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Calcium in PDB 7pod: Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide

Enzymatic activity of Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide

All present enzymatic activity of Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide:
3.2.1.96;

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide, PDB code: 7pod was solved by S.Martinez Caballero, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.25 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.144, 92.522, 124.572, 90, 90, 90
R / Rfree (%) 14.5 / 19.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide (pdb code 7pod). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide, PDB code: 7pod:

Calcium binding site 1 out of 1 in 7pod

Go back to Calcium Binding Sites List in 7pod
Calcium binding site 1 out of 1 in the Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide


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 Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:29.5
occ:1.00
 OE1 A:GLU425 2.2 39.3 1.0
OD2 A:ASP421 2.4 25.6 1.0
OD2 A:ASP423 2.5 41.0 1.0
CG A:ASP421 3.5 21.1 1.0
CD A:GLU425 3.5 37.4 1.0
CG A:ASP423 3.7 34.0 1.0
OD1 A:ASP421 4.0 24.0 1.0
O A:HOH904 4.0 35.6 1.0
O A:HOH801 4.1 35.2 1.0
CB A:ASP423 4.1 30.1 1.0
CG A:GLU425 4.3 29.6 1.0
OE2 A:GLU425 4.4 39.1 1.0
CB A:GLU425 4.4 24.6 1.0
CB A:ASP421 4.7 16.4 1.0
OD1 A:ASP423 4.8 40.6 1.0

Reference:

S.Martinez Caballero, J.A.Hermoso. Crystal Structure of Catalytic Domain of Lytb (E585Q) From Streptococcus Pneumoniae in Complex with Nag-Nam-Nag-Nam Tetrasaccharide To Be Published.
Page generated: Thu Jul 10 00:22:17 2025

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