Atomistry » Sodium » PDB 5jid-5k8r » 5jyx
Atomistry »
  Sodium »
    PDB 5jid-5k8r »
      5jyx »

Sodium in PDB 5jyx: Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like

Protein crystallography data

The structure of Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like, PDB code: 5jyx was solved by X.Mei, M.A.Swairjo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 108.56 / 2.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 215.325, 126.779, 65.083, 90.00, 102.58, 90.00
R / Rfree (%) 17.1 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like (pdb code 5jyx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like, PDB code: 5jyx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5jyx

Go back to Sodium Binding Sites List in 5jyx
Sodium binding site 1 out of 3 in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like


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 the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:37.5
occ:1.00
O C:HOH308 2.5 46.9 1.0
OG C:SER33 2.9 37.4 1.0
OE2 C:GLU31 3.2 55.3 1.0
O C:GLU31 3.4 29.1 1.0
O C:THR85 3.5 29.0 1.0
N C:SER33 3.6 30.8 1.0
C C:GLU31 3.7 31.1 1.0
C C:VAL32 3.8 28.3 1.0
CA C:VAL32 3.8 28.4 1.0
N C:VAL32 3.8 29.4 1.0
CG C:GLU31 3.8 47.6 1.0
CD C:GLU31 3.9 54.2 1.0
CE C:LYS87 4.0 47.1 1.0
CD C:LYS87 4.0 42.7 1.0
CG C:LYS87 4.0 38.6 1.0
CB C:SER33 4.2 33.7 1.0
CB C:GLU31 4.2 40.7 1.0
CG2 C:THR85 4.2 32.5 1.0
N C:LYS87 4.2 32.9 1.0
C C:THR85 4.2 30.4 1.0
CB C:LYS87 4.2 35.6 1.0
CB C:THR85 4.3 31.6 1.0
NZ C:LYS87 4.4 49.6 1.0
CA C:SER33 4.5 31.7 1.0
O C:VAL32 4.5 26.7 1.0
CA C:GLU31 4.5 34.9 1.0
CE C:LYS14 4.6 47.1 1.0
C C:VAL86 4.7 31.8 1.0
N C:VAL86 4.8 30.4 1.0
CA C:VAL86 4.8 30.5 1.0
CA C:LYS87 4.9 34.6 1.0
CG C:LYS14 4.9 38.0 1.0
CA C:THR85 5.0 31.0 1.0

Sodium binding site 2 out of 3 in 5jyx

Go back to Sodium Binding Sites List in 5jyx
Sodium binding site 2 out of 3 in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:42.1
occ:1.00
O E:HOH305 2.3 51.8 1.0
OG E:SER33 3.0 39.7 1.0
O E:GLU31 3.5 34.6 1.0
O E:THR85 3.5 36.4 1.0
N E:SER33 3.5 34.1 1.0
CA E:VAL32 3.8 33.9 1.0
CG2 E:THR85 3.8 35.6 1.0
C E:VAL32 3.8 33.5 1.0
C E:GLU31 3.8 34.2 1.0
CB E:SER33 3.8 35.6 1.0
CE E:LYS87 3.8 40.8 1.0
CD E:LYS87 3.9 38.2 1.0
N E:VAL32 3.9 34.3 1.0
CG E:LYS87 4.0 35.9 1.0
OE1 E:GLU31 4.0 58.0 1.0
C E:THR85 4.0 34.6 1.0
CB E:THR85 4.0 35.9 1.0
CG E:GLU31 4.1 49.5 1.0
N E:LYS87 4.2 31.0 1.0
CA E:SER33 4.3 34.2 1.0
CB E:GLU31 4.4 42.4 1.0
N E:VAL86 4.5 33.9 1.0
CE E:LYS14 4.5 52.9 1.0
CA E:VAL86 4.5 32.3 1.0
CD E:GLU31 4.6 55.5 1.0
CB E:LYS87 4.6 33.7 1.0
O E:VAL32 4.6 31.6 1.0
C E:VAL86 4.6 31.5 1.0
CA E:THR85 4.7 35.5 1.0
NZ E:LYS14 4.7 56.4 1.0
CA E:GLU31 4.8 36.4 1.0

Sodium binding site 3 out of 3 in 5jyx

Go back to Sodium Binding Sites List in 5jyx
Sodium binding site 3 out of 3 in the Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Covalent Thioimide Intermediate of the Archaeosine Synthase Quef-Like within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na202

b:47.3
occ:1.00
N L:SER33 3.6 52.1 1.0
CB L:SER33 3.7 56.8 1.0
O L:THR85 3.8 51.8 1.0
O L:GLU31 3.8 50.3 1.0
C L:GLU31 3.9 49.5 1.0
CD L:LYS87 3.9 54.9 1.0
N L:VAL32 3.9 49.5 1.0
C L:VAL32 4.0 49.6 1.0
CE L:LYS87 4.0 57.0 1.0
CA L:VAL32 4.0 49.4 1.0
CG L:GLU31 4.0 59.3 1.0
CG L:LYS87 4.0 53.4 1.0
CB L:GLU31 4.1 54.8 1.0
NZ L:LYS87 4.1 57.8 1.0
CG2 L:THR85 4.1 55.0 1.0
CA L:SER33 4.3 54.3 1.0
CB L:THR85 4.3 54.5 1.0
C L:THR85 4.3 50.9 1.0
N L:LYS87 4.4 48.9 1.0
CB L:LYS87 4.4 51.9 1.0
OE2 L:GLU31 4.5 63.9 1.0
CD L:GLU31 4.6 62.1 1.0
CA L:GLU31 4.6 51.1 1.0
C L:VAL86 4.6 47.9 1.0
O L:VAL32 4.8 52.2 1.0
CE L:LYS14 4.8 59.0 1.0
CA L:VAL86 4.8 48.9 1.0
CG L:LYS14 4.9 51.1 1.0
N L:VAL86 4.9 50.1 1.0
OG L:SER33 4.9 62.7 1.0
CA L:THR85 5.0 52.7 1.0

Reference:

X.Mei, J.Alvarez, A.Bon Ramos, U.Samanta, D.Iwata-Reuyl, M.A.Swairjo. Crystal Structure of the Archaeosine Synthase Quef-Like-Insights Into Amidino Transfer and Trna Recognition By the Tunnel Fold. Proteins V. 85 103 2017.
ISSN: ESSN 1097-0134
PubMed: 27802572
DOI: 10.1002/PROT.25202
Page generated: Tue Dec 15 11:09:02 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy