Atomistry » Sodium » PDB 5ack-5b07 » 5ah2
Atomistry »
  Sodium »
    PDB 5ack-5b07 »
      5ah2 »

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy