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Calcium in PDB 1jao: Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)

Enzymatic activity of Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)

All present enzymatic activity of Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form):
3.4.24.34;

Protein crystallography data

The structure of Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1jao was solved by F.Grams, P.Reinemer, J.C.Powers, T.Kleine, M.Piper, H.Tschesche, R.Huber, W.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.240, 69.200, 72.330, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / n/a

Other elements in 1jao:

The structure of Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) (pdb code 1jao). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1jao:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1jao

Go back to Calcium Binding Sites List in 1jao
Calcium binding site 1 out of 2 in the Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:12.9
occ:1.00
 H2 A:HOH1027 1.3 15.0 1.0
O A:HOH1027 2.2 3.6 1.0
O A:ASP137 2.2 8.8 1.0
H1 A:HOH1027 2.2 15.0 1.0
O A:GLY171 2.3 11.9 1.0
OD1 A:ASP173 2.3 6.7 1.0
O A:GLY169 2.4 17.1 1.0
C A:ASP137 3.3 9.2 1.0
CG A:ASP173 3.4 9.5 1.0
C A:GLY171 3.5 10.9 1.0
HD22 A:ASN139 3.5 15.0 1.0
C A:GLY169 3.6 17.0 1.0
H A:ASP173 3.7 15.0 1.0
OD2 A:ASP173 3.9 9.8 1.0
N A:GLY171 4.0 11.2 1.0
H A:ASN139 4.0 15.0 1.0
C A:ILE170 4.0 13.8 1.0
N A:ASP173 4.1 5.0 1.0
H A:GLY171 4.2 15.0 1.0
O A:ILE170 4.2 15.1 1.0
N A:ILE138 4.2 7.8 1.0
CA A:GLY171 4.2 10.7 1.0
O A:GLY167 4.2 14.3 1.0
CA A:ASP137 4.2 9.5 1.0
O A:ALA136 4.3 15.0 1.0
CA A:ILE138 4.4 7.0 1.0
ND2 A:ASN139 4.4 10.3 1.0
N A:GLY172 4.5 9.4 1.0
N A:ILE170 4.5 16.1 1.0
H A:GLY169 4.5 15.0 1.0
O A:HOH1026 4.5 53.4 1.0
N A:GLY169 4.5 17.9 1.0
CA A:ILE170 4.5 14.8 1.0
H1 A:HOH1026 4.6 15.0 1.0
CA A:GLY169 4.6 17.0 1.0
CA A:GLY172 4.6 6.2 1.0
CB A:ASP173 4.6 6.5 1.0
C A:GLY172 4.6 6.1 1.0
HD21 A:ASN139 4.7 15.0 1.0
N A:ASN139 4.8 7.4 1.0
CA A:ASP173 4.8 5.7 1.0
O A:HOH1045 4.8 9.3 1.0
C A:GLN168 4.8 19.8 1.0
H1 A:HOH1045 4.9 15.0 1.0

Calcium binding site 2 out of 2 in 1jao

Go back to Calcium Binding Sites List in 1jao
Calcium binding site 2 out of 2 in the Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of 3-Mercapto-2-Benzylpropanoyl-Ala-Gly-NH2 with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:8.8
occ:1.00
 OE2 A:GLU180 2.2 5.3 1.0
OD1 A:ASP154 2.2 10.7 1.0
O A:ILE159 2.2 11.7 1.0
O A:GLY155 2.4 11.1 1.0
O A:ASN157 2.5 8.5 1.0
OD2 A:ASP177 2.5 8.9 1.0
H A:ASP154 3.4 15.0 1.0
C A:ILE159 3.4 10.4 1.0
CG A:ASP177 3.5 8.4 1.0
CG A:ASP154 3.5 8.5 1.0
CD A:GLU180 3.5 5.6 1.0
C A:GLY155 3.5 8.0 1.0
C A:ASN157 3.6 8.1 1.0
C A:PRO156 4.0 10.6 1.0
CB A:ASP177 4.0 10.8 1.0
N A:ASN157 4.0 10.7 1.0
OD2 A:ASP154 4.1 8.4 1.0
N A:GLY155 4.1 8.1 1.0
C A:ASP154 4.1 8.8 1.0
N A:ILE159 4.1 9.5 1.0
O A:PRO156 4.2 10.2 1.0
N A:ASP154 4.2 10.8 1.0
H A:ILE159 4.2 15.0 1.0
H A:GLY155 4.2 15.0 1.0
C A:GLY158 4.3 8.4 1.0
H A:ASN157 4.3 15.0 1.0
OE1 A:GLU180 4.3 5.8 1.0
CA A:ILE159 4.3 11.0 1.0
N A:LEU160 4.3 9.2 1.0
OD1 A:ASP177 4.4 7.7 1.0
CG A:GLU180 4.4 5.7 1.0
CA A:ASN157 4.4 8.5 1.0
CA A:PRO156 4.4 8.0 1.0
N A:PRO156 4.4 6.9 1.0
O A:ASP154 4.4 8.8 1.0
CA A:GLY155 4.5 8.6 1.0
CA A:LEU160 4.5 6.5 1.0
CA A:ASP154 4.5 9.2 1.0
O A:GLY158 4.6 6.9 1.0
CB A:ASP154 4.6 7.8 1.0
N A:GLY158 4.6 7.6 1.0
CA A:GLY158 4.7 7.0 1.0
CD1 A:LEU160 4.9 6.3 1.0
H2 A:HOH1021 4.9 15.0 1.0

Reference:

F.Grams, P.Reinemer, J.C.Powers, T.Kleine, M.Pieper, H.Tschesche, R.Huber, W.Bode. X-Ray Structures of Human Neutrophil Collagenase Complexed with Peptide Hydroxamate and Peptide Thiol Inhibitors. Implications For Substrate Binding and Rational Drug Design. Eur.J.Biochem. V. 228 830 1995.
ISSN: ISSN 0014-2956
PubMed: 7737183
DOI: 10.1111/J.1432-1033.1995.TB20329.X
Page generated: Mon Jul 7 16:04:34 2025

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