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Zinc in PDB 5vo0: Structure of A TRAF6-UBC13~Ub Complex

Enzymatic activity of Structure of A TRAF6-UBC13~Ub Complex

All present enzymatic activity of Structure of A TRAF6-UBC13~Ub Complex:
2.3.2.23; 2.3.2.27;

Protein crystallography data

The structure of Structure of A TRAF6-UBC13~Ub Complex, PDB code: 5vo0 was solved by A.J.Middleton, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 128.40 / 3.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 181.114, 181.114, 97.414, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 29.9

Other elements in 5vo0:

The structure of Structure of A TRAF6-UBC13~Ub Complex also contains other interesting chemical elements:

Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A TRAF6-UBC13~Ub Complex (pdb code 5vo0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of A TRAF6-UBC13~Ub Complex, PDB code: 5vo0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vo0

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Zinc binding site 1 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:77.7
occ:1.00
 SG A:CYS74 2.3 76.5 1.0
SG A:CYS91 2.3 73.3 1.0
SG A:CYS94 2.3 90.4 1.0
SG A:CYS71 2.3 83.7 1.0
CB A:CYS71 3.2 85.6 1.0
CB A:CYS74 3.2 78.9 1.0
CB A:CYS94 3.2 85.9 1.0
CB A:CYS91 3.3 76.5 1.0
N A:CYS74 3.7 75.9 1.0
N A:CYS91 3.9 73.1 1.0
CA A:CYS74 4.1 79.3 1.0
CA A:CYS91 4.2 76.7 1.0
N A:GLY56 4.5 0.7 1.0
CB A:ILE73 4.6 74.0 1.0
CA A:CYS71 4.6 85.3 1.0
CA A:GLY56 4.6 0.1 1.0
CA A:CYS94 4.7 85.0 1.0
C A:ILE73 4.8 76.1 1.0
CG2 A:ILE73 4.8 74.6 1.0

Zinc binding site 2 out of 8 in 5vo0

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Zinc binding site 2 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:77.7
occ:1.00
 OD1 A:ASP109 1.6 0.1 1.0
NE2 A:HIS88 2.2 80.2 1.0
SG A:CYS86 2.3 92.1 1.0
SG A:CYS106 2.3 89.4 1.0
CD2 A:HIS88 2.5 79.6 1.0
CG A:ASP109 2.6 0.5 1.0
OD2 A:ASP109 3.0 0.1 1.0
CE1 A:HIS88 3.2 79.3 1.0
CB A:CYS106 3.3 92.3 1.0
CG A:HIS88 3.4 80.0 1.0
CB A:CYS86 3.4 92.0 1.0
CG1 A:VAL108 3.4 97.2 1.0
ND1 A:HIS88 3.7 79.5 1.0
CB A:ASP109 3.8 0.1 1.0
OG1 A:THR84 4.1 86.4 1.0
N A:ASP109 4.3 95.9 1.0
CB A:HIS88 4.5 80.3 1.0
CA A:CYS86 4.6 94.8 1.0
C A:CYS86 4.7 94.0 1.0
CA A:ASP109 4.7 0.6 1.0
CA A:CYS106 4.7 93.4 1.0
CB A:VAL108 4.8 96.3 1.0
C A:VAL108 4.8 92.4 1.0
N A:HIS88 4.9 80.5 1.0
N A:GLY87 4.9 90.1 1.0
N A:VAL108 4.9 88.9 1.0
CB A:THR84 5.0 85.0 1.0
CG2 A:THR84 5.0 87.8 1.0

