Sodium in PDB 4yhq: Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A

Enzymatic activity of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A

All present enzymatic activity of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A, PDB code: 4yhq was solved by J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.303, 60.303, 86.141, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 21

Other elements in 4yhq:

The structure of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Yttrium (Y) 4 atoms
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A (pdb code 4yhq). 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 Multidrug Resistant Clinical Isolate PR20 with Grl-5010A, PDB code: 4yhq:

Sodium binding site 1 out of 1 in 4yhq

Go back to Sodium Binding Sites List in 4yhq
Sodium binding site 1 out of 1 in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A


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 Multidrug Resistant Clinical Isolate PR20 with Grl-5010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:38.1
occ:0.60
 O A:HOH312 2.7 97.7 0.5
OG1 A:THR89 2.7 13.1 1.0
CA A:GLY73 3.1 18.2 0.5
O A:HOH366 3.1 29.5 0.5
NE2 A:GLN92 3.2 36.1 1.0
CA A:THR89 3.5 12.0 1.0
CB A:THR89 3.6 13.5 1.0
N A:THR74 3.7 15.2 0.5
N A:THR89 3.7 11.6 1.0
C A:GLY73 3.8 16.1 0.5
C A:ASP88 3.9 13.4 1.0
O A:THR74 3.9 14.0 0.5
O A:ASP88 4.0 18.9 1.0
CG1 A:VAL71 4.1 23.7 0.5
OD2 A:ASP88 4.1 24.0 1.0
O A:THR74 4.1 17.1 0.5
CG A:ASP88 4.1 16.2 1.0
CG2 A:THR89 4.2 14.3 1.0
N A:GLY73 4.2 17.4 0.5
CD1 A:ILE64 4.3 22.5 0.5
OD1 A:ASP88 4.4 15.3 1.0
CB A:ASP88 4.4 15.1 1.0
CD A:GLN92 4.5 28.8 1.0
CD1 A:ILE64 4.5 18.4 0.5
O A:ILE72 4.7 20.9 0.5
C A:THR74 4.7 13.6 0.5
CA A:THR74 4.7 15.5 0.5
C A:ILE72 4.8 19.2 0.5
O A:GLY73 4.8 17.1 0.5
OG1 A:THR31 4.8 15.8 1.0
CA A:ASP88 4.8 12.8 1.0
O A:HOH368 4.9 35.2 1.0
C A:THR89 4.9 10.8 1.0
CG2 A:VAL71 5.0 17.7 0.5

Reference:

J.Agniswamy, J.M.Louis, C.H.Shen, S.Yashchuk, A.K.Ghosh, I.T.Weber. Substituted Bis-Thf Protease Inhibitors with Improved Potency Against Highly Resistant Mature Hiv-1 Protease PR20. J.Med.Chem. V. 58 5088 2015.
ISSN: ISSN 0022-2623
PubMed: 26010498
DOI: 10.1021/ACS.JMEDCHEM.5B00474
Page generated: Tue Dec 15 10:03:55 2020

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