Atomistry » Zinc » PDB 5o1j-5of9 » 5o6c
Atomistry »
  Zinc »
    PDB 5o1j-5of9 »
      5o6c »

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

Go back to Zinc Binding Sites List in 5o6c
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

Go back to Zinc Binding Sites List in 5o6c
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

Go back to Zinc Binding Sites List in 5o6c
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

Go back to Zinc Binding Sites List in 5o6c
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: Sun Oct 27 23:16:02 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy