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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: Wed Mar 3 15:28:11 2021

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