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Sodium in PDB 7mcp: Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer:
2.5.1.48; 4.4.1.1; 4.4.1.8;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer, PDB code: 7mcp was solved by A.Nuthanakanti, A.Serganov, A.Kaushik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.40
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.465, 104.465, 286.605, 90, 90, 90
R / Rfree (%) 15 / 17.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer (pdb code 7mcp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer, PDB code: 7mcp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7mcp

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Sodium binding site 1 out of 6 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer


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 Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:54.4
occ:1.00
 O A:HIS9 2.4 31.6 1.0
O A:GLY11 2.6 41.7 1.0
O A:HOH636 2.6 40.0 1.0
O A:HOH562 3.1 35.8 1.0
O A:HOH709 3.3 46.1 1.0
C A:HIS9 3.3 30.4 1.0
C A:GLY11 3.8 37.2 1.0
CA A:HIS9 3.9 36.1 1.0
C A:GLY10 4.2 34.0 1.0
N A:GLY10 4.3 32.0 1.0
O A:GLY10 4.3 34.1 1.0
N A:GLY11 4.4 34.6 1.0
CA A:GLY10 4.5 32.0 1.0
CB A:HIS9 4.6 31.1 1.0
CA A:HIS12 4.7 34.7 1.0
N A:HIS12 4.7 36.3 1.0
CA A:GLY11 4.8 33.0 1.0
N A:THR13 4.9 33.7 1.0
OG1 A:THR13 5.0 32.2 1.0

Sodium binding site 2 out of 6 in 7mcp

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Sodium binding site 2 out of 6 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:52.6
occ:1.00
 O A:VAL117 2.4 35.6 1.0
O A:HOH658 2.5 41.4 1.0
O A:HOH691 2.6 36.8 1.0
O A:HOH616 2.8 50.9 1.0
C A:VAL117 3.6 37.4 1.0
N A:VAL117 3.9 39.7 1.0
NH2 A:ARG133 4.2 35.6 1.0
CA A:VAL117 4.3 33.1 1.0
OE1 A:GLU116 4.4 53.3 1.0
N A:ASP118 4.7 32.3 1.0
CB A:VAL117 4.8 35.0 1.0
OD2 A:ASP118 4.9 34.9 1.0
OD1 A:ASP118 4.9 43.2 1.0
CG A:ASP118 4.9 31.6 1.0
CA A:ASP118 5.0 33.4 1.0

Sodium binding site 3 out of 6 in 7mcp

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Sodium binding site 3 out of 6 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:43.4
occ:1.00
 O A:GLN130 2.5 30.8 1.0
O A:HOH695 2.5 38.6 1.0
O A:HOH647 2.5 46.5 1.0
C A:GLN130 3.6 34.5 1.0
CG A:GLN130 4.1 30.4 1.0
CA A:GLN130 4.4 31.0 1.0
O A:ILE132 4.5 34.3 1.0
N A:ALA131 4.6 31.2 1.0
O A:HOH549 4.7 35.0 1.0
CA A:ALA131 4.8 30.8 1.0
CB A:GLN130 4.9 28.5 1.0
O A:HOH634 4.9 40.7 1.0
C A:ALA131 5.0 29.8 1.0

Sodium binding site 4 out of 6 in 7mcp

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Sodium binding site 4 out of 6 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:57.5
occ:1.00
 O A:HOH617 2.5 49.9 1.0
O A:HOH560 2.6 41.3 1.0
O A:HOH543 2.7 35.0 1.0
O A:HOH756 2.9 59.6 1.0
O A:HOH719 4.0 53.1 1.0
O A:HOH567 4.2 30.4 1.0
O A:HOH661 4.3 41.1 1.0
O A:HOH739 4.3 59.5 1.0
O A:ILE187 4.4 28.1 1.0
O A:GLY186 4.5 32.0 1.0
NZ A:LYS162 4.6 59.8 1.0
OD1 A:ASP188 4.8 40.9 1.0
C A:GLY186 4.8 32.0 1.0
CE A:LYS162 4.8 43.9 1.0
CA A:GLY186 4.9 29.0 1.0
O A:LEU183 5.0 36.5 1.0

Sodium binding site 5 out of 6 in 7mcp

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Sodium binding site 5 out of 6 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na403

b:56.6
occ:1.00
 O H:HOH587 2.5 43.3 1.0
O H:HOH678 2.6 62.0 1.0
O H:HOH729 2.6 44.5 1.0
O H:HOH533 2.6 33.2 1.0
O H:HOH735 2.9 53.0 1.0
O H:HOH620 4.1 32.2 1.0
O H:HOH613 4.2 43.5 1.0
O H:GLY186 4.4 32.2 1.0
O H:ILE187 4.4 35.6 1.0
CA H:GLY186 4.5 33.5 1.0
C H:GLY186 4.5 35.8 1.0
NZ H:LYS162 4.5 60.9 1.0
O H:LEU183 4.7 34.9 1.0
CE H:LYS162 4.7 48.1 1.0

Sodium binding site 6 out of 6 in 7mcp

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Sodium binding site 6 out of 6 in the Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na404

b:56.8
occ:1.00
 O H:HOH653 2.3 43.0 1.0
O H:HOH567 2.5 48.3 1.0
O H:HOH560 2.6 40.0 1.0
O H:GLY11 2.8 37.5 1.0
O H:HIS9 2.9 35.4 1.0
C H:HIS9 3.6 33.4 1.0
O H:HOH665 3.8 54.8 1.0
C H:GLY11 4.0 37.5 1.0
CA H:HIS9 4.0 37.8 1.0
N H:THR13 4.1 32.7 1.0
OG1 H:THR13 4.2 33.5 1.0
O H:GLY10 4.4 31.3 1.0
CA H:HIS12 4.5 40.7 1.0
C H:GLY10 4.5 33.6 1.0
N H:GLY10 4.6 33.0 1.0
N H:HIS12 4.7 34.9 1.0
CB H:HIS9 4.7 32.0 1.0
O H:ILE8 4.8 33.1 1.0
CG2 H:THR14 4.8 29.0 1.0
C H:HIS12 4.9 38.2 1.0
N H:GLY11 4.9 32.0 1.0
CA H:GLY10 5.0 31.7 1.0

Reference:

K.Shatalin, A.Nuthanakanti, A.Kaushik, D.Shishov, A.Peselis, I.Shamovsky, B.Pani, M.Lechpammer, N.Vasilyev, E.Shatalina, D.Rebatchouk, A.Mironov, P.Fedichev, A.Serganov, E.Nudler. Inhibitors of Bacterial H 2 S Biogenesis Targeting Antibiotic Resistance and Tolerance. Science V. 372 1169 2021.
ISSN: ESSN 1095-9203
PubMed: 34112687
DOI: 10.1126/SCIENCE.ABD8377
Page generated: Mon Aug 18 10:55:47 2025

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