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Zinc in PDB 6t7f: Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate

Enzymatic activity of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate

All present enzymatic activity of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate, PDB code: 6t7f was solved by P.D.Mabbitt, S.Virdee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 2.58
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 179.008, 179.008, 87.276, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate (pdb code 6t7f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate, PDB code: 6t7f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6t7f

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Zinc binding site 1 out of 6 in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4701

b:61.8
occ:1.00
 ND1 A:HIS4413 2.2 89.2 1.0
SG A:CYS4416 2.3 66.6 1.0
SG A:CYS4393 2.3 0.5 1.0
SG A:CYS4390 2.3 57.9 1.0
CE1 A:HIS4413 3.0 87.3 1.0
CG A:HIS4413 3.0 92.2 1.0
CB A:CYS4416 3.4 67.7 1.0
CB A:HIS4413 3.4 75.9 1.0
CB A:CYS4390 3.4 71.7 1.0
CB A:CYS4393 3.5 88.9 1.0
N A:CYS4393 3.8 74.4 1.0
NE2 A:HIS4413 4.0 94.6 1.0
CD2 A:HIS4413 4.0 91.7 1.0
O A:CYS4393 4.0 96.7 1.0
CA A:CYS4393 4.2 84.9 1.0
N A:HIS4413 4.2 73.5 1.0
CA A:HIS4413 4.4 71.0 1.0
C A:CYS4393 4.6 89.8 1.0
CB A:ILE4392 4.6 66.4 1.0
CA A:CYS4416 4.7 65.2 1.0
CG2 A:ILE4392 4.8 61.8 1.0
CA A:CYS4390 4.8 80.1 1.0
O A:CYS4390 4.8 0.0 1.0
C A:ILE4392 5.0 73.6 1.0
CB A:GLU4396 5.0 0.8 1.0

Zinc binding site 2 out of 6 in 6t7f

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Zinc binding site 2 out of 6 in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4702

b:69.5
occ:1.00
 NE2 A:HIS4410 1.9 91.8 1.0
SG A:CYS4408 2.3 74.9 1.0
SG A:CYS4437 2.3 86.7 1.0
SG A:CYS4440 2.4 76.3 1.0
CD2 A:HIS4410 2.5 94.4 1.0
CE1 A:HIS4410 2.8 93.5 1.0
CB A:CYS4437 3.2 89.4 1.0
CB A:CYS4408 3.2 83.3 1.0
CG A:HIS4410 3.5 0.6 1.0
CB A:CYS4440 3.5 84.0 1.0
ND1 A:HIS4410 3.6 0.5 1.0
N A:CYS4440 3.8 99.3 1.0
CA A:CYS4440 4.2 90.7 1.0
CA A:CYS4408 4.4 84.8 1.0
C A:CYS4408 4.4 84.0 1.0
O A:CYS4408 4.5 74.0 1.0
N A:HIS4410 4.6 0.1 1.0
CA A:CYS4437 4.6 80.5 1.0
CB A:ILE4439 4.7 90.0 1.0
CB A:HIS4410 4.7 0.4 1.0
N A:SER4409 4.9 97.1 1.0
N A:LYS4441 4.9 91.0 1.0
CG2 A:ILE4439 4.9 93.0 1.0
C A:CYS4440 4.9 94.6 1.0
C A:ILE4439 4.9 94.0 1.0

Zinc binding site 3 out of 6 in 6t7f

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Zinc binding site 3 out of 6 in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4703

b:59.8
occ:1.00
 SG A:CYS4509 2.3 73.2 1.0
SG A:CYS4540 2.3 68.3 1.0
SG A:CYS4537 2.3 71.5 1.0
SG A:CYS4506 2.4 71.8 1.0
CB A:CYS4506 3.3 63.9 1.0
CB A:CYS4509 3.4 80.4 1.0
CB A:CYS4537 3.4 69.9 1.0
CB A:CYS4540 3.5 71.1 1.0
N A:CYS4509 3.6 83.6 1.0
CA A:CYS4509 4.0 81.8 1.0
N A:CYS4537 4.0 65.3 1.0
CA A:CYS4537 4.3 68.0 1.0
N A:CYS4540 4.4 76.8 1.0
CA A:CYS4540 4.6 74.3 1.0
C A:CYS4509 4.6 85.3 1.0
CB A:LYS4508 4.7 72.8 1.0
C A:LYS4508 4.7 88.8 1.0
O A:CYS4537 4.7 62.6 1.0
CA A:CYS4506 4.8 63.8 1.0
C A:CYS4537 4.8 68.9 1.0
N A:LYS4508 4.9 76.7 1.0
CA A:LYS4508 5.0 81.2 1.0

