Sodium in PDB 8c9f: Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue.

Enzymatic activity of Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue.

All present enzymatic activity of Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue.:
6.1.1.5;

Protein crystallography data

The structure of Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue., PDB code: 8c9f 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) 48.81 / 3.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.04, 127.04, 163.38, 90, 90, 120
R / Rfree (%) 23.9 / 27.6

Other elements in 8c9f:

The structure of Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase 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 Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue. (pdb code 8c9f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue., PDB code: 8c9f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8c9f

Go back to Sodium Binding Sites List in 8c9f
Sodium binding site 1 out of 4 in the Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase 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 Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1017

b:124.6
occ:1.00
 OE2 A:GLU520 3.6 109.8 1.0
OE1 A:GLU520 3.8 126.1 1.0
CD A:GLU520 4.0 113.2 1.0
OG1 A:THR521 4.5 140.3 1.0
O A:LYS519 4.5 122.9 1.0
CE2 A:TYR466 4.5 116.8 1.0
CA A:GLU520 4.6 105.9 1.0
N A:THR521 4.7 122.9 1.0
OH A:TYR466 5.0 115.8 1.0

Sodium binding site 2 out of 4 in 8c9f

Go back to Sodium Binding Sites List in 8c9f
Sodium binding site 2 out of 4 in the Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase 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 Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1018

b:78.0
occ:1.00
 O A:ILA1002 3.3 105.9 1.0
OD2 A:ASP556 3.6 144.1 1.0
O2A A:ILA1002 4.0 120.3 1.0
C A:ILA1002 4.3 97.7 1.0
NE2 A:GLN557 4.3 98.2 1.0
CG A:ASP556 4.5 123.8 1.0
CH2 A:TRP527 4.6 87.6 1.0
CZ2 A:TRP527 4.7 108.8 1.0
C8 A:ILA1002 4.7 105.3 1.0
CE2 A:TYR58 4.8 109.8 1.0
CB A:ASP556 5.0 97.7 1.0
N3A A:ILA1002 5.0 85.0 1.0
SA A:ILA1002 5.0 110.2 1.0

Sodium binding site 3 out of 4 in 8c9f

Go back to Sodium Binding Sites List in 8c9f
Sodium binding site 3 out of 4 in the Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase 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 Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1019

b:92.7
occ:1.00
 OG1 A:THR521 3.7 140.3 1.0
CB A:THR521 4.2 141.1 1.0
OD1 A:ASP522 4.3 103.5 1.0
O A:GLN455 4.8 110.5 1.0
O A:THR521 4.9 122.7 1.0
C A:GLN455 4.9 94.6 1.0
CA A:GLN455 4.9 95.5 1.0
CB A:GLN455 4.9 96.0 1.0
C A:THR521 5.0 131.9 1.0
CG A:GLN455 5.0 105.5 1.0

Sodium binding site 4 out of 4 in 8c9f

Go back to Sodium Binding Sites List in 8c9f
Sodium binding site 4 out of 4 in the Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase 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 4 of Priestia Megaterium Inactive High Motif Mutant of TYPE1 Isoleucyl-Trna Synthetase Complexed with An Isoleucyl-Adenylate Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1020

b:153.8
occ:1.00
 OE1 A:GLU115 2.6 182.4 1.0
CD A:GLU115 3.8 178.8 1.0
CB A:GLU115 3.9 148.3 1.0
N A:ASN112 4.4 123.0 1.0
CE A:MET116 4.4 117.6 1.0
CG A:GLU115 4.4 168.8 1.0
OE2 A:GLU115 4.7 184.7 1.0
O A:ASN112 4.8 121.5 1.0
CA A:VAL111 4.9 138.6 1.0
CB A:ASN112 5.0 152.4 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: Wed Oct 9 10:52:43 2024

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