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Sodium in PDB 7bm0: Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp

Enzymatic activity of Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp

All present enzymatic activity of Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp, PDB code: 7bm0 was solved by P.D.Anindita, P.Grinkevich, Z.Franta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.71 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.952, 72.952, 196.45, 90, 90, 90
R / Rfree (%) 21.6 / 22.9

Other elements in 7bm0:

The structure of Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp (pdb code 7bm0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp, PDB code: 7bm0:

Sodium binding site 1 out of 1 in 7bm0

Go back to Sodium Binding Sites List in 7bm0
Sodium binding site 1 out of 1 in the Crystal Structure of the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp


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 the Tick-Borne Encephalitis Virus NS3 Helicase in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:30.8
occ:1.00
 O A:HOH995 2.9 39.6 1.0
O A:HOH981 3.1 32.5 1.0
NH1 A:ARG402 3.3 40.6 1.0
NH2 A:ARG402 3.5 44.0 1.0
O A:VAL388 3.8 31.2 1.0
NH2 A:ARG382 3.8 29.2 1.0
CZ A:ARG402 3.8 40.2 1.0
CA A:ILE389 4.7 30.6 1.0
CG1 A:ILE389 4.7 32.7 1.0
OD2 A:ASP399 4.8 42.6 1.0
CZ A:ARG382 4.8 32.2 1.0
O A:HOH1054 4.9 36.6 1.0
C A:VAL388 4.9 27.3 1.0

Reference:

P.D.Anindita, M.Halbeisen, D.Reha, R.Tuma, Z.Franta. Mechanistic Insight Into the Rna-Stimulated Atpase Activity of Tick-Borne Encephalitis Virus Helicase. J.Biol.Chem. V. 298 02383 2022.
ISSN: ESSN 1083-351X
PubMed: 35987382
DOI: 10.1016/J.JBC.2022.102383
Page generated: Tue Oct 8 16:14:26 2024

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