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Zinc 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:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1jao

Go back to Zinc Binding Sites List in 1jao
Zinc 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 Zinc with other atoms in the Zn 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:Zn998

b:10.9
occ:1.00
 OD2 A:ASP149 1.8 7.6 1.0
ND1 A:HIS175 1.9 9.4 1.0
NE2 A:HIS147 2.0 9.3 1.0
NE2 A:HIS162 2.2 10.2 1.0
CG A:ASP149 2.7 11.6 1.0
CD2 A:HIS147 2.8 9.2 1.0
CE1 A:HIS175 2.8 7.5 1.0
CE1 A:HIS162 3.0 10.3 1.0
CG A:HIS175 3.1 5.6 1.0
CE1 A:HIS147 3.1 8.0 1.0
OD1 A:ASP149 3.2 7.6 1.0
CD2 A:HIS162 3.4 11.0 1.0
CB A:HIS175 3.5 5.7 1.0
NE2 A:HIS175 4.0 7.8 1.0
CG A:HIS147 4.0 7.2 1.0
CB A:ASP149 4.1 13.0 1.0
CD2 A:HIS175 4.1 6.2 1.0
CZ A:PHE164 4.2 11.4 1.0
ND1 A:HIS147 4.2 6.0 1.0
ND1 A:HIS162 4.2 9.5 1.0
CE1 A:PHE164 4.3 8.4 1.0
O A:SER151 4.3 17.4 1.0
CG A:HIS162 4.4 8.9 1.0
CZ A:PHE153 4.7 5.4 1.0
CE2 A:PHE153 4.7 7.5 1.0
H2 A:HOH1073 4.8 15.0 1.0
CB A:SER151 4.8 22.9 1.0
O A:HOH1024 4.8 19.8 1.0
HE2 A:HIS175 4.9 15.0 1.0
H1 A:HOH1073 4.9 15.0 1.0
CA A:HIS175 4.9 5.4 1.0
H A:HIS175 5.0 15.0 1.0

Zinc binding site 2 out of 2 in 1jao

Go back to Zinc Binding Sites List in 1jao
Zinc 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 Zinc with other atoms in the Zn 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:Zn999

b:9.4
occ:1.00
 NE2 A:HIS197 1.9 4.7 1.0
NE2 A:HIS207 2.0 8.3 1.0
NE2 A:HIS201 2.1 5.0 1.0
S' A:0D31 2.2 13.0 1.0
CE1 A:HIS207 2.8 3.9 1.0
CD2 A:HIS197 2.9 2.8 1.0
CE1 A:HIS197 3.0 3.9 1.0
CD2 A:HIS207 3.0 6.9 1.0
CD2 A:HIS201 3.1 4.5 1.0
CE1 A:HIS201 3.1 3.8 1.0
H1 A:HOH1083 3.6 15.0 1.0
C' A:0D31 3.6 17.1 1.0
ND1 A:HIS207 3.9 5.7 1.0
C2 A:0D31 4.0 19.6 1.0
CG A:HIS207 4.0 7.3 1.0
CG A:HIS197 4.0 2.5 1.0
ND1 A:HIS197 4.1 2.7 1.0
OE2 A:GLU198 4.3 6.0 1.0
ND1 A:HIS201 4.3 6.7 1.0
CG A:HIS201 4.3 6.0 1.0
C3 A:0D31 4.4 20.0 1.0
O A:HOH1083 4.5 36.9 1.0
H2 A:HOH1083 4.5 15.0 1.0
C2' A:0D31 4.6 19.6 1.0
CE A:MET215 4.6 3.0 1.0
HD1 A:HIS207 4.8 15.0 1.0
OE1 A:GLU198 4.8 3.7 1.0
C1' A:0D31 4.8 18.8 1.0
CD A:GLU198 4.9 2.3 1.0
HD1 A:HIS197 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: Sun Oct 13 03:28:24 2024

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