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Sodium in PDB 1c82: Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution

Enzymatic activity of Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution

All present enzymatic activity of Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution:
4.2.2.1;

Protein crystallography data

The structure of Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution, PDB code: 1c82 was solved by K.Ponnuraj, M.J.Jedrzejas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.550, 104.190, 99.880, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.7

Other elements in 1c82:

The structure of Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution (pdb code 1c82). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution, PDB code: 1c82:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1c82

Go back to Sodium Binding Sites List in 1c82
Sodium binding site 1 out of 2 in the Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:20.0
occ:1.00
 O2 A:CAC905 2.1 39.7 1.0
AS A:CAC905 3.5 42.6 1.0
N A:SER630 3.5 25.9 1.0
C1 A:CAC907 3.5 41.0 1.0
CB A:ASP629 3.6 26.9 1.0
C2 A:CAC905 3.7 41.0 1.0
CA A:SER630 3.8 26.7 1.0
CB A:SER630 3.8 24.4 1.0
C A:ASP629 3.8 26.4 1.0
O1 A:CAC905 4.1 40.3 1.0
NZ A:LYS584 4.2 42.3 1.0
C2 A:CAC907 4.3 41.0 1.0
O A:ASP629 4.3 27.2 1.0
CA A:ASP629 4.4 26.1 1.0
AS A:CAC907 4.5 42.6 1.0
C1 A:CAC905 4.6 41.0 1.0
OG A:SER630 4.8 25.4 1.0
CG A:ASP629 4.9 27.4 1.0
N A:ASP629 4.9 25.9 1.0
O1 A:CAC907 5.0 40.3 1.0
OD2 A:ASP629 5.0 27.5 1.0

Sodium binding site 2 out of 2 in 1c82

Go back to Sodium Binding Sites List in 1c82
Sodium binding site 2 out of 2 in the Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:20.0
occ:1.00
 O2 A:CAC907 2.0 39.7 1.0
AS A:CAC907 3.4 42.6 1.0
CB A:ALA628 3.7 27.3 1.0
O1 A:CAC907 3.7 40.3 1.0
CA A:ALA628 4.1 26.1 1.0
C1 A:CAC907 4.3 41.0 1.0
C2 A:CAC907 4.5 41.0 1.0
N A:ALA628 4.9 26.4 1.0

Reference:

K.Ponnuraj, M.J.Jedrzejas. Mechanism of Hyaluronan Binding and Degradation: Structure of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Hyaluronic Acid Disaccharide at 1.7 A Resolution. J.Mol.Biol. V. 299 885 2000.
ISSN: ISSN 0022-2836
PubMed: 10843845
DOI: 10.1006/JMBI.2000.3817
Page generated: Sun Oct 6 17:59:09 2024

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