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Sodium in PDB 4d99: Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site

Enzymatic activity of Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site

All present enzymatic activity of Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site:
4.4.1.15;

Protein crystallography data

The structure of Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site, PDB code: 4d99 was solved by S.R.Bharath, B.Shveta, K.H.Rajesh, H.S.Savithri, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.63 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.564, 165.492, 68.876, 90.00, 119.34, 90.00
R / Rfree (%) 21.2 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site (pdb code 4d99). 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 Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site, PDB code: 4d99:

Sodium binding site 1 out of 1 in 4d99

Go back to Sodium Binding Sites List in 4d99
Sodium binding site 1 out of 1 in the Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Typhimurium D-Cysteine Desulfhydrase with L-Ser Bound Non- Covalently at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:38.9
occ:1.00
 O C:THR219 2.7 28.9 1.0
O C:TRP253 2.9 31.9 1.0
N C:TYR256 3.0 32.5 1.0
C C:ASP254 3.2 30.8 1.0
CA C:ASP254 3.3 31.8 1.0
OG1 C:THR219 3.4 30.3 1.0
N C:ASP255 3.5 33.0 1.0
N C:THR219 3.5 29.9 1.0
CA C:TYR256 3.5 31.2 1.0
CG1 C:VAL218 3.6 31.2 1.0
N C:PHE257 3.6 29.6 1.0
C C:THR219 3.6 30.4 1.0
C C:TYR256 3.6 30.2 1.0
CB C:TYR256 3.7 30.7 1.0
O C:ASP254 3.7 31.8 1.0
C C:TRP253 3.7 32.3 1.0
CD2 C:PHE257 3.8 30.2 1.0
CD1 C:TYR256 3.8 32.3 1.0
N C:ASP254 3.9 31.5 1.0
CA C:THR219 3.9 30.0 1.0
CB C:PHE257 4.0 29.5 1.0
C C:ASP255 4.1 34.0 1.0
C C:VAL218 4.1 29.8 1.0
CG C:TYR256 4.2 32.5 1.0
CB C:THR219 4.2 30.7 1.0
O C:TYR256 4.3 30.3 1.0
CA C:ASP255 4.4 34.8 1.0
CG C:PHE257 4.4 29.7 1.0
CA C:PHE257 4.4 29.2 1.0
CA C:VAL218 4.5 30.9 1.0
CB C:ASP254 4.6 31.9 1.0
CB C:VAL218 4.7 31.1 1.0
N C:VAL220 4.8 29.5 1.0
CE2 C:PHE257 4.9 30.2 1.0
O C:VAL218 4.9 29.2 1.0
CE1 C:TYR256 5.0 32.5 1.0

Reference:

S.R.Bharath, S.Bisht, R.K.Harijan, H.S.Savithri, M.R.N.Murthy. Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella Typhimurium D-Cysteine Desulfhydrase. Plos One V. 7 36267 2012.
ISSN: ESSN 1932-6203
PubMed: 22574144
DOI: 10.1371/JOURNAL.PONE.0036267
Page generated: Sun Aug 17 18:55:12 2025

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