in 1eak

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Calcium binding site 3 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca998

b:20.8
occ:1.00
O B:LEU190 2.3 31.3 1.0
OE2 B:GLU211 2.4 15.0 1.0
O B:GLY186 2.4 27.8 1.0
OD1 B:ASP185 2.6 26.9 1.0
O B:ASP188 2.6 37.8 1.0
OD2 B:ASP208 2.7 28.2 1.0
C B:LEU190 3.3 28.2 1.0
C B:GLY186 3.4 26.8 1.0
CG B:ASP208 3.5 26.4 1.0
C B:ASP188 3.5 37.3 1.0
CD B:GLU211 3.6 16.4 1.0
N B:LEU190 3.6 29.5 1.0
CG B:ASP185 3.8 25.2 1.0
N B:ASP188 3.8 36.8 1.0
CA B:LEU190 3.9 28.4 1.0
N B:GLY186 3.9 22.2 1.0
CB B:ASP208 4.0 24.8 1.0
OE1 B:GLU211 4.0 15.9 1.0
C B:LYS187 4.0 35.0 1.0
CA B:ASP188 4.2 37.6 1.0
N B:LYS187 4.3 28.1 1.0
CA B:GLY186 4.3 24.2 1.0
CB B:LEU190 4.3 27.4 1.0
N B:LEU191 4.3 25.6 1.0
C B:GLY189 4.4 33.3 1.0
OD2 B:ASP185 4.4 29.0 1.0
CA B:LYS187 4.4 31.1 1.0
OD1 B:ASP208 4.4 23.2 1.0
N B:ASP185 4.5 16.9 1.0
C B:ASP185 4.5 20.1 1.0
N B:GLY189 4.5 36.3 1.0
O B:LYS187 4.5 39.0 1.0
CA B:LEU191 4.6 22.2 1.0
CA B:GLY189 4.7 35.7 1.0
CG B:GLU211 4.8 16.5 1.0
CD2 B:LEU191 4.8 15.8 1.0
CA B:ASP185 4.8 19.0 1.0
CB B:ASP185 4.9 21.3 1.0

Calcium binding site 4 out of 8 in 1eak

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Calcium binding site 4 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca999

b:0.0
occ:1.00
O B:GLY202 3.0 28.9 1.0
O B:GLY200 3.1 30.3 1.0
O B:ASP168 3.1 26.4 1.0
O B:GLY198 3.4 35.5 1.0
O B:ALA167 3.9 34.8 1.0
C B:ASP168 4.0 24.7 1.0
C B:GLY200 4.0 29.5 1.0
C B:GLY202 4.0 25.9 1.0
CA B:ASP168 4.1 27.2 1.0
N B:GLY202 4.2 24.0 1.0
N B:GLY200 4.3 33.4 1.0
OD1 B:ASP204 4.4 30.2 1.0
C B:THR199 4.5 34.3 1.0
CA B:GLY202 4.5 24.7 1.0
CH2 B:TRP119 4.5 34.8 1.0
C B:VAL201 4.5 25.9 1.0
C B:GLY198 4.6 34.9 1.0
OE2 B:GLU166 4.6 39.6 1.0
CA B:THR199 4.7 34.6 1.0
CA B:GLY200 4.8 31.3 1.0
C B:ALA167 4.8 33.0 1.0
N B:VAL201 4.9 28.0 1.0
O B:VAL201 4.9 24.5 1.0
CA B:VAL201 4.9 26.6 1.0
O B:THR199 5.0 35.2 1.0

Calcium binding site 5 out of 8 in 1eak

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Calcium binding site 5 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca998

b:30.8
occ:1.00
O C:ASP188 2.3 37.0 1.0
OD2 C:ASP208 2.4 29.0 1.0
O C:LEU190 2.5 26.8 1.0
O C:GLY186 2.5 28.2 1.0
OD1 C:ASP185 2.6 34.7 1.0
OE2 C:GLU211 2.7 34.8 1.0
CG C:ASP208 3.4 26.6 1.0
C C:ASP188 3.5 35.6 1.0
C C:LEU190 3.6 26.7 1.0
C C:GLY186 3.7 28.6 1.0
CD C:GLU211 3.7 34.5 1.0
CG C:ASP185 3.7 32.3 1.0
CB C:ASP208 3.9 25.8 1.0
N C:LEU190 3.9 29.9 1.0
C C:LYS187 4.0 33.1 1.0
CG C:GLU211 4.0 33.4 1.0
N C:ASP188 4.0 34.6 1.0
C C:GLY189 4.0 30.2 1.0
O C:LYS187 4.1 34.7 1.0
N C:GLY186 4.2 29.2 1.0
CA C:ASP188 4.3 35.5 1.0
CA C:LEU190 4.3 29.4 1.0
OD2 C:ASP185 4.3 32.7 1.0
CA C:GLY189 4.4 30.0 1.0
OD1 C:ASP208 4.4 26.5 1.0
N C:ASP185 4.4 25.8 1.0
C C:ASP185 4.4 27.5 1.0
N C:GLY189 4.4 33.2 1.0
O C:GLY189 4.5 30.7 1.0
N C:LEU191 4.5 24.1 1.0
CA C:GLY186 4.6 28.6 1.0
CA C:LYS187 4.6 31.8 1.0
CA C:LEU191 4.6 24.5 1.0
N C:LYS187 4.6 29.4 1.0
CD2 C:LEU191 4.6 21.2 1.0
CA C:ASP185 4.7 26.5 1.0
CB C:ASP185 4.8 29.5 1.0
OE1 C:GLU211 4.9 32.9 1.0
CB C:LEU190 5.0 29.6 1.0

