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Sodium in PDB 5ah2: The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product.

Enzymatic activity of The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product.

All present enzymatic activity of The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product.:
2.7.7.7;

Protein crystallography data

The structure of The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product., PDB code: 5ah2 was solved by P.Lukat, A.Kling, D.W.Heinz, R.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.71 / 2.13
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.241, 125.868, 94.899, 90.00, 104.42, 90.00
R / Rfree (%) 18.2 / 23.1

Sodium Binding Sites:

The binding sites of Sodium atom in the The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product. (pdb code 5ah2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product., PDB code: 5ah2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ah2

Go back to Sodium Binding Sites List in 5ah2
Sodium binding site 1 out of 2 in the The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1398

b:45.4
occ:1.00
O A:HOH2228 2.6 43.0 1.0
O A:ALA316 3.1 31.4 1.0
O A:ALA308 3.2 26.4 1.0
N A:ALA316 3.6 35.1 1.0
CB A:ARG315 3.6 36.4 1.0
CB A:SER307 3.7 28.6 1.0
C A:ALA316 3.8 32.8 1.0
N A:ALA308 4.0 25.2 1.0
C A:ALA308 4.0 25.6 1.0
O A:HOH2223 4.1 49.4 1.0
CA A:ARG315 4.2 31.2 1.0
C A:ARG315 4.3 30.4 1.0
CG A:ARG315 4.3 41.4 1.0
CA A:ALA316 4.3 37.0 1.0
CD A:ARG315 4.4 42.9 1.0
OE1 A:GLU317 4.5 55.0 1.0
OG A:SER307 4.5 27.9 1.0
CA A:SER307 4.5 26.1 1.0
CA A:ALA308 4.6 25.9 1.0
C A:SER307 4.7 24.5 1.0
CB A:GLU317 4.7 33.0 1.0
N A:GLU317 4.8 31.2 1.0
O B:HOH2067 4.9 25.4 0.7
N A:GLY309 4.9 27.9 1.0

Sodium binding site 2 out of 2 in 5ah2

Go back to Sodium Binding Sites List in 5ah2
Sodium binding site 2 out of 2 in the The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Sliding Clamp of Mycobacterium Smegmatis in Complex with A Natural Product. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1398

b:56.9
occ:1.00
OG C:SER55 2.3 29.1 1.0
O C:HOH2183 2.7 38.9 1.0
O C:HOH2020 2.8 28.3 1.0
CB C:SER55 3.2 28.1 1.0
OE2 C:GLU64 3.4 49.9 1.0
CD2 C:LEU44 3.5 30.0 1.0
CD2 C:LEU127 3.9 50.3 1.0
CG2 C:THR53 3.9 37.5 1.0
OG1 C:THR46 4.2 32.2 1.0
CD C:GLU64 4.3 49.3 1.0
CG C:LEU44 4.3 32.9 1.0
CG C:GLU64 4.5 40.2 1.0
CA C:SER55 4.5 27.9 1.0
O C:HOH2022 4.5 37.0 1.0
CB C:LEU44 4.5 32.5 1.0
O C:HOH2055 4.5 39.5 1.0
N C:SER55 4.6 27.2 1.0
CD1 C:LEU127 4.7 46.6 1.0
O C:LEU44 4.7 29.1 1.0
CG C:LEU127 4.9 45.7 1.0

Reference:

A.Kling, P.Lukat, D.V.Almeida, A.Bauer, E.Fontaine, S.Sordello, N.Zaburannyi, J.Herrmann, S.C.Wenzel, C.Koenig, N.C.Ammermann, M.B.Barrio, K.Borchers, F.Bordon-Pallier, M.Broenstrup, G.Courtemanche, M.Gerlitz, M.Geslin, P.Hammann, D.W.Heinz, H.Hoffmann, S.Klieber, M.Kohlmann, M.Kurz, C.Lair, H.Matter, E.Nuermberger, S.Tyagi, L.Fraisse, J.H.Grosset, S.Lagrange, R.Mueller. Antibiotics. Targeting Dnan For Tuberculosis Therapy Using Novel Griselimycins. Science V. 348 1106 2015.
ISSN: ISSN 0036-8075
PubMed: 26045430
DOI: 10.1126/SCIENCE.AAA4690
Page generated: Tue Dec 15 10:23:19 2020

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