Zinc binding site 4 out of 6 in 6t7f

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Zinc binding site 4 out of 6 in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4704

b:84.1
occ:1.00
 ND1 A:HIS4552 2.2 88.9 1.0
SG A:CYS4634 2.3 71.1 1.0
SG A:CYS4631 2.3 0.7 1.0
SG A:CYS4549 2.4 81.3 1.0
CE1 A:HIS4552 3.1 89.3 1.0
CG A:HIS4552 3.2 84.2 1.0
CB A:CYS4631 3.4 95.3 1.0
CB A:CYS4634 3.4 96.6 1.0
CB A:HIS4552 3.5 78.8 1.0
CB A:CYS4549 3.7 0.4 1.0
N A:HIS4552 3.8 0.1 1.0
O A:HIS4552 4.2 0.4 1.0
CA A:HIS4552 4.2 93.8 1.0
NE2 A:HIS4552 4.3 87.5 1.0
CG2 A:VAL4633 4.3 94.5 1.0
CD2 A:HIS4552 4.3 92.4 1.0
CB A:LYS4551 4.4 86.1 1.0
CA A:CYS4634 4.6 0.0 1.0
N A:CYS4634 4.7 0.8 1.0
C A:HIS4552 4.7 96.1 1.0
CA A:CYS4631 4.8 90.1 1.0
C A:LYS4551 4.9 0.2 1.0

Zinc binding site 5 out of 6 in 6t7f

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Zinc binding site 5 out of 6 in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4705

b:45.6
occ:1.00
 SG A:CYS4579 2.3 53.6 1.0
SG A:CYS4561 2.3 66.8 1.0
SG A:CYS4582 2.3 61.4 1.0
SG A:CYS4564 2.3 59.0 1.0
CB A:CYS4582 3.2 52.4 1.0
CB A:CYS4561 3.3 70.9 1.0
CB A:CYS4579 3.3 61.5 1.0
CB A:CYS4564 3.5 58.6 1.0
N A:CYS4564 3.9 57.5 1.0
N A:CYS4579 4.0 57.8 1.0
CA A:CYS4564 4.2 58.4 1.0
CA A:PRO4604 4.2 49.7 1.0
CA A:CYS4579 4.3 56.6 1.0
CB A:PRO4604 4.4 48.5 1.0
N A:CYS4582 4.4 67.8 1.0
C A:TYR4563 4.4 56.4 1.0
CA A:CYS4582 4.4 58.7 1.0
CG A:PRO4604 4.7 44.4 1.0
CB A:TYR4563 4.8 49.6 1.0
CA A:CYS4561 4.8 68.2 1.0
C A:CYS4564 4.8 56.8 1.0
N A:TYR4563 4.8 55.9 1.0
CA A:TYR4563 4.8 54.0 1.0
C A:CYS4579 4.9 60.2 1.0
O A:CYS4564 4.9 60.3 1.0
CB A:SER4566 4.9 55.0 1.0
O A:TYR4563 5.0 60.9 1.0
OG A:SER4566 5.0 69.4 1.0

Zinc binding site 6 out of 6 in 6t7f

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Zinc binding site 6 out of 6 in the Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rcr E3 Ligase E2-Ubiquitin Transthiolation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4706

b:55.5
occ:1.00
 NE2 A:HIS4620 2.1 60.2 1.0
SG A:CYS4600 2.3 65.1 1.0
SG A:CYS4614 2.3 67.1 1.0
SG A:CYS4565 2.3 66.5 1.0
CE1 A:HIS4620 3.1 70.3 1.0
CD2 A:HIS4620 3.1 74.4 1.0
CB A:CYS4600 3.2 59.0 1.0
CB A:CYS4614 3.2 64.3 1.0
CB A:CYS4565 3.4 62.1 1.0
CA A:CYS4600 4.0 59.4 1.0
CA A:CYS4614 4.0 71.6 1.0
ND1 A:HIS4620 4.2 71.0 1.0
CG A:HIS4620 4.2 74.7 1.0
CD A:PRO4615 4.2 64.2 1.0
CA A:CYS4565 4.5 58.3 1.0
CA A:PRO4601 4.6 56.5 1.0
N A:PRO4615 4.7 69.2 1.0
C A:CYS4614 4.7 72.4 1.0
NZ A:LYS4560 4.8 71.7 1.0
N A:ALA4602 4.9 61.8 1.0
O A:VAL4618 4.9 89.1 1.0
C A:CYS4600 4.9 58.2 1.0

Reference:

P.D.Mabbitt, A.Loreto, M.A.Dery, A.J.Fletcher, M.Stanley, K.C.Pao, N.T.Wood, M.P.Coleman, S.Virdee. Structural Basis For Ring-Cys-Relay E3 Ligase Activity and Its Role in Axon Integrity. Nat.Chem.Biol. V. 16 1227 2020.
ISSN: ESSN 1552-4469
PubMed: 32747811
DOI: 10.1038/S41589-020-0598-6
Page generated: Tue Oct 29 07:52:02 2024

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