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Sodium in PDB 5t73: Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151

Enzymatic activity of Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151

All present enzymatic activity of Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151:
1.2.1.12;

Protein crystallography data

The structure of Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151, PDB code: 5t73 was solved by A.J.Pietrzyk-Brzezinska, M.C.Wahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.16 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.692, 111.456, 128.063, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 26

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 (pdb code 5t73). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151, PDB code: 5t73:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5t73

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Sodium binding site 1 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


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 S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:15.1
occ:1.00
 O A:ASP34 2.4 37.0 1.0
O A:THR36 2.5 37.4 1.0
OG A:SER76 2.7 40.6 1.0
OD1 A:ASP38 3.0 39.1 1.0
O A:PHE75 3.5 38.4 1.0
C A:ASP34 3.6 36.2 1.0
C A:THR36 3.7 37.6 1.0
OG A:SER74 3.8 39.7 1.0
O A:HOH542 3.9 30.0 1.0
CD1 A:LEU41 3.9 35.0 1.0
CB A:SER76 4.0 41.3 1.0
CG A:ASP38 4.2 40.2 1.0
C A:PHE75 4.2 39.7 1.0
N A:ASP38 4.3 39.4 1.0
C A:ASP37 4.3 39.7 1.0
CA A:ASP37 4.3 40.3 1.0
C A:LEU35 4.4 38.0 1.0
CA A:SER76 4.4 40.4 1.0
CA A:ASP34 4.4 35.1 1.0
N A:ASP34 4.4 35.5 1.0
N A:ASP37 4.4 38.5 1.0
N A:THR36 4.4 36.8 1.0
O A:LEU35 4.5 39.2 1.0
N A:LEU35 4.6 36.4 1.0
CB A:ASP34 4.6 34.1 1.0
N A:SER76 4.6 40.7 1.0
CA A:THR36 4.7 36.9 1.0
CA A:LEU35 4.7 37.8 1.0
CA A:ASP38 4.7 38.9 1.0
O A:ASP37 4.8 38.1 1.0
OD2 A:ASP38 4.9 41.5 1.0

Sodium binding site 2 out of 8 in 5t73

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Sodium binding site 2 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


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 S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:8.5
occ:1.00
 O A:VAL24 2.1 40.6 1.0
O A:HOH530 2.5 36.4 1.0
O A:ILE21 2.6 37.9 1.0
O A:LEU27 2.7 40.1 1.0
C A:VAL24 3.2 41.0 1.0
C A:ILE21 3.7 36.7 1.0
C A:LEU27 3.9 39.8 1.0
O A:GLN22 3.9 41.0 1.0
CA A:GLU25 4.0 51.2 1.0
N A:VAL24 4.0 39.4 1.0
C A:GLN22 4.0 39.3 1.0
N A:GLU25 4.0 49.1 1.0
OE2 A:GLU28 4.1 53.5 1.0
CG2 A:ILE21 4.1 36.2 1.0
CA A:GLN22 4.1 38.3 1.0
CA A:VAL24 4.2 39.8 1.0
N A:LEU27 4.2 41.1 1.0
N A:GLN22 4.4 36.8 1.0
CD A:GLU28 4.5 51.6 1.0
CA A:LEU27 4.5 39.7 1.0
N A:GLY26 4.6 46.4 1.0
C A:GLU25 4.6 50.9 1.0
OE1 A:GLU28 4.7 51.3 1.0
N A:GLU23 4.7 38.5 1.0
CB A:LEU27 4.7 38.0 1.0
CB A:VAL24 4.8 38.3 1.0
CA A:ILE21 4.8 35.2 1.0
N A:GLU28 4.9 43.5 1.0

Sodium binding site 3 out of 8 in 5t73

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Sodium binding site 3 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


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 S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:23.8
occ:1.00
 O B:ASP34 2.4 40.1 1.0
O B:THR36 2.7 37.7 1.0
O B:HOH534 2.9 30.4 1.0
OG B:SER76 3.0 44.4 1.0
OD1 B:ASP38 3.2 38.1 1.0
O B:PHE75 3.4 41.9 1.0
C B:ASP34 3.4 39.2 1.0
CD1 B:LEU41 3.6 35.1 1.0
C B:THR36 3.9 37.9 1.0
C B:PHE75 4.0 42.8 1.0
N B:ASP34 4.0 39.5 1.0
CA B:ASP34 4.1 38.0 1.0
CB B:SER76 4.2 45.5 1.0
CA B:SER76 4.3 44.8 1.0
CB B:ASP34 4.3 37.8 1.0
N B:THR36 4.3 37.0 1.0
N B:SER76 4.3 44.2 1.0
CG B:ASP38 4.3 39.1 1.0
C B:LEU35 4.4 38.2 1.0
N B:LEU35 4.5 36.8 1.0
N B:PHE75 4.6 41.3 1.0
CB B:SER74 4.6 40.0 1.0
N B:ASP38 4.7 39.1 1.0
CA B:THR36 4.7 37.1 1.0
CA B:LEU35 4.8 38.1 1.0
N B:ASP37 4.9 38.8 1.0
CA B:PHE75 4.9 42.6 1.0
O B:LEU35 4.9 39.5 1.0
OG B:SER74 4.9 41.0 1.0
C B:ASP37 4.9 38.6 1.0
CG B:LEU41 4.9 34.6 1.0
CA B:ASP37 4.9 39.6 1.0
OD2 B:ASP38 4.9 40.0 1.0

