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Sodium in PDB 7tin: The Structure of S. Aureus Mend

Enzymatic activity of The Structure of S. Aureus Mend

All present enzymatic activity of The Structure of S. Aureus Mend:
2.2.1.9;

Protein crystallography data

The structure of The Structure of S. Aureus Mend, PDB code: 7tin was solved by J.M.Johnston, T.Stanborough, N.A.T.Ho, E.W.Akazong, W.Jiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.445, 166.489, 168.035, 90, 90, 90
R / Rfree (%) 18.7 / 23.6

Other elements in 7tin:

The structure of The Structure of S. Aureus Mend also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of S. Aureus Mend (pdb code 7tin). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of S. Aureus Mend, PDB code: 7tin:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7tin

Go back to Sodium Binding Sites List in 7tin
Sodium binding site 1 out of 4 in the The Structure of S. Aureus Mend


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of S. Aureus Mend within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:60.2
occ:1.00
 O A:HIS45 2.5 59.8 1.0
O A:GLU43 2.5 56.4 1.0
O A:PHE42 2.6 61.5 1.0
O A:ILE48 2.7 55.4 1.0
C A:GLU43 3.0 64.2 1.0
CA A:GLU43 3.5 57.4 1.0
C A:HIS45 3.5 59.8 1.0
C A:PHE42 3.7 59.9 1.0
N A:HIS45 3.8 60.0 1.0
C A:ILE48 3.9 52.3 1.0
N A:ALA44 4.0 58.2 1.0
N A:GLU43 4.0 60.0 1.0
C A:ALA44 4.1 63.8 1.0
CA A:HIS45 4.2 58.6 1.0
N A:ILE48 4.4 57.6 1.0
CA A:ALA44 4.5 62.2 1.0
O A:ALA44 4.5 59.0 1.0
CG2 A:THR50 4.5 56.4 1.0
N A:PRO46 4.5 58.7 1.0
CA A:ILE48 4.6 59.4 1.0
CB A:HIS45 4.7 54.0 1.0
CA A:PRO46 4.7 61.1 1.0
CB A:ILE48 4.8 55.1 1.0
CB A:GLU43 4.8 56.8 1.0
C A:PRO46 4.8 60.7 1.0
N A:LYS49 4.9 49.6 1.0

Sodium binding site 2 out of 4 in 7tin

Go back to Sodium Binding Sites List in 7tin
Sodium binding site 2 out of 4 in the The Structure of S. Aureus Mend


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of S. Aureus Mend within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:53.9
occ:1.00
 O B:HIS45 2.3 52.0 1.0
O B:ILE48 2.5 53.6 1.0
O B:HOH756 2.5 60.1 1.0
O B:PHE42 2.5 49.5 1.0
O B:GLU43 2.7 53.6 1.0
C B:GLU43 3.2 53.8 1.0
C B:HIS45 3.5 52.4 1.0
CA B:GLU43 3.5 52.7 1.0
C B:PHE42 3.6 50.2 1.0
C B:ILE48 3.7 51.0 1.0
N B:HIS45 3.9 49.2 1.0
N B:GLU43 4.1 48.5 1.0
CA B:HIS45 4.1 51.0 1.0
N B:ALA44 4.2 53.2 1.0
C B:ALA44 4.3 48.4 1.0
N B:ILE48 4.3 49.7 1.0
CA B:ILE48 4.4 51.2 1.0
CB B:HIS45 4.5 50.9 1.0
N B:PRO46 4.5 49.9 1.0
CB B:ILE48 4.5 51.4 1.0
CA B:PRO46 4.6 45.4 1.0
CG2 B:THR50 4.6 48.5 1.0
N B:LYS49 4.7 52.9 1.0
C B:PRO46 4.7 52.7 1.0
CA B:ALA44 4.8 50.1 1.0
O B:ALA44 4.8 55.2 1.0
O B:HOH757 4.8 52.3 1.0
CB B:GLU43 4.9 51.0 1.0
CA B:PHE42 4.9 50.6 1.0
CA B:LYS49 4.9 50.7 1.0
N B:ASN47 4.9 54.9 1.0

