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Sodium in PDB 8c9e: Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue

Enzymatic activity of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue

All present enzymatic activity of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue:
6.1.1.5;

Protein crystallography data

The structure of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue, PDB code: 8c9e was solved by A.Brkic, M.Leibundgut, J.Jablonska, V.Zanki, Z.Car, V.Petrovic Perokovic, N.Ban, I.Gruic-Sovulj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.77 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.09, 127.09, 163.22, 90, 90, 120
R / Rfree (%) 24.2 / 26.9

Other elements in 8c9e:

The structure of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue (pdb code 8c9e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue, PDB code: 8c9e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8c9e

Go back to Sodium Binding Sites List in 8c9e
Sodium binding site 1 out of 3 in the Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1016

b:119.1
occ:1.00
 OE1 A:GLU520 3.0 124.1 1.0
OE2 A:GLU520 3.2 101.4 1.0
CD A:GLU520 3.4 102.4 1.0
OG1 A:THR521 4.2 133.5 1.0
NZ A:LYS179 4.5 118.5 1.0
N A:THR521 4.6 123.3 1.0
OH A:TYR466 4.7 114.1 1.0
OD2 A:ASP522 4.7 95.5 1.0
CG A:GLU520 4.8 102.3 1.0
CA A:GLU520 4.9 98.5 1.0
CE2 A:TYR466 4.9 115.7 1.0

Sodium binding site 2 out of 3 in 8c9e

Go back to Sodium Binding Sites List in 8c9e
Sodium binding site 2 out of 3 in the Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1017

b:146.2
occ:1.00
 OE1 A:GLU115 2.8 189.2 1.0
CD A:GLU115 4.0 185.5 1.0
CB A:GLU115 4.2 149.6 1.0
N A:ASN112 4.7 142.8 1.0
CG A:GLU115 4.8 172.8 1.0
CE A:MET116 4.8 142.1 1.0
OE2 A:GLU115 4.9 183.6 1.0

Sodium binding site 3 out of 3 in 8c9e

Go back to Sodium Binding Sites List in 8c9e
Sodium binding site 3 out of 3 in the Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Priestia Megaterium Mupirocin-Sensitive Isoleucyl-Trna Synthetase 1 Complexed with An Isoleucyl-Adenylate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1018

b:125.1
occ:1.00
 OG1 A:THR521 3.5 133.5 1.0
CB A:THR521 3.9 115.3 1.0
OD1 A:ASP522 4.3 89.5 1.0
O A:THR521 4.6 109.1 1.0
C A:THR521 4.7 107.9 1.0
CG2 A:THR521 4.8 131.7 1.0
CA A:THR521 5.0 116.8 1.0

Reference:

A.Brkic, M.Leibundgut, J.Jablonska, V.Zanki, Z.Car, V.Petrovic Perokovic, N.Ban, I.Gruic-Sovulj. Antibiotic Hyper-Resistance in A Class I Aminoacyl-Trna Synthetase with Altered Active Site Signature Motif To Be Published.
Page generated: Mon Aug 18 13:24:27 2025

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