Zinc binding site 3 out of 8 in 5vo0

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Zinc binding site 3 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:0.2
occ:1.00
 NE2 A:HIS152 2.2 0.0 1.0
SG A:CYS156 2.3 0.9 1.0
SG A:CYS135 2.4 0.2 1.0
SG A:CYS140 2.4 0.9 1.0
CB A:CYS140 3.2 0.3 1.0
CD2 A:HIS152 3.2 0.4 1.0
CE1 A:HIS152 3.2 0.8 1.0
CB A:CYS135 3.3 0.5 1.0
CB A:CYS156 3.6 0.6 1.0
CA A:CYS156 4.2 0.5 1.0
CA A:CYS140 4.3 0.9 1.0
ND1 A:HIS152 4.3 0.1 1.0
CG A:HIS152 4.3 0.6 1.0
N A:ARG157 4.4 0.7 1.0
CA A:CYS135 4.7 0.5 1.0
C A:CYS156 4.9 0.7 1.0
CB A:GLU142 5.0 0.8 1.0

Zinc binding site 4 out of 8 in 5vo0

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Zinc binding site 4 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:64.0
occ:1.00
 SG D:CYS91 2.3 67.9 1.0
SG D:CYS74 2.3 65.4 1.0
SG D:CYS94 2.3 74.2 1.0
SG D:CYS71 2.3 63.6 1.0
CB D:CYS71 3.2 64.8 1.0
CB D:CYS91 3.2 73.1 1.0
CB D:CYS94 3.3 76.1 1.0
CB D:CYS74 3.3 67.1 1.0
N D:CYS74 3.9 68.3 1.0
N D:CYS91 4.0 71.5 1.0
CA D:CYS74 4.2 67.8 1.0
CA D:CYS91 4.2 74.4 1.0
N D:GLY56 4.3 86.5 1.0
CA D:GLY56 4.6 82.9 1.0
CA D:CYS71 4.6 65.1 1.0
CA D:CYS94 4.7 79.5 1.0
CB D:ILE73 4.8 65.5 1.0

Zinc binding site 5 out of 8 in 5vo0

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Zinc binding site 5 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:87.0
occ:1.00
 CD2 D:HIS88 1.7 93.2 1.0
OD1 D:ASP109 1.9 0.0 1.0
NE2 D:HIS88 1.9 90.0 1.0
SG D:CYS86 2.4 0.5 1.0
SG D:CYS106 2.4 79.7 1.0
CG D:ASP109 2.7 0.4 1.0
CB D:CYS86 2.9 0.8 1.0
CG D:HIS88 2.9 97.6 1.0
OD2 D:ASP109 3.0 0.8 1.0
CE1 D:HIS88 3.1 91.7 1.0
CB D:CYS106 3.2 85.3 1.0
ND1 D:HIS88 3.6 95.4 1.0
CB D:HIS88 4.0 99.7 1.0
OG1 D:THR84 4.0 74.6 1.0
CB D:ASP109 4.0 0.8 1.0
CA D:CYS86 4.0 0.1 1.0
C D:CYS86 4.0 0.5 1.0
O D:CYS86 4.1 0.5 1.0
O D:ASP109 4.2 0.1 1.0
N D:ASP109 4.3 0.1 1.0
CA D:ASP109 4.6 0.5 1.0
N D:GLY87 4.6 0.3 1.0
CA D:CYS106 4.7 87.8 1.0
C D:GLY87 4.7 0.1 1.0
C D:ASP109 4.8 0.0 1.0
O D:GLY87 4.8 0.6 1.0
N D:HIS88 4.8 0.1 1.0
N D:CYS86 4.8 0.4 1.0
CB D:GLU111 4.9 0.7 1.0
CA D:HIS88 4.9 99.2 1.0
CB D:THR84 5.0 76.2 1.0

