Atomistry » Sodium » PDB 6toy-6u6c » 6txb
Atomistry »
  Sodium »
    PDB 6toy-6u6c »
      6txb »

Sodium in PDB 6txb: Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin

Enzymatic activity of Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin

All present enzymatic activity of Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin, PDB code: 6txb was solved by S.A.Abdul Rehman, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.84 / 2.18
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.032, 74.032, 202.853, 90, 90, 90
R / Rfree (%) 21.3 / 24.7

Other elements in 6txb:

The structure of Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin (pdb code 6txb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin, PDB code: 6txb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6txb

Go back to Sodium Binding Sites List in 6txb
Sodium binding site 1 out of 4 in the Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin


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 MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:84.0
occ:1.00
 N A:PHE359 3.9 53.3 1.0
CA A:CYS358 4.1 57.5 1.0
CB A:CYS358 4.5 62.2 1.0
O A:SER367 4.5 72.5 1.0
C A:CYS358 4.5 53.9 1.0
O A:PHE359 4.6 50.5 1.0
O A:SER357 4.7 55.4 1.0
CA A:PHE359 4.9 53.6 1.0
CB A:PHE359 4.9 55.8 1.0

Sodium binding site 2 out of 4 in 6txb

Go back to Sodium Binding Sites List in 6txb
Sodium binding site 2 out of 4 in the Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin


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 MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:67.3
occ:1.00
 O A:HOH548 2.4 75.2 1.0
O A:HOH544 3.5 52.6 1.0
N A:TYR296 3.6 47.4 1.0
CA A:THR295 4.0 44.8 1.0
CB A:THR295 4.1 44.6 1.0
CB A:TYR296 4.2 52.3 1.0
C A:THR295 4.3 45.5 1.0
CA A:TYR296 4.5 49.9 1.0
CG2 A:THR295 4.6 44.8 1.0

Sodium binding site 3 out of 4 in 6txb

Go back to Sodium Binding Sites List in 6txb
Sodium binding site 3 out of 4 in the Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin


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 MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:78.3
occ:1.00
 N A:LEU311 3.2 43.2 1.0
O A:HOH502 3.2 52.2 1.0
NE2 A:GLN149 3.3 52.9 1.0
CA A:GLU310 3.6 50.4 1.0
C A:GLU310 3.9 46.6 1.0
CG A:GLU310 4.0 55.4 1.0
O A:GLY309 4.0 52.5 1.0
CB A:LEU311 4.1 41.6 1.0
CA A:LEU311 4.2 42.1 1.0
CG A:LEU311 4.3 44.5 1.0
CB A:GLU310 4.3 53.0 1.0
O A:LEU311 4.4 43.2 1.0
CD A:GLN149 4.5 52.7 1.0
CD1 A:LEU311 4.6 46.4 1.0
N A:GLU310 4.7 50.4 1.0
O A:HOH547 4.7 60.2 1.0
C A:GLY309 4.8 51.6 1.0
C A:LEU311 4.8 41.0 1.0
CG A:GLN149 4.9 50.8 1.0

Sodium binding site 4 out of 4 in 6txb

Go back to Sodium Binding Sites List in 6txb
Sodium binding site 4 out of 4 in the Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of MINDY1 Mutant (P138A) in Complex with LYS48 Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:94.0
occ:1.00
 CE1 A:HIS270 3.6 98.8 1.0
CE D:LYS6 3.7 99.9 1.0
NE2 D:HIS68 3.8 71.2 1.0
CE1 D:HIS68 3.8 70.3 1.0
CD D:LYS6 4.1 96.7 1.0
NE2 A:HIS270 4.2 97.0 1.0
ND1 A:HIS270 4.7 97.1 1.0
NZ D:LYS6 4.8 105.0 1.0
CG2 D:THR66 4.8 72.7 1.0

Reference:

S.A.Abdul Rehman, Y.Kulathu. Structural Basis For the Activation and Regulation of Deubiquitinase Activity in MINDY1 and MINDY2 To Be Published.
Page generated: Tue Oct 8 14:06:58 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy