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Zinc in PDB 5vzw: TRIM23 Ring Domain in Complex with UBCH5-Ub

Enzymatic activity of TRIM23 Ring Domain in Complex with UBCH5-Ub

All present enzymatic activity of TRIM23 Ring Domain in Complex with UBCH5-Ub:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of TRIM23 Ring Domain in Complex with UBCH5-Ub, PDB code: 5vzw was solved by O.Pornillos, D.Dawidziak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.57 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.830, 109.355, 122.963, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the TRIM23 Ring Domain in Complex with UBCH5-Ub (pdb code 5vzw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the TRIM23 Ring Domain in Complex with UBCH5-Ub, PDB code: 5vzw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5vzw

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Zinc binding site 1 out of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:47.7
occ:1.00
OD2 F:ASP75 2.1 50.4 1.0
ND1 F:HIS53 2.1 48.8 1.0
SG F:CYS51 2.3 44.8 1.0
SG F:CYS72 2.3 44.3 1.0
CG F:ASP75 2.8 45.7 1.0
HB2 F:HIS53 2.9 53.0 1.0
HB2 F:CYS51 2.9 60.8 1.0
CE1 F:HIS53 3.0 52.4 1.0
OD1 F:ASP75 3.0 51.3 1.0
HB2 F:CYS72 3.1 61.3 1.0
CB F:CYS72 3.1 51.1 1.0
CG F:HIS53 3.1 51.3 1.0
HB3 F:CYS72 3.1 61.3 1.0
CB F:CYS51 3.1 50.7 1.0
HE1 F:HIS53 3.2 62.9 1.0
CB F:HIS53 3.5 44.2 1.0
HB3 F:CYS51 3.5 60.8 1.0
HB2 F:PHE74 3.7 59.9 1.0
H F:HIS53 3.8 55.8 1.0
HD2 F:PHE74 3.8 56.9 1.0
H F:ASP75 4.0 55.6 1.0
HB3 F:HIS53 4.1 53.0 1.0
NE2 F:HIS53 4.2 49.7 1.0
CB F:ASP75 4.2 50.0 1.0
CD2 F:HIS53 4.2 50.3 1.0
HB2 F:GLN77 4.3 53.2 1.0
HB3 F:ASP75 4.3 60.0 1.0
H F:PHE74 4.3 57.9 1.0
N F:ASP75 4.4 46.4 1.0
N F:HIS53 4.4 46.5 1.0
CA F:CYS51 4.5 47.7 1.0
HD12 F:LEU49 4.5 57.2 1.0
CA F:CYS72 4.6 50.7 1.0
HB2 F:LEU49 4.6 58.0 1.0
CA F:HIS53 4.6 49.2 1.0
CB F:PHE74 4.6 49.9 1.0
C F:CYS51 4.7 48.9 1.0
CD2 F:PHE74 4.7 47.4 1.0
H F:CYS51 4.7 58.5 1.0
H F:GLN77 4.8 60.0 1.0
O F:HOH405 4.8 45.2 1.0
HB2 F:ASP75 4.8 60.0 1.0
O F:CYS51 4.8 47.5 1.0
HA F:CYS72 4.9 60.9 1.0
HD13 F:LEU49 4.9 57.2 1.0
CA F:ASP75 4.9 47.8 1.0
HE2 F:HIS53 4.9 59.7 1.0

