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Zinc in PDB 6s53: Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate

Enzymatic activity of Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate

All present enzymatic activity of Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate:
2.3.2.23; 2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate, PDB code: 6s53 was solved by L.Kiss, A.Boland, D.Neuhaus, L.C.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.76 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.750, 83.310, 86.750, 89.90, 89.05, 88.70
R / Rfree (%) 20.9 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate (pdb code 6s53). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate, PDB code: 6s53:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6s53

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Zinc binding site 1 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


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 TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:55.9
occ:1.00
 SG B:CYS39 2.2 53.4 1.0
SG B:CYS36 2.3 59.8 1.0
SG B:CYS19 2.4 60.1 1.0
SG B:CYS16 2.5 54.0 1.0
CB B:CYS36 3.0 50.6 1.0
CB B:CYS16 3.1 52.6 1.0
CB B:CYS19 3.2 58.0 1.0
CB B:CYS39 3.3 54.9 1.0
N B:CYS19 3.8 52.2 1.0
N B:CYS36 4.0 51.7 1.0
CA B:CYS19 4.1 54.8 1.0
CA B:CYS36 4.1 51.0 1.0
CA B:CYS16 4.6 55.7 1.0
CA B:CYS39 4.7 55.7 1.0
CB B:ILE18 4.7 56.1 1.0
C B:ILE18 4.9 55.3 1.0
C B:CYS19 4.9 50.9 1.0
N B:CYS39 5.0 59.5 1.0

Zinc binding site 2 out of 8 in 6s53

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Zinc binding site 2 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


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 TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:59.2
occ:1.00
 ND1 B:HIS33 2.2 44.0 1.0
SG B:CYS54 2.2 54.3 1.0
SG B:CYS31 2.2 52.9 1.0
SG B:CYS51 2.3 53.8 1.0
CE1 B:HIS33 3.0 44.8 1.0
CB B:CYS31 3.1 53.9 1.0
CB B:CYS51 3.1 56.7 1.0
CG B:HIS33 3.2 47.0 1.0
CB B:CYS54 3.6 50.5 1.0
CB B:HIS33 3.6 48.3 1.0
N B:CYS54 3.8 55.6 1.0
NE2 B:HIS33 4.2 48.6 1.0
CA B:CYS54 4.3 54.4 1.0
CD2 B:HIS33 4.3 51.4 1.0
CB B:VAL53 4.4 55.7 1.0
CA B:CYS31 4.4 53.6 1.0
N B:HIS33 4.6 53.0 1.0
CA B:CYS51 4.6 52.8 1.0
CD1 B:ILE29 4.7 58.2 1.0
C B:VAL53 4.7 56.1 1.0
C B:CYS31 4.7 56.0 1.0
CA B:HIS33 4.8 51.1 1.0
CB B:GLN56 4.8 54.5 1.0
C B:CYS54 4.9 55.5 1.0
CA B:VAL53 4.9 55.0 1.0
N B:VAL53 4.9 47.6 1.0
N B:ARG55 4.9 52.3 1.0
O B:CYS31 5.0 54.6 1.0

Zinc binding site 3 out of 8 in 6s53

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Zinc binding site 3 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


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 TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:49.1
occ:1.00
 SG A:CYS39 2.2 51.6 1.0
SG A:CYS19 2.3 54.8 1.0
SG A:CYS36 2.3 49.0 1.0
SG A:CYS16 2.4 49.8 1.0
CB A:CYS36 2.9 51.2 1.0
CB A:CYS16 3.0 51.7 1.0
CB A:CYS19 3.2 49.9 1.0
CB A:CYS39 3.4 50.9 1.0
N A:CYS19 3.7 51.7 1.0
N A:CYS36 4.0 59.1 1.0
CA A:CYS19 4.0 55.4 1.0
CA A:CYS36 4.1 56.1 1.0
CA A:CYS16 4.5 51.9 1.0
CA A:CYS39 4.7 51.0 1.0
CB A:ILE18 4.8 45.6 1.0
C A:ILE18 4.9 49.6 1.0
C A:CYS19 4.9 57.4 1.0
N A:CYS39 4.9 53.8 1.0

Zinc binding site 4 out of 8 in 6s53

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Zinc binding site 4 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


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 TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:51.6
occ:1.00
 ND1 A:HIS33 2.1 56.7 1.0
SG A:CYS31 2.1 51.5 1.0
SG A:CYS51 2.2 49.1 1.0
SG A:CYS54 2.2 60.9 1.0
CE1 A:HIS33 3.0 57.5 1.0
CB A:CYS51 3.1 48.1 1.0
CB A:CYS31 3.1 50.8 1.0
CG A:HIS33 3.2 50.9 1.0
CB A:CYS54 3.5 55.5 1.0
CB A:HIS33 3.6 50.9 1.0
N A:CYS54 3.8 49.1 1.0
CA A:CYS54 4.1 53.7 1.0
NE2 A:HIS33 4.2 52.8 1.0
CD2 A:HIS33 4.3 51.5 1.0
CB A:VAL53 4.5 56.0 1.0
CA A:CYS31 4.5 50.3 1.0
CA A:CYS51 4.5 48.6 1.0
CD1 A:ILE29 4.6 53.9 1.0
N A:HIS33 4.6 47.7 1.0
C A:VAL53 4.7 49.5 1.0
CA A:HIS33 4.7 50.7 1.0
C A:CYS31 4.8 50.9 1.0
C A:CYS54 4.8 50.3 1.0
N A:VAL53 4.9 49.1 1.0
N A:ARG55 4.9 47.6 1.0
CB A:GLN56 4.9 57.4 1.0
CA A:VAL53 4.9 54.2 1.0

Zinc binding site 5 out of 8 in 6s53

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Zinc binding site 5 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


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 TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn101

b:54.7
occ:1.00
 ND1 H:HIS33 2.0 49.1 1.0
SG H:CYS54 2.2 56.9 1.0
SG H:CYS31 2.2 50.3 1.0
SG H:CYS51 2.3 47.6 1.0
CE1 H:HIS33 2.8 49.6 1.0
CB H:CYS31 3.0 44.9 1.0
CG H:HIS33 3.1 39.8 1.0
CB H:CYS51 3.1 54.6 1.0
CB H:CYS54 3.5 52.3 1.0
CB H:HIS33 3.6 41.7 1.0
N H:CYS54 3.8 47.8 1.0
NE2 H:HIS33 4.0 51.0 1.0
CD2 H:HIS33 4.1 45.1 1.0
CA H:CYS54 4.2 50.1 1.0
CB H:VAL53 4.4 43.9 1.0
CA H:CYS31 4.4 46.5 1.0
N H:HIS33 4.6 43.5 1.0
CA H:CYS51 4.6 53.8 1.0
CD1 H:ILE29 4.6 51.5 1.0
CA H:HIS33 4.7 42.2 1.0
C H:VAL53 4.7 43.3 1.0
C H:CYS31 4.7 45.4 1.0
C H:CYS54 4.9 47.4 1.0
N H:VAL53 4.9 43.6 1.0
CA H:VAL53 4.9 42.0 1.0
N H:ARG55 4.9 50.0 1.0
O H:CYS31 5.0 55.1 1.0

Zinc binding site 6 out of 8 in 6s53

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Zinc binding site 6 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


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 TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn102

b:52.8
occ:1.00
 SG H:CYS39 2.1 54.5 1.0
SG H:CYS36 2.3 52.8 1.0
SG H:CYS19 2.3 51.4 1.0
SG H:CYS16 2.5 45.9 1.0
CB H:CYS36 2.9 57.2 1.0
CB H:CYS19 3.1 45.4 1.0
CB H:CYS16 3.1 51.2 1.0
CB H:CYS39 3.3 54.1 1.0
N H:CYS19 3.7 47.5 1.0
CA H:CYS19 4.0 48.1 1.0
N H:CYS36 4.0 58.4 1.0
CA H:CYS36 4.1 59.2 1.0
CA H:CYS39 4.6 55.7 1.0
CA H:CYS16 4.6 56.2 1.0
CB H:ILE18 4.6 54.8 1.0
C H:ILE18 4.8 51.7 1.0
N H:CYS39 4.9 61.5 1.0
C H:CYS19 4.9 49.1 1.0

