Potassium in PDB 7wik: Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155

Enzymatic activity of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155

All present enzymatic activity of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155:
3.1.13.3;

Protein crystallography data

The structure of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155, PDB code: 7wik was solved by P.Badhwar, B.Taneja, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.07 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.25, 97.26, 146.73, 90, 90, 90
R / Rfree (%) 17.9 / 22.2

Other elements in 7wik:

The structure of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155 (pdb code 7wik). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155, PDB code: 7wik:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7wik

Go back to Potassium Binding Sites List in 7wik
Potassium binding site 1 out of 4 in the Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:75.5
occ:1.00
 OE2 A:GLU11 3.0 33.9 1.0
O A:HOH736 3.1 41.5 1.0
O A:CYS10 3.1 25.0 1.0
OD1 A:ASP9 3.1 39.1 1.0
OD2 A:ASP9 3.1 37.8 1.0
OE1 A:GLU11 3.3 31.5 1.0
OD2 A:ASP162 3.4 38.8 1.0
CD A:GLU11 3.4 30.3 1.0
CG A:ASP9 3.5 30.7 1.0
C A:CYS10 4.3 26.4 1.0
C3 A:GOL605 4.5 45.8 1.0
CG A:ASP162 4.6 38.5 1.0
O A:HOH824 4.7 45.3 1.0
CG A:GLU11 4.7 28.6 1.0
N A:CYS10 4.9 24.6 1.0
OD1 A:ASP110 5.0 25.5 0.5
O3 A:GOL605 5.0 32.7 1.0

Potassium binding site 2 out of 4 in 7wik

Go back to Potassium Binding Sites List in 7wik
Potassium binding site 2 out of 4 in the Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K302

b:77.4
occ:1.00
 O B:HOH433 2.7 34.3 1.0
OD1 B:ASP9 3.2 33.0 1.0
OE2 B:GLU11 3.3 31.0 1.0
O B:CYS10 3.4 30.3 1.0
OD2 B:ASP9 3.4 34.0 1.0
OE1 B:GLU11 3.4 30.1 1.0
OD2 B:ASP162 3.4 38.0 1.0
CD B:GLU11 3.6 26.7 1.0
CG B:ASP9 3.7 30.7 1.0
O C:HOH458 4.1 53.2 1.0
C1 B:GOL307 4.3 47.0 1.0
O B:HOH432 4.5 47.0 1.0
CG B:ASP162 4.5 35.3 1.0
NH1 C:ARG65 4.5 35.7 0.6
C B:CYS10 4.6 30.5 1.0
O1 B:GOL307 4.9 31.8 1.0
CG B:GLU11 5.0 27.6 1.0

Potassium binding site 3 out of 4 in 7wik

Go back to Potassium Binding Sites List in 7wik
Potassium binding site 3 out of 4 in the Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K302

b:64.9
occ:1.00
 OE2 C:GLU11 3.0 29.6 1.0
OE1 C:GLU11 3.1 25.9 1.0
O C:HOH431 3.2 36.3 1.0
O C:CYS10 3.3 22.7 1.0
OD2 C:ASP9 3.3 30.7 1.0
CD C:GLU11 3.3 26.5 1.0
OD2 C:ASP162 3.3 33.2 1.0
OD1 C:ASP9 3.4 38.2 1.0
O C:HOH527 3.5 49.4 1.0
O C:HOH507 3.5 54.8 1.0
CG C:ASP9 3.7 31.3 1.0
C1 C:GOL309 4.0 41.9 1.0
C C:CYS10 4.4 22.7 1.0
CG C:ASP162 4.5 33.7 1.0
NH1 B:ARG65 4.6 49.8 1.0
CG C:GLU11 4.7 24.7 1.0
O C:HOH441 4.7 42.7 1.0
C2 C:GOL309 4.9 47.2 1.0
O1 C:GOL309 5.0 32.1 1.0

Potassium binding site 4 out of 4 in 7wik

Go back to Potassium Binding Sites List in 7wik
Potassium binding site 4 out of 4 in the Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Oligoribonuclease of Mycobacterium Smegmatis MC2 155 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:63.8
occ:1.00
 OE2 D:GLU11 2.9 30.5 1.0
OD2 D:ASP9 3.0 30.1 1.0
OD2 D:ASP162 3.2 37.2 1.0
OD1 D:ASP9 3.2 28.9 1.0
O D:CYS10 3.2 24.4 1.0
OE1 D:GLU11 3.2 27.6 1.0
O D:HOH660 3.3 29.6 1.0
CD D:GLU11 3.3 26.5 1.0
CG D:ASP9 3.5 30.1 1.0
O D:HOH646 3.6 51.2 1.0
CG D:ASP162 4.3 33.4 1.0
O D:HOH730 4.4 48.3 1.0
C D:CYS10 4.4 28.0 1.0
C1 D:GOL508 4.4 33.6 0.4
C3 D:GOL508 4.5 53.7 0.6
CG D:GLU11 4.6 25.5 1.0
O D:HOH610 4.7 37.0 1.0
CB D:ASP162 4.8 31.7 1.0
O1 D:GOL508 4.9 26.1 0.4
O3 D:GOL508 4.9 43.7 0.6

Reference:

P.Badhwar, S.H.Khan, B.Taneja. Three-Dimensional Structure of A Mycobacterial Oligoribonuclease Reveals A Unique C-Terminal Tail That Stabilizes the Homodimer. J.Biol.Chem. V. 298 02595 2022.
ISSN: ESSN 1083-351X
PubMed: 36244449
DOI: 10.1016/J.JBC.2022.102595
Page generated: Wed Apr 5 10:25:22 2023

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