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Sodium in PDB 1rwf: Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide

Enzymatic activity of Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide

All present enzymatic activity of Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide:
4.2.2.5;

Protein crystallography data

The structure of Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide, PDB code: 1rwf was solved by V.V.Lunin, Y.Li, H.Miyazono, M.Kyogashima, A.W.Bell, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.12 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.889, 86.914, 81.504, 90.00, 107.00, 90.00
R / Rfree (%) 13.8 / 17.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide (pdb code 1rwf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide, PDB code: 1rwf:

Sodium binding site 1 out of 1 in 1rwf

Go back to Sodium Binding Sites List in 1rwf
Sodium binding site 1 out of 1 in the Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase in Complex with Chondroitin Tetrasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na900

b:21.0
occ:1.00
 O A:HOH1320 2.1 25.5 1.0
O A:HIS233 2.2 14.1 1.0
O A:TRP465 2.2 17.3 1.0
O A:HOH1059 2.5 15.0 1.0
O A:HOH1967 2.5 47.1 1.0
OG1 A:THR235 2.8 13.1 1.0
C A:TRP465 3.3 15.3 1.0
O A:GLY466 3.4 16.6 1.0
C A:HIS233 3.4 13.0 1.0
C A:GLY466 3.5 16.0 1.0
CA A:GLY466 3.5 15.1 1.0
CB A:HIS233 3.8 11.9 1.0
N A:GLY466 3.8 14.5 1.0
N A:THR235 3.9 10.5 1.0
O A:HOH1860 4.1 40.8 1.0
CB A:THR235 4.1 12.6 1.0
CA A:HIS233 4.2 12.1 1.0
O A:HOH1801 4.2 39.8 1.0
N A:ALA467 4.3 16.7 1.0
CA A:TRP465 4.4 14.6 1.0
CB A:SER234 4.4 15.5 1.0
O6 A:ASG812 4.5 31.3 0.6
N A:SER234 4.5 12.7 1.0
CG2 A:THR235 4.6 16.2 1.0
CA A:THR235 4.6 11.7 1.0
O A:HOH1958 4.6 48.4 1.0
CB A:TRP465 4.7 15.0 1.0
OE2 A:GLU407 4.8 13.2 1.0
OG1 A:THR236 4.8 11.7 1.0
CA A:SER234 4.8 13.3 1.0
C A:SER234 4.8 12.8 1.0
CA A:ALA467 4.9 17.4 1.0

Reference:

V.V.Lunin, Y.Li, R.J.Linhardt, H.Miyazono, M.Kyogashima, T.Kaneko, A.W.Bell, M.Cygler. High-Resolution Crystal Structure of Arthrobacter Aurescens Chondroitin Ac Lyase: An Enzyme-Substrate Complex Defines the Catalytic Mechanism J.Mol.Biol. V. 337 367 2004.
ISSN: ISSN 0022-2836
PubMed: 15003453
DOI: 10.1016/J.JMB.2003.12.071
Page generated: Sun Aug 17 07:32:01 2025

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