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Calcium in PDB 3ayu: Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor

Enzymatic activity of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor

All present enzymatic activity of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor:
3.4.24.24;

Protein crystallography data

The structure of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor, PDB code: 3ayu was solved by H.Hashimoto, T.Takeuchi, K.Komatsu, K.Miyazaki, M.Sato, S.Higashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.881, 76.060, 37.082, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.5

Other elements in 3ayu:

The structure of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor (pdb code 3ayu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor, PDB code: 3ayu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3ayu

Go back to Calcium Binding Sites List in 3ayu
Calcium binding site 1 out of 3 in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor


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 Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca417

b:11.9
occ:1.00
 O A:LEU81 2.2 16.7 1.0
O A:GLY77 2.3 19.8 1.0
O A:ASP79 2.3 20.6 1.0
OD2 A:ASP99 2.3 15.1 1.0
OE2 A:GLU102 2.4 16.8 1.0
OD2 A:ASP76 2.4 18.3 1.0
CG A:ASP99 3.4 14.9 1.0
C A:LEU81 3.4 16.8 1.0
C A:ASP79 3.5 21.0 1.0
C A:GLY77 3.5 20.0 1.0
CD A:GLU102 3.6 16.4 1.0
CG A:ASP76 3.6 18.8 1.0
N A:ASP79 3.9 21.5 1.0
N A:LEU81 3.9 18.5 1.0
CB A:ASP99 4.1 14.6 1.0
C A:LYS78 4.1 21.5 1.0
CA A:LEU81 4.2 17.6 1.0
C A:GLY80 4.2 19.2 1.0
N A:GLY77 4.2 19.5 1.0
OD1 A:ASP76 4.2 18.8 1.0
O A:HOH237 4.3 39.0 1.0
CA A:LYS78 4.3 21.1 1.0
C A:ASP76 4.3 19.4 1.0
N A:ASP76 4.3 18.3 1.0
OD1 A:ASP99 4.3 15.0 1.0
CA A:ASP79 4.3 21.7 1.0
CG A:GLU102 4.4 15.9 1.0
N A:LYS78 4.4 20.7 1.0
N A:LEU82 4.4 15.9 1.0
CA A:GLY77 4.5 19.9 1.0
N A:GLY80 4.5 20.6 1.0
OE1 A:GLU102 4.5 16.7 1.0
CB A:LEU81 4.5 17.7 1.0
CA A:GLY80 4.6 20.2 1.0
O A:LYS78 4.6 22.2 1.0
O A:GLY80 4.6 19.0 1.0
CA A:ASP76 4.7 19.1 1.0
CA A:LEU82 4.7 15.3 1.0
O A:ASP76 4.7 19.5 1.0
CB A:ASP76 4.7 19.2 1.0

Calcium binding site 2 out of 3 in 3ayu

Go back to Calcium Binding Sites List in 3ayu
Calcium binding site 2 out of 3 in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor


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 Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca418

b:12.7
occ:1.00
 O A:GLY93 2.3 15.7 1.0
O A:ASP59 2.3 15.5 1.0
O A:GLY91 2.3 16.6 1.0
O A:HOH303 2.4 14.7 1.0
O A:HOH212 2.4 12.4 1.0
OD1 A:ASP95 2.4 15.4 1.0
CG A:ASP95 3.4 15.6 1.0
C A:GLY93 3.5 15.7 1.0
C A:ASP59 3.5 15.7 1.0
C A:GLY91 3.5 17.4 1.0
OD2 A:ASP95 3.8 15.9 1.0
C A:VAL92 3.9 16.5 1.0
N A:GLY93 3.9 16.7 1.0
O A:ALA58 4.1 16.9 1.0
N A:ASP95 4.1 15.2 1.0
O A:VAL92 4.2 16.0 1.0
CA A:GLY93 4.3 16.3 1.0
CA A:ASP59 4.3 16.1 1.0
CA A:VAL92 4.3 17.0 1.0
O A:GLY89 4.3 17.2 1.0
N A:VAL92 4.4 17.5 1.0
O A:HOH349 4.4 22.9 1.0
N A:GLY94 4.5 15.3 1.0
N A:GLY91 4.5 18.4 1.0
N A:ILE60 4.5 15.1 1.0
CA A:GLY91 4.5 18.3 1.0
O A:HOH177 4.5 24.1 1.0
CB A:ASP95 4.6 15.2 1.0
CA A:GLY94 4.6 15.0 1.0
C A:GLY94 4.6 14.9 1.0
O A:HOH311 4.6 21.8 1.0
CA A:ILE60 4.7 14.9 1.0
N A:MET61 4.7 15.1 1.0
CH2 A:TRP10 4.7 19.4 1.0
CA A:ASP95 4.7 14.9 1.0
C A:THR90 4.8 18.6 1.0
CG A:MET61 4.9 16.1 1.0
O A:THR90 5.0 18.6 1.0

Calcium binding site 3 out of 3 in 3ayu

Go back to Calcium Binding Sites List in 3ayu
Calcium binding site 3 out of 3 in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor


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 Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca419

b:25.9
occ:1.00
 O A:GLU102 2.3 16.2 1.0
O A:ASP100 2.3 15.9 1.0
OD2 A:ASP25 2.4 17.6 1.0
OD1 A:ASP100 2.4 15.8 1.0
O A:HOH215 2.5 26.7 1.0
CG A:ASP25 3.1 18.2 1.0
OD1 A:ASP25 3.2 18.4 1.0
C A:ASP100 3.2 15.8 1.0
CG A:ASP100 3.4 16.1 1.0
C A:GLU102 3.5 16.2 1.0
CA A:ASP100 3.7 15.4 1.0
OG1 A:THR23 3.9 17.7 1.0
CB A:ASP100 4.0 15.8 1.0
CD1 A:TRP104 4.1 14.6 1.0
CA A:LEU103 4.1 16.4 1.0
N A:LEU103 4.2 16.4 1.0
OD2 A:ASP100 4.2 16.8 1.0
N A:GLU102 4.3 16.1 1.0
N A:ASP101 4.3 15.9 1.0
O A:HOH267 4.4 26.3 1.0
O A:HOH259 4.4 62.0 1.0
N A:TRP104 4.5 15.4 1.0
C A:ASP101 4.5 16.5 1.0
CA A:GLU102 4.5 16.1 1.0
CB A:ASP25 4.5 18.2 1.0
NE1 A:TRP104 4.6 14.4 1.0
CA A:ASP101 4.6 16.4 1.0
NH2 A:ARG66 4.8 22.1 1.0
C A:LEU103 4.8 16.0 1.0

Reference:

H.Hashimoto, T.Takeuchi, K.Komatsu, K.Miyazaki, M.Sato, S.Higashi. Structural Basis For Matrix Metalloproteinase-2 (Mmp-2)-Selective Inhibitory Action of {Beta}-Amyloid Precursor Protein-Derived Inhibitor J.Biol.Chem. 2011.
ISSN: ESSN 1083-351X
PubMed: 21813640
DOI: 10.1074/JBC.M111.264176
Page generated: Sat Dec 12 04:05:20 2020

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