Sodium binding site 4 out of 8 in 5t73

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Sodium binding site 4 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


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 S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:13.7
occ:1.00
 O B:HOH541 2.3 43.4 1.0
O B:VAL24 2.3 36.2 1.0
O B:LEU27 2.4 35.8 1.0
O B:ILE21 2.6 36.0 1.0
O B:HOH542 2.9 39.9 1.0
C B:VAL24 3.4 36.6 1.0
C B:LEU27 3.6 35.7 1.0
OE2 B:GLU28 3.7 48.5 1.0
C B:ILE21 3.8 35.2 1.0
N B:LEU27 3.9 36.7 1.0
CD B:GLU28 4.1 47.2 1.0
CA B:GLU25 4.1 45.4 1.0
N B:GLU25 4.2 43.6 1.0
N B:VAL24 4.2 35.5 1.0
CA B:LEU27 4.2 35.8 1.0
CG2 B:ILE21 4.2 34.3 1.0
N B:GLY26 4.3 38.7 1.0
CA B:GLN22 4.3 34.5 1.0
O B:GLN22 4.3 36.3 1.0
C B:GLN22 4.3 35.2 1.0
CA B:VAL24 4.3 35.9 1.0
OE1 B:GLU28 4.4 47.1 1.0
C B:GLU25 4.5 44.4 1.0
CB B:LEU27 4.5 34.8 1.0
N B:GLN22 4.5 33.5 1.0
N B:GLU28 4.6 39.9 1.0
CG B:GLU28 4.9 45.8 1.0
CA B:GLU28 4.9 41.1 1.0
CA B:ILE21 4.9 34.4 1.0
CB B:VAL24 4.9 35.1 1.0
N B:GLU23 4.9 34.8 1.0

Sodium binding site 5 out of 8 in 5t73

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Sodium binding site 5 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


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 S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:17.4
occ:1.00
 O C:HOH532 2.2 21.7 1.0
O C:ASP34 2.5 37.1 1.0
O C:THR36 2.7 36.6 1.0
O C:PHE75 3.3 39.6 1.0
CB C:SER76 3.5 39.6 1.0
OD1 C:ASP38 3.5 37.6 1.0
C C:ASP34 3.6 36.7 1.0
C C:THR36 3.7 36.8 1.0
OG C:SER74 3.8 38.9 1.0
CD1 C:LEU41 3.9 34.8 1.0
C C:PHE75 4.0 40.5 1.0
CA C:SER76 4.1 40.2 1.0
N C:THR36 4.2 36.7 1.0
C C:LEU35 4.3 37.7 1.0
OG C:SER76 4.4 40.3 1.0
N C:ASP38 4.4 37.7 1.0
N C:SER76 4.4 40.8 1.0
N C:ASP34 4.4 36.6 1.0
CG C:ASP38 4.4 38.4 1.0
N C:LEU35 4.5 37.0 1.0
CA C:ASP34 4.5 36.1 1.0
CA C:LEU35 4.6 37.9 1.0
CA C:ASP37 4.6 38.0 1.0
N C:ASP37 4.6 37.4 1.0
C C:ASP37 4.6 37.2 1.0
CA C:THR36 4.6 36.5 1.0
CB C:ASP34 4.7 35.1 1.0
O C:LEU35 4.8 38.5 1.0
CA C:ASP38 5.0 37.3 1.0

Sodium binding site 6 out of 8 in 5t73

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Sodium binding site 6 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