Calcium binding site 6 out of 8 in 1eak

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Calcium binding site 6 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca999

b:94.8
occ:1.00
O C:GLY202 3.1 40.9 1.0
O C:GLY200 3.1 38.9 1.0
O C:ASP168 3.2 42.1 1.0
O C:GLY198 3.4 33.5 1.0
O C:ALA167 3.9 48.0 1.0
C C:ASP168 4.0 40.1 1.0
C C:GLY200 4.1 36.8 1.0
CA C:ASP168 4.1 41.4 1.0
C C:GLY202 4.2 38.5 1.0
N C:GLY200 4.2 34.6 1.0
C C:THR199 4.3 34.0 1.0
N C:GLY202 4.3 36.2 1.0
CA C:THR199 4.5 33.5 1.0
C C:GLY198 4.5 33.9 1.0
OD1 C:ASP204 4.5 38.3 1.0
CH2 C:TRP119 4.6 49.8 1.0
CA C:GLY202 4.6 37.9 1.0
CA C:GLY200 4.7 36.5 1.0
C C:VAL201 4.7 35.9 1.0
O C:THR199 4.8 33.1 1.0
C C:ALA167 4.9 47.2 1.0
OE2 C:GLU166 5.0 63.2 1.0

Calcium binding site 7 out of 8 in 1eak

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Calcium binding site 7 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca998

b:34.1
occ:1.00
OD1 D:ASP185 2.4 34.2 1.0
O D:GLY186 2.4 21.4 1.0
O D:LEU190 2.4 37.2 1.0
OE2 D:GLU211 2.7 32.3 1.0
O D:ASP188 2.9 31.8 1.0
OD2 D:ASP208 3.1 47.4 1.0
CG D:ASP208 3.3 43.3 1.0
C D:GLY186 3.4 24.4 1.0
CG D:ASP185 3.5 30.8 1.0
C D:LEU190 3.6 37.8 1.0
N D:GLY186 3.7 25.2 1.0
CB D:ASP208 3.7 39.0 1.0
OD1 D:ASP208 3.7 44.5 1.0
CD D:GLU211 3.8 30.0 1.0
C D:ASP188 3.8 31.4 1.0
CA D:GLY186 4.1 24.4 1.0
N D:ASP188 4.1 30.9 1.0
OD2 D:ASP185 4.2 31.5 1.0
N D:ASP185 4.2 27.3 1.0
N D:LEU190 4.3 37.7 1.0
C D:ASP185 4.3 25.3 1.0
CG D:GLU211 4.3 28.3 1.0
C D:GLY189 4.4 37.2 1.0
CA D:ASP188 4.4 29.7 1.0
CA D:LEU190 4.4 38.0 1.0
N D:LYS187 4.5 26.6 1.0
N D:LEU191 4.5 37.0 1.0
C D:LYS187 4.5 30.4 1.0
CA D:LEU191 4.5 35.4 1.0
CA D:ASP185 4.6 25.8 1.0
O D:GLY189 4.6 38.0 1.0
CB D:ASP185 4.7 26.4 1.0
CA D:LYS187 4.7 28.7 1.0
N D:GLY189 4.7 33.8 1.0
OE1 D:GLU211 4.8 31.7 1.0
CB D:LEU190 4.8 38.2 1.0
CA D:GLY189 4.9 35.6 1.0
CB D:PHE184 5.0 30.8 1.0

Calcium binding site 8 out of 8 in 1eak

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Calcium binding site 8 out of 8 in the Catalytic Domain of Prommp-2 E404Q Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Catalytic Domain of Prommp-2 E404Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca999

b:0.0
occ:1.00
O D:GLY200 3.2 54.7 1.0
O D:ALA167 3.2 48.6 1.0
O D:ASP168 3.2 44.6 1.0
O D:GLY202 3.7 58.0 1.0
CA D:ASP168 3.7 46.1 1.0
C D:ASP168 3.8 45.4 1.0
O D:GLY198 4.1 56.4 1.0
OE1 D:GLU166 4.1 60.5 1.0
C D:ALA167 4.2 48.7 1.0
C D:GLY200 4.3 55.8 1.0
N D:ASP168 4.5 47.4 1.0
OE2 D:GLU166 4.6 59.1 1.0
CD D:GLU166 4.7 58.2 1.0
N D:GLY200 4.7 57.4 1.0
C D:GLY202 4.8 56.3 1.0
OD1 D:ASP204 4.9 48.7 1.0
CB D:ASP168 4.9 47.6 1.0
N D:GLY202 4.9 57.4 1.0
C D:THR199 4.9 57.8 1.0
N D:ILE169 5.0 44.2 1.0

Reference:

U.Bergmann, A.Tuuttila, E.Morgunova, K.Tryggvason. Crystal Structure of Human Mmp-2 Reveals A New P To Be Published.
Page generated: Sat Dec 12 02:54:01 2020

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