Zinc binding site 2 out of 4 in 5vzw

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Zinc binding site 2 out of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:55.5
occ:1.00
SG F:CYS59 2.3 51.6 1.0
SG F:CYS56 2.4 57.7 1.0
SG F:CYS31 2.4 49.8 1.0
SG F:CYS34 2.4 59.0 1.0
H F:CYS34 2.9 72.6 1.0
HB3 F:CYS31 2.9 73.0 1.0
HB3 F:CYS56 2.9 64.2 1.0
HB2 F:CYS59 3.0 62.9 1.0
CB F:CYS31 3.1 60.9 1.0
HB3 F:CYS34 3.2 70.7 1.0
CB F:CYS56 3.2 53.5 1.0
CB F:CYS59 3.3 52.5 1.0
HB2 F:CYS31 3.3 73.0 1.0
CB F:CYS34 3.4 58.9 1.0
H F:CYS56 3.4 61.5 1.0
HZ2 F:LYS44 3.5 85.7 1.0
HB F:VAL33 3.5 65.8 1.0
H F:CYS59 3.6 62.9 1.0
N F:CYS34 3.7 60.5 1.0
HB3 F:CYS59 3.9 62.9 1.0
HZ3 F:LYS44 3.9 85.7 1.0
HB2 F:CYS56 4.0 64.2 1.0
N F:CYS56 4.1 51.2 1.0
CA F:CYS34 4.1 60.0 1.0
NZ F:LYS44 4.2 71.4 1.0
H F:VAL33 4.2 63.9 1.0
HB2 F:CYS34 4.2 70.7 1.0
CA F:CYS56 4.2 53.0 1.0
HG13 F:VAL55 4.2 61.6 1.0
N F:CYS59 4.3 52.5 1.0
CA F:CYS59 4.4 55.1 1.0
CB F:VAL33 4.5 54.9 1.0
HG12 F:VAL55 4.5 61.6 1.0
HD2 F:LYS44 4.5 89.7 1.0
H F:GLU35 4.5 79.7 1.0
CA F:CYS31 4.6 61.6 1.0
HD3 F:LYS44 4.6 89.7 1.0
H F:ASP36 4.6 83.5 1.0
O F:CYS56 4.6 51.8 1.0
HZ1 F:LYS44 4.7 85.7 1.0
HB2 F:ASP36 4.7 83.7 1.0
C F:CYS56 4.8 52.4 1.0
C F:VAL33 4.8 56.0 1.0
HA F:CYS59 4.8 66.1 1.0
CG1 F:VAL55 4.8 51.3 1.0
HG12 F:VAL33 4.8 65.5 1.0
N F:VAL33 4.9 53.3 1.0
HB3 F:ASP58 4.9 73.2 1.0
HA F:CYS34 4.9 72.0 1.0
C F:CYS31 4.9 56.7 1.0
CD F:LYS44 5.0 74.7 1.0
C F:CYS34 5.0 69.7 1.0
CA F:VAL33 5.0 58.1 1.0
N F:GLU35 5.0 66.4 1.0
HE1 F:PHE38 5.0 74.0 1.0

Zinc binding site 3 out of 4 in 5vzw

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Zinc binding site 3 out of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:44.9
occ:1.00
OD2 G:ASP75 1.9 53.3 1.0
ND1 G:HIS53 2.1 46.2 1.0
SG G:CYS51 2.2 46.9 1.0
SG G:CYS72 2.2 46.1 1.0
CG G:ASP75 2.7 44.0 1.0
HB2 G:CYS51 2.9 51.6 1.0
OD1 G:ASP75 2.9 50.0 1.0
HB2 G:HIS53 2.9 51.5 1.0
CE1 G:HIS53 3.0 50.8 1.0
CB G:CYS51 3.1 43.0 1.0
CB G:CYS72 3.1 44.4 1.0
HB2 G:CYS72 3.1 53.3 1.0
HE1 G:HIS53 3.1 60.9 1.0
HB3 G:CYS72 3.1 53.3 1.0
CG G:HIS53 3.2 50.4 1.0
HB3 G:CYS51 3.5 51.6 1.0
CB G:HIS53 3.6 42.9 1.0
HB2 G:PHE74 3.7 53.7 1.0
H G:HIS53 3.8 47.8 1.0
HD2 G:PHE74 3.9 60.8 1.0
H G:ASP75 4.0 57.8 1.0
CB G:ASP75 4.1 46.6 1.0
HB3 G:HIS53 4.2 51.5 1.0
NE2 G:HIS53 4.2 48.3 1.0
HB3 G:ASP75 4.2 55.9 1.0
HB2 G:GLN77 4.3 59.8 1.0
CD2 G:HIS53 4.3 43.3 1.0
HD12 G:LEU49 4.3 62.2 1.0
H G:PHE74 4.3 58.2 1.0
N G:ASP75 4.4 48.2 1.0
CA G:CYS51 4.4 45.5 1.0
N G:HIS53 4.5 39.8 1.0
HB2 G:LEU49 4.5 52.8 1.0
CA G:CYS72 4.6 44.7 1.0
HD13 G:LEU49 4.6 62.2 1.0
CA G:HIS53 4.6 45.8 1.0
C G:CYS51 4.6 47.9 1.0
CB G:PHE74 4.6 44.8 1.0
HB2 G:ASP75 4.7 55.9 1.0
H G:CYS51 4.7 50.9 1.0
O G:HOH403 4.7 49.8 1.0
H G:GLN77 4.7 60.9 1.0
CD2 G:PHE74 4.7 50.7 1.0
O G:CYS51 4.8 46.2 1.0
CA G:ASP75 4.8 48.6 1.0
HA G:CYS72 4.9 53.7 1.0
CD1 G:LEU49 4.9 51.8 1.0
HE2 G:HIS53 4.9 58.0 1.0