Sodium binding site 3 out of 4 in 7tin

Go back to Sodium Binding Sites List in 7tin
Sodium binding site 3 out of 4 in the The Structure of S. Aureus Mend


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of S. Aureus Mend within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:58.8
occ:1.00
 O C:HIS45 2.4 56.9 1.0
O C:PHE42 2.5 54.6 1.0
O C:GLU43 2.5 52.6 1.0
O C:ILE48 2.6 55.5 1.0
O C:HOH733 2.8 57.9 1.0
O C:HOH754 3.0 56.7 1.0
C C:GLU43 3.0 58.5 1.0
O C:HOH757 3.2 57.9 1.0
CA C:GLU43 3.3 56.5 1.0
C C:HIS45 3.5 56.8 1.0
C C:PHE42 3.5 54.3 1.0
N C:HIS45 3.8 55.4 1.0
C C:ILE48 3.8 53.2 1.0
N C:GLU43 3.9 56.6 1.0
N C:ALA44 3.9 55.6 1.0
CA C:HIS45 4.1 55.6 1.0
C C:ALA44 4.2 56.8 1.0
OE2 C:GLU43 4.4 64.7 1.0
N C:ILE48 4.4 52.4 1.0
CA C:ILE48 4.5 54.2 1.0
CA C:ALA44 4.5 53.3 1.0
N C:PRO46 4.5 56.0 1.0
CB C:HIS45 4.6 50.8 1.0
CG2 C:THR50 4.6 48.2 1.0
CB C:ILE48 4.6 57.2 1.0
CD C:GLU43 4.7 66.4 1.0
CA C:PRO46 4.7 51.8 1.0
CB C:GLU43 4.7 49.3 1.0
O C:ALA44 4.8 57.0 1.0
N C:LYS49 4.8 48.4 1.0
CA C:PHE42 4.9 53.3 1.0
C C:PRO46 5.0 54.3 1.0
CG C:GLU43 5.0 59.0 1.0

Sodium binding site 4 out of 4 in 7tin

Go back to Sodium Binding Sites List in 7tin
Sodium binding site 4 out of 4 in the The Structure of S. Aureus Mend


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of S. Aureus Mend within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na603

b:57.2
occ:1.00
 O D:HIS45 2.4 51.9 1.0
O D:HOH757 2.6 63.5 1.0
O D:ILE48 2.6 46.3 1.0
O D:PHE42 2.6 53.1 1.0
O D:HOH763 2.6 56.4 1.0
O D:GLU43 2.7 59.8 1.0
C D:GLU43 3.3 56.9 1.0
C D:HIS45 3.6 54.4 1.0
CA D:GLU43 3.6 55.6 1.0
C D:PHE42 3.7 51.3 1.0
C D:ILE48 3.8 49.2 1.0
N D:HIS45 4.0 52.6 1.0
N D:GLU43 4.1 50.1 1.0
CA D:HIS45 4.2 53.3 1.0
N D:ALA44 4.3 53.9 1.0
C D:ALA44 4.3 57.1 1.0
N D:ILE48 4.4 55.8 1.0
CG2 D:THR50 4.5 53.5 1.0
CA D:ILE48 4.5 50.2 1.0
CB D:HIS45 4.6 54.2 1.0
OE1 D:GLU43 4.6 64.5 1.0
N D:PRO46 4.6 54.1 1.0
CB D:ILE48 4.7 49.0 1.0
CA D:PRO46 4.8 50.5 1.0
C D:PRO46 4.8 49.2 1.0
N D:LYS49 4.8 45.2 1.0
CA D:ALA44 4.8 54.2 1.0
O D:ALA44 4.8 58.7 1.0
O D:PRO46 4.9 51.0 1.0
CB D:GLU43 4.9 58.8 1.0
CA D:PHE42 5.0 49.7 1.0
CA D:LYS49 5.0 48.5 1.0

Reference:

T.Stanborough, N.A.T.Ho, W.Jiao, E.W.Akazong, G.Bashiri, S.S.Dawes, E.M.M.Bulloch, J.M.Johnston. 1,4-Dihydroxy-2-Naphthoic Acid Is An Allosteric Inhibitor of Staphylococcus Aureus Mend To Be Published.
Page generated: Fri Apr 7 16:32:49 2023

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