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Sodium in PDB 5dx5: Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes

Enzymatic activity of Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes

All present enzymatic activity of Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes:
4.4.1.11;

Protein crystallography data

The structure of Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes, PDB code: 5dx5 was solved by S.V.Revtovich, A.D.Nikulin, E.A.Morozova, N.V.Anufrieva, T.V.Demidkina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.37
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.090, 91.090, 175.929, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 22.5

Other elements in 5dx5:

The structure of Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes (pdb code 5dx5). 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 Methionine Gamma-Lyase From Clostridium Sporogenes, PDB code: 5dx5:

Sodium binding site 1 out of 1 in 5dx5

Go back to Sodium Binding Sites List in 5dx5
Sodium binding site 1 out of 1 in the Crystal Structure of Methionine Gamma-Lyase From Clostridium Sporogenes


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 Methionine Gamma-Lyase From Clostridium Sporogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:35.5
occ:1.00
 O B:HOH676 2.4 32.3 1.0
CB B:ASP344 2.6 26.4 1.0
OE1 B:GLU346 2.9 34.3 1.0
N B:SER345 3.0 25.2 1.0
CG B:ASP344 3.1 35.3 1.0
CA B:ASP344 3.1 28.5 1.0
C B:HIS217 3.1 23.1 1.0
OD1 B:ASP344 3.2 36.9 1.0
CA B:HIS217 3.4 19.7 1.0
N B:GLY218 3.4 23.3 1.0
O B:HIS217 3.4 22.7 1.0
O B:GLY216 3.5 22.2 1.0
C B:ASP344 3.5 25.5 1.0
O B:HOH680 3.8 34.4 1.0
CA B:GLY218 3.8 23.8 1.0
OD2 B:ASP344 3.9 41.6 1.0
CD B:GLU346 4.0 36.5 1.0
N B:HIS217 4.1 22.6 1.0
OG B:SER345 4.1 31.2 1.0
CA B:SER345 4.2 25.0 1.0
C B:GLY216 4.2 21.8 1.0
CB B:SER345 4.2 23.3 1.0
N B:GLU346 4.3 23.8 1.0
OE2 B:GLU346 4.3 33.0 1.0
N B:ASP344 4.4 24.6 1.0
O B:HOH613 4.6 22.9 1.0
CB B:HIS217 4.6 17.7 1.0
O B:ASP344 4.8 22.4 1.0
C B:SER345 4.8 27.2 1.0
C B:GLY218 5.0 23.2 1.0

Reference:

S.Revtovich, N.Anufrieva, E.Morozova, V.Kulikova, A.Nikulin, T.Demidkina. Structure of Methionine Gamma-Lyase From Clostridium Sporogenes. Acta Crystallogr.,Sect.F V. 72 65 2016.
ISSN: ESSN 2053-230X
PubMed: 26750487
DOI: 10.1107/S2053230X15023869
Page generated: Sun Aug 17 23:33:44 2025

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