Atomistry » Sodium » PDB 2yfa-2zgb » 2ynx
Atomistry »
  Sodium »
    PDB 2yfa-2zgb »
      2ynx »

Sodium in PDB 2ynx: Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period

Enzymatic activity of Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period

All present enzymatic activity of Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period:
1.8.1.9;

Protein crystallography data

The structure of Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period, PDB code: 2ynx was solved by J.A.Gavira, A.Ingles-Prieto, B.Ibarra-Molero, J.M.Sanchez-Ruiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.322 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 32.153, 36.294, 48.118, 90.76, 107.97, 111.01
R / Rfree (%) 16.03 / 21.64

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period (pdb code 2ynx). 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 Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period, PDB code: 2ynx:

Sodium binding site 1 out of 1 in 2ynx

Go back to Sodium Binding Sites List in 2ynx
Sodium binding site 1 out of 1 in the Crystal Structure of Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period


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 Ancestral Thioredoxin Relative to Last Archaea Common Ancestor (Laca) From the Precambrian Period within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1107

b:33.4
occ:1.00
HG3 B:LYS45 2.7 30.5 0.5
O B:GLU41 2.9 15.6 1.0
HG3 B:GLU41 2.9 37.3 0.4
H1 B:SER1 2.9 57.7 1.0
HA B:SER1 3.0 44.4 1.0
H3 B:SER1 3.0 57.7 1.0
HZ3 B:LYS45 3.0 49.8 0.5
OE1 B:GLU41 3.1 31.3 0.6
HB1 B:ALA44 3.1 15.5 1.0
OE1 B:GLU41 3.2 34.5 0.4
CD B:GLU41 3.3 36.7 0.4
HA B:GLU41 3.3 20.8 0.4
HA B:GLU41 3.3 11.2 0.6
N B:SER1 3.3 48.1 1.0
HB3 B:GLU41 3.3 30.2 0.6
O B:HOH2003 3.5 33.6 1.0
CG B:GLU41 3.5 31.1 0.4
CG B:LYS45 3.5 25.4 0.5
CA B:SER1 3.6 37.0 1.0
HB2 B:LYS45 3.6 16.3 0.5
HE3 B:LYS45 3.6 46.7 0.5
HG2 B:LYS45 3.6 30.5 0.5
C B:GLU41 3.7 16.0 1.0
H B:LYS45 3.7 16.7 0.5
NZ B:LYS45 3.8 41.5 0.5
H B:LYS45 3.8 17.1 0.5
OE2 B:GLU41 3.8 36.6 0.4
CA B:GLU41 3.8 9.4 0.6
CA B:GLU41 3.8 17.4 0.4
H B:VAL2 3.9 19.9 1.0
HZ2 B:LYS45 4.0 49.8 0.5
CB B:ALA44 4.0 12.9 1.0
CB B:GLU41 4.0 25.1 0.6
CE B:LYS45 4.1 38.9 0.5
N B:LYS45 4.1 13.9 0.5
HB2 B:ALA44 4.1 15.5 1.0
N B:LYS45 4.1 14.2 0.5
HG22 B:VAL2 4.1 26.1 1.0
HG21 B:VAL2 4.2 26.1 1.0
CD B:GLU41 4.2 35.7 0.6
H2 B:SER1 4.2 57.7 1.0
CB B:GLU41 4.2 26.8 0.4
C B:SER1 4.3 23.9 1.0
N B:VAL2 4.3 16.6 1.0
HG2 B:GLU41 4.3 37.3 0.4
CD B:LYS45 4.4 30.8 0.5
CB B:LYS45 4.4 13.6 0.5
HZ1 B:LYS45 4.5 49.8 0.5
O B:HOH2001 4.5 56.5 1.0
CB B:LYS45 4.5 14.1 0.5
HA B:LYS45 4.5 19.0 0.5
HA B:LYS45 4.6 19.0 0.5
HB3 B:ALA44 4.6 15.5 1.0
CG2 B:VAL2 4.6 21.8 1.0
C B:ALA44 4.6 15.2 1.0
CA B:LYS45 4.6 15.8 0.5
HB2 B:GLU41 4.6 32.1 0.4
HB3 B:LYS45 4.6 16.3 0.5
CA B:LYS45 4.7 15.9 0.5
HB2 B:LYS45 4.7 16.9 0.5
CG B:GLU41 4.7 27.7 0.6
HB2 B:GLU41 4.8 30.2 0.6
CA B:ALA44 4.8 10.9 1.0
HD2 B:LYS45 4.8 36.9 0.5
HB2 B:SER1 4.8 49.7 1.0
CB B:SER1 4.9 41.4 1.0
HA B:GLU42 4.9 17.9 0.3
N B:GLU42 4.9 13.5 1.0
H B:ALA44 4.9 12.6 1.0
HE2 B:LYS45 5.0 46.7 0.5
HB3 B:GLU41 5.0 32.1 0.4

Reference:

A.Ingles-Prieto, B.Ibarra-Molero, A.Delgado-Delgado, R.Perez-Jimenez, J.M.Fernandez, E.A.Gaucher, J.M.Sanchez-Ruiz, J.A.Gavira. Conservation of Protein Structure Over Four Billion Years Structure V. 21 1690 2013.
ISSN: ISSN 0969-2126
PubMed: 23932589
DOI: 10.1016/J.STR.2013.06.020
Page generated: Tue Dec 15 06:00:46 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