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Sodium in PDB 8i4d: X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K

Enzymatic activity of X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K

All present enzymatic activity of X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K:
4.2.2.28;

Protein crystallography data

The structure of X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K, PDB code: 8i4d was solved by N.Yano, T.Kondo, K.Kusaka, T.Yamada, T.Arakawa, T.Sakamoto, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.65 / 1.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.313, 65.23, 108.224, 90, 90, 90
R / Rfree (%) 17.2 / 18.3

Other elements in 8i4d:

The structure of X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K (pdb code 8i4d). 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 X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K, PDB code: 8i4d:

Sodium binding site 1 out of 1 in 8i4d

Go back to Sodium Binding Sites List in 8i4d
Sodium binding site 1 out of 1 in the X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of A L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase From Fusarium Oxysporum 12S, L-Rha Complex at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:14.5
occ:1.00
 O A:GLU221 2.4 13.1 1.0
O A:HOH1084 2.4 29.9 1.0
O A:HOH1008 2.4 29.4 1.0
O A:HOH1061 2.4 25.3 1.0
O A:ASP198 2.5 13.1 1.0
O A:HOH839 2.5 23.1 1.0
O A:GLY171 2.5 14.3 1.0
C A:ASP198 3.3 10.5 1.0
C A:GLY171 3.6 13.8 1.0
C A:GLU221 3.6 11.4 1.0
CA A:GLY171 3.9 14.2 1.0
OG A:SER172 4.0 19.7 0.4
CA A:ASP198 4.1 13.0 1.0
N A:ASN199 4.1 10.2 1.0
CB A:ASP198 4.3 16.5 1.0
CA A:ASN199 4.3 9.9 1.0
CA A:GLU221 4.4 10.9 1.0
N A:THR222 4.5 11.1 1.0
O A:HOH722 4.6 26.8 1.0
CA A:THR222 4.6 12.5 1.0
CG2 A:THR222 4.7 16.3 1.0
N A:SER172 4.7 13.4 0.6
N A:SER172 4.7 13.4 0.4
OE1 A:GLU221 4.8 14.8 1.0
O A:HOH707 4.9 30.8 1.0
CB A:ASN199 5.0 10.8 1.0

Reference:

N.Yano, A.G.Santiago, T.Kondo, K.Kusaka, T.Yamada, T.Arakawa, T.Sakamoto, S.Fushinobu. Charge Neutralization and Beta-Elimination Cleavage Mechanism of Family 42 L-Rhamnose-Alpha-1,4-D-Glucuronate Lyase Revealed Using Neutron Crystallography To Be Published.
Page generated: Wed Oct 9 12:22:51 2024

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