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Chlorine in PDB 6z49: Crystal Structure of Deubiquitinase MINDY2

Enzymatic activity of Crystal Structure of Deubiquitinase MINDY2

All present enzymatic activity of Crystal Structure of Deubiquitinase MINDY2:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of Deubiquitinase MINDY2, PDB code: 6z49 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) 47.72 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.115, 120.42, 78.378, 90, 92.94, 90
R / Rfree (%) 21.5 / 25.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Deubiquitinase MINDY2 (pdb code 6z49). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Deubiquitinase MINDY2, PDB code: 6z49:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6z49

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Chlorine binding site 1 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:72.2
occ:1.00
 CE1 A:TYR455 3.9 42.8 1.0
CG A:LYS251 4.1 53.8 1.0
CD1 A:TYR455 4.2 42.1 1.0
CH2 A:TRP250 4.3 35.1 1.0
CE2 A:PHE493 4.5 33.8 1.0
CZ3 A:TRP250 4.6 33.8 1.0
O A:HOH711 4.7 32.4 1.0
CE A:LYS251 4.7 66.4 1.0
CD A:LYS251 4.7 60.2 1.0
CZ2 A:TRP250 4.8 32.1 1.0
CZ A:TYR455 4.9 46.0 1.0

Chlorine binding site 2 out of 7 in 6z49

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Chlorine binding site 2 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:53.5
occ:1.00
 N B:ARG347 3.2 37.1 1.0
N B:VAL346 3.3 32.5 1.0
C B:GLY345 3.5 30.1 1.0
CA B:GLY345 3.5 31.9 1.0
CB B:ARG347 3.6 43.1 1.0
O B:HOH726 3.7 51.7 1.0
CG2 B:VAL348 3.8 38.7 1.0
CA B:ARG347 3.9 38.3 1.0
C B:VAL346 4.1 35.8 1.0
CG2 B:VAL346 4.2 35.1 1.0
O B:GLY345 4.2 33.3 1.0
CA B:VAL346 4.2 34.7 1.0
N B:VAL348 4.3 36.1 1.0
CG B:ARG347 4.3 48.1 1.0
C B:ARG347 4.4 34.6 1.0
CD B:ARG347 4.6 56.6 1.0
N B:GLY345 4.8 34.5 1.0
CB B:VAL346 4.8 34.9 1.0
CB B:VAL348 5.0 33.9 1.0

Chlorine binding site 3 out of 7 in 6z49

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Chlorine binding site 3 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:69.4
occ:1.00
 NZ B:LYS282 3.3 57.8 1.0
CE B:LYS282 3.5 54.7 1.0
CD2 B:TRP279 3.6 42.4 1.0
CG B:TRP279 3.6 40.4 1.0
CE3 B:TRP279 3.9 45.8 1.0
CB B:TRP279 3.9 34.6 1.0
CD1 B:TRP279 4.1 41.5 1.0
CE2 B:TRP279 4.1 42.4 1.0
NE1 B:TRP279 4.3 40.1 1.0
CZ3 B:TRP279 4.6 44.7 1.0
CG B:GLU253 4.6 55.1 1.0
CZ2 B:TRP279 4.8 46.9 1.0
CD B:GLU253 4.8 57.1 1.0
CB B:GLU253 4.8 48.0 1.0
OE1 B:GLU253 5.0 54.9 1.0

Chlorine binding site 4 out of 7 in 6z49

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Chlorine binding site 4 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl603

b:77.9
occ:1.00
 CE2 B:TYR302 4.1 38.8 1.0
CZ B:TYR302 4.2 41.7 1.0
O B:TYR302 4.2 52.5 1.0
OH B:TYR302 4.3 44.0 1.0
O B:LEU360 4.4 50.7 1.0
O B:MET303 4.6 60.9 1.0
CD2 B:TYR302 4.7 36.1 1.0
CE1 B:TYR302 4.9 39.2 1.0
CA B:MET303 4.9 54.8 1.0

Chlorine binding site 5 out of 7 in 6z49

Go back to Chlorine Binding Sites List in 6z49
Chlorine binding site 5 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:70.0
occ:1.00
 O C:HOH709 2.9 45.1 1.0
NZ C:LYS280 3.0 56.7 1.0
CB C:ALA278 3.5 35.6 1.0
CE C:LYS280 3.6 49.7 1.0
CD C:LYS280 3.9 51.3 1.0
O C:HOH712 4.5 37.9 1.0
CG1 C:VAL274 4.6 26.3 1.0
CB C:LEU440 4.8 28.8 1.0
CD1 C:LEU440 4.8 31.9 1.0
CA C:ALA278 4.9 35.7 1.0

Chlorine binding site 6 out of 7 in 6z49

Go back to Chlorine Binding Sites List in 6z49
Chlorine binding site 6 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl601

b:56.1
occ:1.00
 NH2 D:ARG496 3.2 50.3 1.0
CE D:LYS473 3.6 65.8 1.0
NE D:ARG496 3.7 54.0 1.0
NZ D:LYS473 3.8 71.0 1.0
CZ D:ARG496 3.9 51.0 1.0
CD D:PRO497 4.1 56.2 1.0
CG D:PRO497 4.3 62.0 1.0
CD D:LYS473 4.7 61.8 1.0
CD D:ARG496 4.9 49.8 1.0

Chlorine binding site 7 out of 7 in 6z49

Go back to Chlorine Binding Sites List in 6z49
Chlorine binding site 7 out of 7 in the Crystal Structure of Deubiquitinase MINDY2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Deubiquitinase MINDY2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl602

b:82.8
occ:1.00
 NE2 D:GLN422 3.1 42.0 1.0
CZ D:TYR387 3.9 54.6 1.0
OH D:TYR387 4.1 58.4 1.0
CE1 D:TYR387 4.1 54.9 1.0
ND2 D:ASN447 4.3 62.2 1.0
CE2 D:TYR387 4.3 49.1 1.0
CD D:GLN422 4.4 41.2 1.0
CD1 D:TYR387 4.7 53.3 1.0
CH2 D:TRP369 4.8 45.0 1.0
CD2 D:TYR387 4.8 47.3 1.0
OE1 D:GLN422 4.8 42.8 1.0
CZ3 D:TRP369 4.9 45.9 1.0
CG D:TYR387 5.0 45.6 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: Mon Jul 29 17:56:57 2024

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