Zinc binding site 7 out of 8 in 6s53

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Zinc binding site 7 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn101

b:51.1
occ:1.00
 ND1 G:HIS33 2.3 44.1 1.0
SG G:CYS51 2.3 44.8 1.0
SG G:CYS31 2.4 51.3 1.0
CB G:CYS54 2.6 70.3 1.0
SG G:CYS54 2.9 0.0 1.0
CB G:CYS51 3.1 51.7 1.0
CB G:CYS31 3.1 50.0 1.0
CE1 G:HIS33 3.2 44.4 1.0
CG G:HIS33 3.4 43.8 1.0
N G:CYS54 3.5 65.3 1.0
CA G:CYS54 3.6 67.4 1.0
CB G:HIS33 3.7 44.7 1.0
NE2 G:HIS33 4.4 43.8 1.0
CB G:VAL53 4.4 56.1 1.0
C G:VAL53 4.4 55.4 1.0
CD2 G:HIS33 4.5 45.7 1.0
CA G:CYS51 4.6 50.9 1.0
CA G:CYS31 4.6 51.8 1.0
C G:CYS54 4.7 60.7 1.0
N G:HIS33 4.7 50.2 1.0
CD1 G:ILE29 4.8 56.0 1.0
CA G:VAL53 4.8 52.0 1.0
CB G:GLN56 4.8 66.6 1.0
N G:VAL53 4.8 46.8 1.0
N G:ARG55 4.8 57.0 1.0
CA G:HIS33 4.9 49.0 1.0
C G:CYS31 4.9 49.9 1.0
O J:GLY35 5.0 49.6 1.0
N G:GLN56 5.0 61.5 1.0
CG1 G:VAL53 5.0 55.3 1.0

Zinc binding site 8 out of 8 in 6s53

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Zinc binding site 8 out of 8 in the Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of TRIM21 Ring Domain in Complex with An Isopeptide- Linked UBE2N~Ubiquitin Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn102

b:52.8
occ:1.00
 SG G:CYS39 2.2 56.1 1.0
SG G:CYS36 2.3 50.0 1.0
SG G:CYS19 2.4 56.5 1.0
SG G:CYS16 2.4 47.3 1.0
CB G:CYS36 2.9 51.5 1.0
CB G:CYS16 3.0 51.4 1.0
CB G:CYS19 3.2 56.0 1.0
CB G:CYS39 3.4 52.0 1.0
N G:CYS19 3.7 52.6 1.0
N G:CYS36 3.9 58.4 1.0
CA G:CYS36 4.0 54.7 1.0
CA G:CYS19 4.0 56.3 1.0
CA G:CYS16 4.5 54.8 1.0
CB G:ILE18 4.7 52.6 1.0
CA G:CYS39 4.7 55.3 1.0
C G:ILE18 4.8 53.3 1.0
C G:CYS19 4.9 53.5 1.0
N G:CYS39 4.9 57.1 1.0
N G:LEU20 5.0 53.7 1.0
C G:CYS36 5.0 58.0 1.0

Reference:

L.Kiss, J.Zeng, C.F.Dickson, D.L.Mallery, J.C.Yang, S.H.Mclaughlin, A.Boland, D.Neuhaus, L.C.James. A Tri-Ionic Anchor Mechanism Drives UBE2N-Specific Recruitment and K63-Chain Ubiquitination in Trim Ligases. Nat Commun V. 10 4502 2019.
ISSN: ESSN 2041-1723
PubMed: 31582740
DOI: 10.1038/S41467-019-12388-Y
Page generated: Tue Oct 29 07:02:04 2024

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