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Sodium in PDB 2c3f: The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity.

Enzymatic activity of The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity.

All present enzymatic activity of The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity.:
4.2.2.1;

Protein crystallography data

The structure of The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity., PDB code: 2c3f was solved by E.J.Taylor, N.L.Smith, A.-M.Linsay, S.J.Charnock, J.P.Turkenburg, E.J.Dodson, G.J.Davies, G.W.Black, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 196.12 / 1.81
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 58.534, 58.534, 586.585, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity. (pdb code 2c3f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity., PDB code: 2c3f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2c3f

Go back to Sodium Binding Sites List in 2c3f
Sodium binding site 1 out of 3 in the The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1337

b:31.2
occ:0.50
NA A:NA1337 0.0 31.2 0.5
NA A:NA1337 2.1 31.2 0.5
O A:HOH2223 2.4 36.1 1.0
O A:SER282 2.5 25.3 1.0
C A:SER282 3.6 25.4 1.0
CA A:ASP283 4.1 23.2 1.0
N A:ASP283 4.2 22.6 1.0
O A:HOH2227 4.3 28.0 1.0
NH2 A:ARG279 4.3 29.2 1.0
CB A:SER282 4.5 25.6 1.0
OD1 A:ASP283 4.6 28.9 1.0
O A:LEU281 4.6 25.9 1.0
CB A:ASP283 4.6 24.0 1.0
CA A:SER282 4.7 25.0 1.0

Sodium binding site 2 out of 3 in 2c3f

Go back to Sodium Binding Sites List in 2c3f
Sodium binding site 2 out of 3 in the The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1337

b:31.2
occ:0.50
NA A:NA1337 0.0 31.2 0.5
NA A:NA1337 2.1 31.2 0.5
OD1 A:ASP283 3.1 28.9 1.0
O A:HOH2227 3.1 28.0 1.0
O A:SER282 3.6 25.3 1.0
O A:HOH2223 3.8 36.1 1.0
CA A:ASP283 3.8 23.2 1.0
CG A:ASP283 4.0 27.1 1.0
CB A:ASP283 4.2 24.0 1.0
C A:SER282 4.5 25.4 1.0
NH2 A:ARG279 4.7 29.2 1.0
N A:ASP283 4.7 22.6 1.0
N A:ASP284 4.8 22.4 1.0
C A:ASP283 4.9 22.2 1.0
O A:HOH2226 5.0 31.1 1.0

Sodium binding site 3 out of 3 in 2c3f

Go back to Sodium Binding Sites List in 2c3f
Sodium binding site 3 out of 3 in the The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of A Group A Streptococcal Phage-Encoded Tail-Fibre Showing Hyaluronan Lyase Activity. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1338

b:32.6
occ:1.00
O A:THR272 2.3 22.6 1.0
O A:HOH2232 2.5 32.1 1.0
C A:THR272 3.5 22.5 1.0
O A:HOH2219 3.6 38.5 1.0
O A:HOH2235 3.7 26.0 1.0
O A:HOH2060 4.0 28.9 0.5
CB A:THR272 4.1 22.6 1.0
O A:HOH2111 4.2 42.0 1.0
CA A:THR272 4.3 21.8 1.0
N A:GLY273 4.5 21.2 1.0
CA A:GLY273 4.6 21.4 1.0
OG1 A:THR272 4.6 22.2 1.0
O A:HOH2221 4.7 23.4 1.0
OG A:SER290 4.8 26.0 1.0
C A:GLY273 4.9 20.4 1.0

Reference:

N.L.Smith, E.J.Taylor, A.-M.Linsay, S.J.Charnock, J.P.Turkenburg, E.J.Dodson, G.J.Davies, G.W.Black. Structure of A Group A Streptococcal Phage-Encoded Virulence Factor Reveals Catalytically Active Triple-Stranded Beta-Helix Proc.Natl.Acad.Sci.Usa V. 102 17652 2005.
ISSN: ISSN 0027-8424
PubMed: 16314578
DOI: 10.1073/PNAS.0504782102
Page generated: Tue Dec 15 05:46:28 2020

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