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Zinc in PDB 5o6c: Crystal Structure of A Threonine-Selective Rcr E3 Ligase

Enzymatic activity of Crystal Structure of A Threonine-Selective Rcr E3 Ligase

All present enzymatic activity of Crystal Structure of A Threonine-Selective Rcr E3 Ligase:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of A Threonine-Selective Rcr E3 Ligase, PDB code: 5o6c was solved by K.-C.Pao, K.Z.Rafie, D.Van Aalten, S.Virdee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.75
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 82.578, 82.578, 103.303, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase (pdb code 5o6c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase, PDB code: 5o6c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5o6c

Go back to Zinc Binding Sites List in 5o6c
Zinc binding site 1 out of 6 in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Threonine-Selective Rcr E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4701

b:27.0
occ:1.00
 ND1 A:HIS4413 2.1 23.6 1.0
SG A:CYS4390 2.3 25.9 1.0
SG A:CYS4393 2.3 26.7 1.0
SG A:CYS4416 2.3 24.6 1.0
CB A:CYS4390 3.0 25.3 1.0
CE1 A:HIS4413 3.1 27.6 1.0
CG A:HIS4413 3.1 23.9 1.0
CB A:CYS4393 3.3 25.7 1.0
CB A:CYS4416 3.4 20.6 1.0
CB A:HIS4413 3.4 24.8 1.0
N A:CYS4393 3.7 24.3 1.0
CA A:CYS4393 4.0 25.3 1.0
NE2 A:HIS4413 4.2 26.6 1.0
CD2 A:HIS4413 4.2 28.3 1.0
N A:HIS4413 4.4 26.1 1.0
CA A:CYS4390 4.4 24.1 1.0
CA A:HIS4413 4.5 24.2 1.0
CB A:ILE4392 4.7 22.7 1.0
CA A:CYS4416 4.7 19.5 1.0
C A:ILE4392 4.8 23.5 1.0
C A:CYS4390 4.8 21.4 1.0
O A:HOH4981 4.9 32.9 1.0
O A:CYS4390 4.9 24.1 1.0

Zinc binding site 2 out of 6 in 5o6c

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Zinc binding site 2 out of 6 in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Threonine-Selective Rcr E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4702

b:28.4
occ:1.00
 ND1 A:HIS4410 2.1 28.4 1.0
SG A:CYS4408 2.3 27.7 1.0
SG A:CYS4437 2.3 23.7 1.0
SG A:CYS4440 2.3 28.9 1.0
CE1 A:HIS4410 3.1 33.6 1.0
CB A:CYS4437 3.1 25.9 1.0
CG A:HIS4410 3.1 28.6 1.0
CB A:CYS4408 3.3 28.4 1.0
CB A:CYS4440 3.4 32.5 1.0
CB A:HIS4410 3.4 28.4 1.0
N A:CYS4440 3.7 25.4 1.0
CA A:CYS4440 4.1 30.8 1.0
NE2 A:HIS4410 4.2 31.2 1.0
CD2 A:HIS4410 4.2 33.5 1.0
N A:HIS4410 4.2 27.7 1.0
O A:CYS4408 4.3 33.9 1.0
C A:CYS4408 4.4 34.2 1.0
CA A:CYS4408 4.4 31.3 1.0
CA A:HIS4410 4.5 29.2 1.0
CA A:CYS4437 4.6 22.8 1.0
CB A:ILE4439 4.6 28.3 1.0
C A:ILE4439 4.8 27.2 1.0
C A:CYS4440 4.8 31.9 1.0
N A:LYS4441 4.9 29.1 1.0

Zinc binding site 3 out of 6 in 5o6c

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Zinc binding site 3 out of 6 in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Threonine-Selective Rcr E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4703

b:22.1
occ:1.00
 SG A:CYS4506 2.3 19.6 1.0
SG A:CYS4540 2.3 23.0 1.0
SG A:CYS4509 2.3 21.8 1.0
SG A:CYS4537 2.4 21.2 1.0
CB A:CYS4540 3.2 21.5 1.0
CB A:CYS4506 3.2 18.7 1.0
CB A:CYS4509 3.2 23.5 1.0
CB A:CYS4537 3.5 19.2 1.0
N A:CYS4509 3.6 20.8 1.0
CA A:CYS4509 4.0 21.4 1.0
N A:CYS4537 4.0 18.1 1.0
N A:CYS4540 4.2 19.5 1.0
CA A:CYS4537 4.3 18.5 1.0
CA A:CYS4540 4.3 20.6 1.0
CE A:LYS4511 4.5 50.1 1.0
CG A:LYS4511 4.6 40.2 1.0
CA A:CYS4506 4.6 18.0 1.0
CB A:LYS4508 4.7 25.6 1.0
CD A:LYS4511 4.7 47.7 1.0
C A:LYS4508 4.7 22.9 1.0
C A:CYS4509 4.8 23.1 1.0
C A:CYS4537 4.8 20.2 1.0
O A:CYS4537 4.9 20.2 1.0
N A:ARG4510 5.0 20.3 1.0
NZ A:LYS4511 5.0 46.0 1.0