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 S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:21.5
occ:1.00
 O C:VAL24 2.4 43.0 1.0
O C:LEU27 2.8 42.1 1.0
O C:HOH538 2.8 39.9 1.0
O C:ILE21 2.9 39.6 1.0
C C:VAL24 3.4 47.1 1.0
OE1 C:GLU28 3.6 48.3 1.0
O C:GLN22 3.6 41.2 1.0
C C:LEU27 3.9 42.1 1.0
C C:GLN22 4.0 39.9 1.0
CD C:GLU28 4.0 49.1 1.0
C C:ILE21 4.0 38.4 1.0
N C:VAL24 4.1 41.2 1.0
CA C:GLN22 4.2 38.9 1.0
N C:GLU25 4.2 58.1 1.0
N C:LEU27 4.3 44.0 1.0
CA C:GLU25 4.3 57.9 1.0
CA C:VAL24 4.3 42.2 1.0
OE2 C:GLU28 4.4 50.3 1.0
N C:GLY26 4.4 46.8 1.0
NZ C:LYS70 4.6 44.1 1.0
N C:GLN22 4.6 37.9 1.0
CA C:LEU27 4.6 42.8 1.0
CG2 C:ILE21 4.7 38.4 1.0
C C:GLU25 4.8 56.3 1.0
N C:GLU23 4.8 39.5 1.0
CG C:GLU28 4.8 48.2 1.0
OE1 C:GLU25 4.9 59.4 1.0
CB C:VAL24 4.9 41.3 1.0
N C:GLU28 5.0 45.2 1.0

Sodium binding site 7 out of 8 in 5t73

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Sodium binding site 7 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:15.9
occ:1.00
 O D:ASP34 2.5 35.7 1.0
OG D:SER76 2.6 38.7 1.0
O D:THR36 2.7 35.4 1.0
O D:HOH516 3.1 35.2 1.0
O D:PHE75 3.3 35.3 1.0
OD1 D:ASP38 3.3 35.6 1.0
C D:ASP34 3.6 35.4 1.0
OG D:SER74 3.7 39.5 1.0
CD1 D:LEU41 3.8 33.4 1.0
C D:PHE75 3.8 36.3 1.0
C D:THR36 3.8 35.6 1.0
CB D:SER76 3.8 39.6 1.0
CA D:SER76 4.1 39.8 1.0
O D:HOH539 4.1 14.3 1.0
N D:SER76 4.2 41.4 1.0
N D:ASP34 4.2 34.7 1.0
CA D:ASP34 4.3 34.6 1.0
C D:ASP37 4.4 35.5 1.0
N D:THR36 4.5 35.6 1.0
CB D:ASP34 4.5 33.7 1.0
CG D:ASP38 4.5 36.0 1.0
N D:ASP38 4.5 35.8 1.0
CA D:ASP37 4.6 36.3 1.0
N D:LEU35 4.6 35.9 1.0
C D:LEU35 4.6 36.6 1.0
N D:ASP37 4.7 36.5 1.0
N D:PHE75 4.7 36.3 1.0
O D:ASP37 4.7 34.7 1.0
CA D:THR36 4.8 35.5 1.0
CA D:PHE75 4.8 37.0 1.0
CA D:LEU35 4.9 36.8 1.0
CA D:ASP38 5.0 35.2 1.0

Sodium binding site 8 out of 8 in 5t73

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Sodium binding site 8 out of 8 in the Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of S.Aureus Glyceraldehyde-3-Phosphate-Dehydrogenase (Gap) Containing Oxidized CYS151 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:12.6
occ:1.00
 O D:HOH544 2.3 32.1 1.0
O D:VAL24 2.4 50.4 1.0
O D:ILE21 2.7 35.6 1.0
O D:LEU27 2.9 49.1 1.0
C D:VAL24 3.4 51.1 1.0
C D:ILE21 3.9 34.6 1.0
C D:GLN22 4.0 36.0 1.0
O D:GLN22 4.0 37.0 1.0
C D:LEU27 4.0 47.9 1.0
N D:VAL24 4.1 48.2 1.0
CA D:GLN22 4.1 35.2 1.0
N D:GLU25 4.2 54.5 1.0
CA D:GLU25 4.3 57.0 1.0
CA D:VAL24 4.4 48.9 1.0
N D:LEU27 4.4 50.4 1.0
N D:GLN22 4.5 37.3 1.0
N D:GLU23 4.5 47.4 1.0
CA D:LEU27 4.6 47.4 1.0
N D:GLY26 4.7 56.5 1.0
CG2 D:ILE21 4.7 34.2 1.0
CB D:LEU27 4.7 44.8 1.0
C D:GLU25 4.8 56.0 1.0
C D:GLU23 4.9 51.6 1.0

Reference:

M.Imber, N.T.T.Huyen, A.J.Pietrzyk-Brzezinska, V.V.Loi, M.Hillion, J.Bernhardt, L.Tharichen, K.Kolsek, M.Saleh, C.J.Hamilton, L.Adrian, F.Grater, M.C.Wahl, H.Antelmann. Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus Aureus Under Hypochlorite Stress. Antioxid. Redox Signal. V. 28 410 2018.
ISSN: ESSN 1557-7716
PubMed: 27967218
DOI: 10.1089/ARS.2016.6897
Page generated: Tue Oct 8 00:03:41 2024

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