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Calcium in PDB 1zvx: Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer)

Enzymatic activity of Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer)

All present enzymatic activity of Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer):
3.4.24.34;

Protein crystallography data

The structure of Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer), PDB code: 1zvx was solved by G.Pochetti, E.Gavuzzo, C.Campestre, M.Agamennone, P.Tortorella, V.Consalvi, C.Gallina, O.Hiller, H.Tschesche, P.A.Tucker, F.Mazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.706, 54.754, 68.413, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.4

Other elements in 1zvx:

The structure of Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer) (pdb code 1zvx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer), PDB code: 1zvx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1zvx

Go back to Calcium Binding Sites List in 1zvx
Calcium binding site 1 out of 2 in the Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer)


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 Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:14.9
occ:1.00
O A:ASP137 2.4 12.0 1.0
O A:GLY169 2.5 16.9 1.0
OD1 A:ASP173 2.5 12.3 1.0
O A:GLY171 2.5 16.4 1.0
O A:HOH1060 2.6 14.4 1.0
O A:HOH1101 2.7 16.9 1.0
CG A:ASP173 3.3 12.7 1.0
C A:ASP137 3.5 14.6 1.0
C A:GLY171 3.6 16.4 1.0
C A:GLY169 3.7 17.8 1.0
OD2 A:ASP173 3.8 14.2 1.0
C A:ILE170 3.9 16.9 1.0
N A:ASP173 4.0 14.2 1.0
N A:GLY171 4.1 17.0 1.0
O A:ALA136 4.1 17.7 1.0
O A:ILE170 4.1 15.8 1.0
ND2 A:ASN139 4.2 20.5 1.0
CA A:ASP137 4.3 15.7 1.0
N A:ILE138 4.3 14.7 1.0
CA A:ILE170 4.3 17.3 1.0
O A:GLY167 4.3 21.2 1.0
CB A:ASP173 4.4 12.0 1.0
CA A:ILE138 4.4 13.7 1.0
N A:ILE170 4.4 16.4 1.0
CA A:GLY171 4.5 17.0 1.0
C A:GLY172 4.5 14.7 1.0
N A:GLY172 4.6 15.4 1.0
CA A:ASP173 4.6 12.8 1.0
O A:HOH1014 4.6 28.0 1.0
N A:ASN139 4.6 14.0 1.0
CA A:GLY172 4.6 15.8 1.0
CH2 A:TRP88 4.7 18.1 1.0
N A:GLY169 4.7 17.2 1.0
CA A:GLY169 4.7 17.2 1.0
OE2 A:GLU135 4.7 22.9 1.0
C A:GLN168 4.8 18.6 1.0
O A:GLN168 4.9 16.2 1.0
CG A:ASN139 5.0 18.9 1.0

Calcium binding site 2 out of 2 in 1zvx

Go back to Calcium Binding Sites List in 1zvx
Calcium binding site 2 out of 2 in the Crystal Structure of the Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer)


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 Complex Between Mmp-8 and A Phosphonate Inhibitor (R-Enantiomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:16.5
occ:1.00
O A:GLY155 2.4 14.4 1.0
O A:ILE159 2.4 15.8 1.0
OE2 A:GLU180 2.4 12.0 1.0
O A:ASN157 2.5 16.3 1.0
OD2 A:ASP177 2.5 11.1 1.0
OD1 A:ASP154 2.5 11.0 1.0
CG A:ASP177 3.3 10.9 1.0
C A:ILE159 3.4 13.0 1.0
C A:ASN157 3.6 15.3 1.0
C A:GLY155 3.6 14.9 1.0
CG A:ASP154 3.6 13.2 1.0
CD A:GLU180 3.7 16.6 1.0
N A:ILE159 3.7 12.7 1.0
CB A:ASP177 3.8 9.5 1.0
N A:ASN157 3.9 16.0 1.0
N A:GLY155 4.0 13.8 1.0
CA A:ILE159 4.1 13.8 1.0
C A:PRO156 4.1 14.9 1.0
OD1 A:ASP177 4.2 12.5 1.0
N A:ASP154 4.2 13.1 1.0
C A:ASP154 4.2 14.1 1.0
OD2 A:ASP154 4.2 14.1 1.0
CA A:ASN157 4.3 15.8 1.0
C A:GLY158 4.3 13.2 1.0
OE1 A:GLU180 4.4 12.7 1.0
CB A:ILE159 4.4 13.6 1.0
CA A:GLY155 4.4 13.0 1.0
N A:LEU160 4.4 11.8 1.0
N A:PRO156 4.5 14.7 1.0
CA A:PRO156 4.5 14.7 1.0
O A:PRO156 4.5 15.0 1.0
N A:GLY158 4.5 14.4 1.0
CA A:ASP154 4.6 13.5 1.0
CG A:GLU180 4.6 12.7 1.0
CA A:GLY158 4.7 13.1 1.0
O A:ASP154 4.7 14.0 1.0
CA A:LEU160 4.7 12.4 1.0
CB A:ASP154 4.7 12.8 1.0
O A:GLY158 5.0 12.2 1.0

Reference:

G.Pochetti, E.Gavuzzo, C.Campestre, M.Agamennone, P.Tortorella, V.Consalvi, C.Gallina, O.Hiller, H.Tschesche, P.A.Tucker, F.Mazza. Structural Insight Into the Stereoselective Inhibition of Mmp-8 By Enantiomeric Sulfonamide Phosphonates. J.Med.Chem. V. 49 923 2006.
ISSN: ISSN 0022-2623
PubMed: 16451058
DOI: 10.1021/JM050787+
Page generated: Sat Dec 12 03:30:27 2020

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