Potassium in PDB 6z7v: Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2)

Enzymatic activity of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2)

All present enzymatic activity of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2):
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2), PDB code: 6z7v was solved by S.A.Abdul Rehman, S.M.Lange, Y.Kulathu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.79 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.011, 117.597, 125.884, 90, 90, 90
R / Rfree (%) 21.3 / 25.4

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2) (pdb code 6z7v). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2), PDB code: 6z7v:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6z7v

Go back to Potassium Binding Sites List in 6z7v
Potassium binding site 1 out of 4 in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:89.4
occ:1.00
 O A:GLN389 4.0 49.4 1.0
CB A:GLN389 4.5 51.6 1.0
CB A:LYS393 4.5 57.7 1.0
N A:LYS393 4.6 53.9 1.0
CG A:GLN389 4.7 52.8 1.0
CA A:LYS393 4.7 54.4 1.0
C A:GLN389 4.7 50.2 1.0
CA A:GLN389 4.8 48.6 1.0
CB A:GLU392 4.8 51.8 1.0

Potassium binding site 2 out of 4 in 6z7v

Go back to Potassium Binding Sites List in 6z7v
Potassium binding site 2 out of 4 in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:119.3
occ:1.00
 OE2 B:GLU253 3.4 83.1 1.0
OE1 B:GLU253 3.7 74.0 1.0
CD B:GLU253 3.9 71.5 1.0
O B:GLU252 4.4 72.3 1.0

Potassium binding site 3 out of 4 in 6z7v

Go back to Potassium Binding Sites List in 6z7v
Potassium binding site 3 out of 4 in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:83.7
occ:1.00
 NZ B:LYS282 3.5 77.9 1.0
CE B:LYS282 3.8 73.6 1.0
OE1 B:GLU253 4.2 74.0 1.0
CD2 B:TRP279 4.3 58.8 1.0
CB B:GLU253 4.3 64.9 1.0
CG B:TRP279 4.3 59.7 1.0
CG B:GLU253 4.3 71.9 1.0
CE2 B:TRP279 4.4 56.1 1.0
CD1 B:TRP279 4.5 59.7 1.0
NE1 B:TRP279 4.5 53.8 1.0
CD B:GLU253 4.6 71.5 1.0
CD B:LYS282 4.6 60.8 1.0
CE3 B:TRP279 4.7 65.7 1.0
CB B:TRP279 4.9 57.6 1.0
CZ2 B:TRP279 5.0 59.1 1.0

Potassium binding site 4 out of 4 in 6z7v

Go back to Potassium Binding Sites List in 6z7v
Potassium binding site 4 out of 4 in the Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of MINDY2 (C266A) in Complex with LYS48 Linked Di- Ubiquitin (K48-UB2) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K101

b:95.5
occ:1.00
 ND1 G:HIS68 4.0 61.3 1.0
CG G:HIS68 4.1 62.4 1.0
CD2 G:LEU8 4.4 70.8 1.0
CE1 G:HIS68 4.4 66.9 1.0
CB G:HIS68 4.4 55.2 1.0
CD2 G:HIS68 4.6 64.7 1.0
OE1 A:GLN321 4.7 85.8 1.0
NE2 G:HIS68 4.7 67.1 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: Sat Jul 10 16:25:27 2021

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