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Sodium in PDB 5ccx: Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate

Enzymatic activity of Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate

All present enzymatic activity of Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate:
2.1.1.220;

Protein crystallography data

The structure of Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate, PDB code: 5ccx was solved by J.Finer-Moore, N.Czudnochowski, J.D.O'connell Iii, A.L.Wang, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.13 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.770, 136.770, 177.160, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate (pdb code 5ccx). 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 Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate, PDB code: 5ccx:

Sodium binding site 1 out of 1 in 5ccx

Go back to Sodium Binding Sites List in 5ccx
Sodium binding site 1 out of 1 in the Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Product Complex of Trna M1A58 Methyltransferase with TRNA3LYS As Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na101

b:42.4
occ:1.00
 O N:HOH269 2.1 52.8 1.0
O N:HOH263 2.2 49.5 1.0
O N:HOH239 2.2 43.7 1.0
OP2 N:A9 2.2 47.8 1.0
OP1 N:U8 2.2 51.2 1.0
O N:HOH217 2.5 49.3 1.0
P N:A9 3.4 43.4 1.0
P N:U8 3.6 45.8 1.0
O N:HOH261 3.8 54.7 1.0
OP1 N:A9 3.8 40.5 1.0
OP2 N:U12 3.9 55.2 1.0
O N:HOH240 4.0 49.2 1.0
O N:HOH226 4.0 39.0 1.0
O3' N:U8 4.3 40.8 1.0
O5' N:U8 4.3 50.9 1.0
OP2 N:U8 4.4 39.0 1.0
O N:HOH231 4.5 54.0 1.0
OP2 N:C11 4.5 54.8 1.0
O N:HOH251 4.5 43.3 1.0
O5' N:A9 4.5 47.0 1.0
C5' N:U8 4.6 42.0 1.0
O3' N:A7 4.6 51.4 1.0
C3' N:U8 4.7 36.1 1.0
C5 N:U12 4.8 45.4 1.0

Reference:

J.Finer-Moore, N.Czudnochowski, J.D.O'connell, A.L.Wang, R.M.Stroud. Crystal Structure of the Human Trna M(1)A58 Methyltransferase-TRNA3(Lys) Complex: Refolding of Substrate Trna Allows Access to the Methylation Target. J.Mol.Biol. V. 427 3862 2015.
ISSN: ESSN 1089-8638
PubMed: 26470919
DOI: 10.1016/J.JMB.2015.10.005
Page generated: Mon Oct 7 20:17:01 2024

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