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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

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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

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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

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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

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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

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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

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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

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