Zinc binding site 4 out of 6 in 5o6c

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Zinc binding site 4 out of 6 in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Threonine-Selective Rcr E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4704

b:28.1
occ:1.00
 ND1 A:HIS4552 2.1 28.5 1.0
SG A:CYS4631 2.3 23.3 1.0
SG A:CYS4634 2.3 29.1 1.0
SG A:CYS4549 2.3 30.0 1.0
CE1 A:HIS4552 3.0 29.7 1.0
CG A:HIS4552 3.1 28.8 1.0
CB A:CYS4631 3.2 24.7 1.0
CB A:CYS4634 3.3 26.3 1.0
CB A:HIS4552 3.5 26.0 1.0
CB A:CYS4549 3.5 31.1 1.0
N A:CYS4634 4.0 22.6 1.0
CG2 A:VAL4633 4.0 25.4 1.0
N A:HIS4552 4.1 29.6 1.0
O A:HOH5054 4.2 38.4 1.0
NE2 A:HIS4552 4.2 30.4 1.0
CA A:CYS4634 4.2 26.9 1.0
CD2 A:HIS4552 4.2 29.9 1.0
O A:HOH4961 4.4 24.1 1.0
CB A:LYS4551 4.4 34.8 1.0
CA A:HIS4552 4.4 28.4 1.0
O A:HOH5048 4.5 42.9 1.0
CA A:CYS4631 4.6 22.7 1.0
CA A:CYS4549 4.9 31.5 1.0
C A:LYS4551 5.0 34.3 1.0

Zinc binding site 5 out of 6 in 5o6c

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Zinc binding site 5 out of 6 in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Threonine-Selective Rcr E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4705

b:23.6
occ:1.00
 SG A:CYS4564 2.3 22.1 1.0
SG A:CYS4582 2.3 21.9 1.0
SG A:CYS4561 2.3 21.5 1.0
SG A:CYS4579 2.4 22.4 1.0
CB A:CYS4582 3.1 21.4 1.0
CB A:CYS4561 3.3 20.8 1.0
CB A:CYS4564 3.4 21.7 1.0
CB A:CYS4579 3.5 20.9 1.0
N A:CYS4564 3.9 24.1 1.0
N A:CYS4579 4.0 19.6 1.0
CA A:CYS4564 4.2 21.5 1.0
CB A:PRO4604 4.2 29.8 1.0
CA A:PRO4604 4.2 26.6 1.0
N A:CYS4582 4.2 23.1 1.0
CA A:CYS4582 4.2 22.8 1.0
CA A:CYS4579 4.3 19.2 1.0
C A:TYR4563 4.4 21.8 1.0
CG A:PRO4604 4.6 30.1 1.0
CB A:SER4566 4.6 24.2 1.0
OG A:SER4566 4.7 26.1 1.0
CA A:CYS4561 4.7 20.0 1.0
CB A:TYR4563 4.7 22.9 1.0
O A:TYR4563 4.8 22.2 1.0
C A:CYS4564 4.8 21.4 1.0
CA A:TYR4563 4.8 22.8 1.0
N A:TYR4563 4.8 18.9 1.0
O A:CYS4564 4.9 20.7 1.0
C A:CYS4579 4.9 20.9 1.0

Zinc binding site 6 out of 6 in 5o6c

Go back to Zinc Binding Sites List in 5o6c
Zinc binding site 6 out of 6 in the Crystal Structure of A Threonine-Selective Rcr E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Threonine-Selective Rcr E3 Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4706

b:30.5
occ:1.00
 NE2 A:HIS4620 2.1 23.9 1.0
SG A:CYS4565 2.3 26.6 1.0
SG A:CYS4614 2.3 29.5 1.0
SG A:CYS4600 2.3 29.4 1.0
CE1 A:HIS4620 3.0 22.2 1.0
CD2 A:HIS4620 3.1 23.8 1.0
CB A:CYS4600 3.2 31.6 1.0
CB A:CYS4614 3.2 32.2 1.0
CB A:CYS4565 3.3 25.0 1.0
CA A:CYS4614 3.9 31.1 1.0
O A:HOH4905 3.9 42.6 1.0
CA A:CYS4600 3.9 29.4 1.0
ND1 A:HIS4620 4.2 25.0 1.0
CD A:PRO4615 4.2 30.0 1.0
CG A:HIS4620 4.2 24.8 1.0
CA A:CYS4565 4.3 23.1 1.0
CA A:PRO4601 4.6 30.0 1.0
O A:HOH4964 4.6 22.8 1.0
C A:CYS4614 4.7 31.5 1.0
N A:PRO4615 4.8 29.6 1.0
O A:VAL4618 4.8 33.6 1.0
C A:CYS4600 4.8 33.5 1.0
N A:ALA4602 4.9 26.0 1.0
N A:PRO4601 5.0 32.3 1.0

Reference:

K.C.Pao, N.T.Wood, A.Knebel, K.Rafie, M.Stanley, P.D.Mabbitt, R.Sundaramoorthy, K.Hofmann, D.M.F.Van Aalten, S.Virdee. Activity-Based E3 Ligase Profiling Uncovers An E3 Ligase with Esterification Activity. Nature V. 556 381 2018.
ISSN: ESSN 1476-4687
PubMed: 29643511
DOI: 10.1038/S41586-018-0026-1
Page generated: Wed Dec 16 06:37:15 2020

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