Atomistry » Zinc » PDB 5tt5-5u0c » 5tte
Atomistry »
  Zinc »
    PDB 5tt5-5u0c »
      5tte »

Zinc in PDB 5tte: Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic

Enzymatic activity of Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic

All present enzymatic activity of Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic:
2.3.2.23;

Protein crystallography data

The structure of Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic, PDB code: 5tte was solved by L.Yuan, Z.Lv, S.K.Olsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 3.50
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 154.234, 154.234, 285.501, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic (pdb code 5tte). 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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic, PDB code: 5tte:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5tte

Go back to Zinc Binding Sites List in 5tte
Zinc binding site 1 out of 6 in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic


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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:0.5
occ:1.00
 SG B:CYS347 2.3 96.9 1.0
SG B:CYS367 2.3 0.4 1.0
SG B:CYS362 2.3 0.8 1.0
SG B:CYS344 2.4 0.8 1.0
CB B:CYS362 2.5 0.2 1.0
O B:CYS367 3.0 94.0 1.0
CB B:CYS347 3.3 0.8 1.0
CB B:CYS367 3.4 0.3 1.0
CB B:CYS344 3.7 0.8 1.0
N B:CYS347 3.8 0.8 1.0
C B:CYS367 3.9 0.3 1.0
CA B:CYS362 4.1 0.7 1.0
CA B:CYS347 4.2 0.9 1.0
CA B:CYS367 4.3 0.6 1.0
CB B:ALA369 4.3 0.6 1.0
N B:ALA369 4.4 0.3 1.0
CB B:LYS346 4.6 82.5 1.0
O B:ALA369 4.7 0.3 1.0
N B:CYS362 4.8 91.7 1.0
C B:LYS346 4.8 0.7 1.0
C B:CYS362 4.9 0.9 1.0
CA B:ALA369 4.9 0.5 1.0

Zinc binding site 2 out of 6 in 5tte

Go back to Zinc Binding Sites List in 5tte
Zinc binding site 2 out of 6 in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic


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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:0.5
occ:1.00
 NE2 B:HIS382 2.0 87.8 1.0
SG B:CYS375 2.4 87.0 1.0
SG B:CYS372 2.4 0.6 1.0
SG B:CYS389 2.4 90.1 1.0
CD2 B:HIS382 2.9 88.2 1.0
CE1 B:HIS382 3.1 0.6 1.0
CB B:CYS389 3.1 98.2 1.0
CB B:CYS372 3.2 0.8 1.0
CB B:CYS375 3.3 86.9 1.0
N B:CYS375 3.9 0.4 1.0
CG B:HIS382 4.1 88.0 1.0
ND1 B:HIS382 4.1 87.5 1.0
CA B:CYS375 4.2 87.2 1.0
CA B:CYS389 4.6 87.0 1.0
CB B:VAL374 4.7 89.8 1.0
CA B:CYS372 4.7 91.9 1.0
C B:VAL374 5.0 0.4 1.0
C B:CYS375 5.0 86.8 1.0

Zinc binding site 3 out of 6 in 5tte

Go back to Zinc Binding Sites List in 5tte
Zinc binding site 3 out of 6 in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic


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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:0.1
occ:1.00
 SG B:CYS208 2.3 80.6 1.0
SG B:CYS186 2.3 84.5 1.0
SG B:CYS189 2.3 79.9 1.0
SG B:CYS211 2.3 77.4 1.0
CB B:CYS186 3.2 0.3 1.0
CB B:CYS208 3.2 80.3 1.0
CB B:CYS211 3.6 75.9 1.0
CB B:CYS189 3.6 80.7 1.0
N B:CYS189 3.9 0.3 1.0
N B:CYS208 4.1 79.3 1.0
CA B:CYS208 4.3 78.2 1.0
CA B:CYS189 4.4 92.5 1.0
N B:CYS211 4.4 92.8 1.0
CA B:CYS186 4.6 91.0 1.0
CA B:CYS211 4.6 76.3 1.0
CB B:ILE188 4.7 75.1 1.0
O B:CYS208 4.8 95.9 1.0
N B:ILE188 4.8 75.6 1.0
C B:ILE188 4.8 0.2 1.0
C B:CYS208 4.9 92.6 1.0

Zinc binding site 4 out of 6 in 5tte

Go back to Zinc Binding Sites List in 5tte
Zinc binding site 4 out of 6 in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic


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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:0.4
occ:1.00
 ND1 B:HIS205 2.0 72.8 1.0
SG B:CYS231 2.1 68.8 1.0
SG B:CYS203 2.1 69.6 1.0
SG B:CYS236 2.2 87.6 1.0
CB B:CYS231 2.8 68.2 1.0
CE1 B:HIS205 2.9 69.1 1.0
CG B:HIS205 3.0 99.6 1.0
CB B:CYS236 3.1 0.7 1.0
CB B:HIS205 3.4 0.6 1.0
CB B:CYS203 3.4 77.0 1.0
NE2 B:HIS205 4.1 85.8 1.0
CD2 B:HIS205 4.1 97.0 1.0
CB B:ALA233 4.1 98.6 1.0
CG2 B:ILE238 4.2 67.5 1.0
CA B:CYS231 4.2 68.4 1.0
CA B:CYS236 4.5 68.7 1.0
C B:CYS231 4.6 68.9 1.0
N B:HIS205 4.6 0.8 1.0
CA B:HIS205 4.6 1.0 1.0
O B:CYS231 4.7 0.9 1.0
CA B:CYS203 4.8 68.5 1.0

Zinc binding site 5 out of 6 in 5tte

Go back to Zinc Binding Sites List in 5tte
Zinc binding site 5 out of 6 in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic


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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:0.9
occ:1.00
 SG B:CYS281 2.3 0.1 1.0
SG B:CYS297 2.3 98.8 1.0
SG B:CYS299 2.3 0.9 1.0
SG B:CYS276 2.4 0.0 1.0
CB B:CYS281 3.1 0.9 1.0
CB B:CYS276 3.4 0.7 1.0
CB B:ALA278 3.6 0.6 1.0
CB B:CYS297 3.7 98.0 1.0
O B:CYS297 3.7 83.8 1.0
CB B:CYS299 4.0 0.0 1.0
C B:CYS297 4.5 98.7 1.0
CA B:CYS281 4.5 0.6 1.0
N B:CYS299 4.6 0.7 1.0
O B:CYS281 4.6 0.5 1.0
CA B:CYS297 4.7 87.4 1.0
C B:CYS281 4.7 0.3 1.0
CB B:HIS283 4.8 0.2 1.0
O B:CYS299 4.8 0.3 1.0
ND1 B:HIS283 4.8 0.0 1.0
CA B:CYS299 4.8 0.8 1.0
CA B:CYS276 4.8 0.6 1.0
CA B:ALA278 4.9 0.8 1.0

Zinc binding site 6 out of 6 in 5tte

Go back to Zinc Binding Sites List in 5tte
Zinc binding site 6 out of 6 in the Crystal Structure of An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic


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 An Rbr E3 Ubiquitin Ligase in Complex with An E2- Ub Thioester Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn606

b:0.3
occ:1.00
 NE2 B:HIS312 2.0 0.4 1.0
CE1 B:HIS312 2.2 0.4 1.0
SG B:CYS307 2.3 0.3 1.0
SG B:CYS304 2.3 0.8 1.0
SG B:CYS317 2.3 0.6 1.0
CB B:CYS307 3.0 0.9 1.0
CB B:CYS304 3.0 0.2 1.0
CD2 B:HIS312 3.4 0.5 1.0
N B:CYS307 3.4 0.8 1.0
ND1 B:HIS312 3.4 0.5 1.0
CB B:CYS317 3.5 0.0 1.0
CA B:CYS307 3.8 0.1 1.0
CG B:HIS312 4.0 0.3 1.0
CA B:CYS317 4.1 0.9 1.0
CB B:ASN306 4.4 0.2 1.0
CA B:CYS304 4.4 0.6 1.0
N B:GLY308 4.4 0.2 1.0
C B:ASN306 4.5 0.1 1.0
C B:CYS307 4.7 0.2 1.0
C B:CYS304 4.7 0.7 1.0
O B:CYS304 4.8 1.0 1.0
CA B:ASN306 4.8 0.6 1.0
N B:ASN306 4.8 0.2 1.0
N B:CYS317 4.9 0.1 1.0

Reference:

L.Yuan, Z.Lv, J.H.Atkison, S.K.Olsen. Structural Insights Into the Mechanism and E2 Specificity of the Rbr E3 Ubiquitin Ligase Hhari. Nat Commun V. 8 211 2017.
ISSN: ESSN 2041-1723
PubMed: 28790309
DOI: 10.1038/S41467-017-00272-6
Page generated: Mon Oct 28 08:48:19 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