Zinc binding site 4 out of 4 in 5vzw

Go back to Zinc Binding Sites List in 5vzw
Zinc binding site 4 out of 4 in the TRIM23 Ring Domain in Complex with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TRIM23 Ring Domain in Complex with UBCH5-Ub within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:55.0
occ:1.00
SG G:CYS59 2.2 50.7 1.0
SG G:CYS31 2.3 52.8 1.0
SG G:CYS56 2.4 52.6 1.0
SG G:CYS34 2.4 57.9 1.0
HB3 G:CYS31 2.8 65.6 1.0
HB3 G:CYS56 2.9 63.2 1.0
H G:CYS34 2.9 72.3 1.0
HB2 G:CYS59 2.9 62.0 1.0
CB G:CYS31 3.0 54.6 1.0
HB2 G:CYS31 3.2 65.6 1.0
CB G:CYS59 3.2 51.7 1.0
CB G:CYS56 3.2 52.6 1.0
HB3 G:CYS34 3.3 67.2 1.0
H G:CYS56 3.4 61.4 1.0
CB G:CYS34 3.4 56.0 1.0
HZ2 G:LYS44 3.5 86.0 1.0
HB G:VAL33 3.6 67.7 1.0
H G:CYS59 3.6 57.7 1.0
N G:CYS34 3.7 60.3 1.0
HB3 G:CYS59 3.8 62.0 1.0
HZ3 G:LYS44 3.8 86.0 1.0
HB2 G:CYS56 3.9 63.2 1.0
N G:CYS56 4.1 51.1 1.0
NZ G:LYS44 4.1 71.7 1.0
H G:VAL33 4.1 68.8 1.0
CA G:CYS56 4.2 49.8 1.0
CA G:CYS34 4.2 62.0 1.0
HG13 G:VAL55 4.2 62.3 1.0
HB2 G:CYS34 4.2 67.2 1.0
N G:CYS59 4.3 48.1 1.0
CA G:CYS59 4.3 53.7 1.0
HG12 G:VAL55 4.5 62.3 1.0
CA G:CYS31 4.5 56.9 1.0
HD2 G:LYS44 4.5 88.2 1.0
CB G:VAL33 4.5 56.4 1.0
H G:GLU35 4.5 77.4 1.0
HZ1 G:LYS44 4.6 86.0 1.0
HD3 G:LYS44 4.6 88.2 1.0
O G:CYS56 4.6 50.0 1.0
H G:ASP36 4.7 87.1 1.0
HA G:CYS59 4.7 64.5 1.0
C G:CYS56 4.7 49.5 1.0
HE1 G:PHE38 4.8 70.5 1.0
C G:VAL33 4.8 56.6 1.0
CG1 G:VAL55 4.8 51.9 1.0
N G:VAL33 4.9 57.4 1.0
HB2 G:ASP36 4.9 84.9 1.0
C G:CYS31 4.9 57.4 1.0
HG12 G:VAL33 4.9 61.6 1.0
HA G:CYS31 4.9 68.3 1.0
CD G:LYS44 4.9 73.5 1.0
HB3 G:ASP58 4.9 77.2 1.0
HA G:CYS34 4.9 74.4 1.0
CA G:VAL33 5.0 57.5 1.0
N G:GLU35 5.0 64.5 1.0
C G:CYS34 5.0 62.0 1.0
HA G:CYS56 5.0 59.8 1.0

Reference:

D.M.Dawidziak, J.G.Sanchez, J.M.Wagner, B.K.Ganser-Pornillos, O.Pornillos. Structure and Catalytic Activation of the TRIM23 Ring E3 Ubiquitin Ligase. Proteins V. 85 1957 2017.
ISSN: ESSN 1097-0134
PubMed: 28681414
DOI: 10.1002/PROT.25348
Page generated: Mon Oct 28 13:34:44 2024

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