Zinc binding site 6 out of 8 in 5vo0

Go back to Zinc Binding Sites List in 5vo0
Zinc binding site 6 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:84.5
occ:1.00
 NE2 D:HIS152 2.1 91.2 1.0
SG D:CYS140 2.3 0.2 1.0
SG D:CYS156 2.3 0.9 1.0
SG D:CYS135 2.3 89.6 1.0
CE1 D:HIS152 3.1 91.9 1.0
CD2 D:HIS152 3.2 91.0 1.0
CB D:CYS140 3.2 0.3 1.0
CB D:CYS135 3.5 82.2 1.0
CB D:CYS156 3.5 0.2 1.0
CA D:CYS156 3.9 0.4 1.0
CA D:CYS140 4.0 0.2 1.0
ND1 D:HIS152 4.2 91.7 1.0
N D:ARG157 4.2 0.1 1.0
CG D:HIS152 4.3 92.7 1.0
C D:CYS156 4.6 0.8 1.0
O D:CYS140 4.6 1.0 1.0
C D:CYS140 4.6 0.2 1.0
CB D:GLU142 4.7 0.2 1.0
OE1 D:GLU142 4.7 0.3 1.0
CA D:CYS135 4.9 80.2 1.0
OD1 D:ASN137 5.0 92.6 1.0

Zinc binding site 7 out of 8 in 5vo0

Go back to Zinc Binding Sites List in 5vo0
Zinc binding site 7 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:0.8
occ:1.00
 NE2 D:HIS178 2.3 0.5 1.0
SG D:CYS166 2.3 0.8 1.0
SG D:CYS163 2.3 0.6 1.0
SG D:CYS183 2.4 0.5 1.0
CB D:CYS183 2.8 0.3 1.0
CB D:CYS166 3.0 0.1 1.0
CD2 D:HIS178 3.1 0.9 1.0
CE1 D:HIS178 3.3 0.9 1.0
N D:CYS166 3.3 0.5 1.0
CB D:CYS163 3.5 0.4 1.0
CA D:CYS166 3.8 0.7 1.0
CA D:CYS183 4.1 0.0 1.0
CB D:GLN165 4.2 0.6 1.0
CG D:HIS178 4.3 0.2 1.0
C D:GLN165 4.3 0.7 1.0
ND1 D:HIS178 4.3 0.5 1.0
C D:CYS183 4.6 0.8 1.0
CA D:GLN165 4.6 0.6 1.0
N D:GLN165 4.7 0.7 1.0
OE1 D:GLN165 4.7 0.5 1.0
C D:CYS166 4.8 0.3 1.0
O D:HIS178 4.9 0.6 1.0
N D:LEU184 4.9 0.6 1.0
CA D:CYS163 4.9 0.5 1.0

Zinc binding site 8 out of 8 in 5vo0

Go back to Zinc Binding Sites List in 5vo0
Zinc binding site 8 out of 8 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn305

b:0.1
occ:1.00
 NE2 D:HIS205 2.1 0.9 1.0
SG D:CYS193 2.3 0.3 1.0
SG D:CYS190 2.3 0.4 1.0
SG D:CYS209 2.3 0.2 1.0
CE1 D:HIS205 3.0 0.1 1.0
CD2 D:HIS205 3.0 0.0 1.0
CB D:CYS193 3.1 0.6 1.0
CB D:CYS190 3.5 0.5 1.0
CB D:CYS209 3.5 0.5 1.0
ND1 D:HIS205 4.1 0.4 1.0
CG D:HIS205 4.1 0.5 1.0
CA D:CYS209 4.2 0.7 1.0
O D:PHE208 4.2 1.0 1.0
CA D:CYS193 4.4 0.8 1.0
N D:CYS209 4.5 0.8 1.0
C D:PHE208 4.6 0.4 1.0
O D:HIS205 4.6 0.3 1.0
N D:CYS193 4.8 0.2 1.0
CA D:CYS190 4.9 1.0 1.0
C D:CYS193 4.9 0.3 1.0

Reference:

A.J.Middleton, R.Budhidarmo, A.Das, J.Zhu, M.Foglizzo, P.D.Mace, C.L.Day. The Activity of Traf Ring Homo- and Heterodimers Is Regulated By Zinc Finger 1. Nat Commun V. 8 1788 2017.
ISSN: ESSN 2041-1723
PubMed: 29176576
DOI: 10.1038/S41467-017-01665-3
Page generated: Mon Oct 28 13:16:53 2024

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