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Zinc in PDB 3hcu: Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group

Enzymatic activity of Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group

All present enzymatic activity of Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group, PDB code: 3hcu was solved by Q.Yin, S.-C.Lin, B.Lamothe, M.Lu, Y.-C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.493, 41.387, 123.745, 90.00, 116.20, 90.00
R / Rfree (%) 25.6 / 33.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group (pdb code 3hcu). 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 TRAF6 in Complex with UBC13 in the C2 Space Group, PDB code: 3hcu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3hcu

Go back to Zinc Binding Sites List in 3hcu
Zinc binding site 1 out of 6 in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group


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 TRAF6 in Complex with UBC13 in the C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:48.3
occ:1.00
 SG A:CYS90 2.3 46.6 1.0
SG A:CYS70 2.3 50.5 1.0
SG A:CYS93 2.4 52.4 1.0
SG A:CYS73 2.5 53.2 1.0
CB A:CYS70 3.1 46.5 1.0
CB A:CYS90 3.1 51.5 1.0
CB A:CYS93 3.4 56.3 1.0
CB A:CYS73 3.4 49.8 1.0
N A:CYS90 3.9 46.1 1.0
N A:CYS73 3.9 50.4 1.0
CA A:CYS90 4.1 49.9 1.0
CA A:CYS73 4.2 51.5 1.0
N A:GLY55 4.4 59.2 1.0
CA A:GLY55 4.5 57.7 1.0
CA A:CYS70 4.6 46.2 1.0
CA A:CYS93 4.7 58.2 1.0
C A:ILE72 4.8 49.0 1.0
C A:GLN54 4.9 59.9 1.0
O A:CYS90 4.9 52.8 1.0
CB A:ILE72 4.9 49.9 1.0
N A:CYS93 5.0 58.4 1.0
N A:GLN54 5.0 57.3 1.0
C A:CYS73 5.0 52.0 1.0

Zinc binding site 2 out of 6 in 3hcu

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Zinc binding site 2 out of 6 in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group


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 TRAF6 in Complex with UBC13 in the C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:66.8
occ:1.00
 ND1 A:HIS87 2.3 58.8 1.0
SG A:CYS85 2.4 52.4 1.0
SG A:CYS105 2.5 59.7 1.0
OD1 A:ASP108 2.5 68.1 1.0
CE1 A:HIS87 2.8 58.7 1.0
CG A:ASP108 3.1 66.1 1.0
OD2 A:ASP108 3.2 66.4 1.0
CB A:CYS85 3.2 48.6 1.0
CG A:HIS87 3.2 56.0 1.0
CB A:CYS105 3.3 62.2 1.0
NE2 A:HIS87 3.8 59.5 1.0
CB A:HIS87 3.9 54.6 1.0
CD2 A:HIS87 4.0 58.6 1.0
CB A:VAL107 4.1 61.5 1.0
OG1 A:THR83 4.1 49.6 1.0
O A:CYS85 4.3 54.5 1.0
CB A:ASP108 4.3 66.6 1.0
CA A:CYS85 4.4 50.4 1.0
N A:ASP108 4.4 67.7 1.0
C A:CYS85 4.4 52.1 1.0
N A:HIS87 4.7 54.3 1.0
CA A:CYS105 4.7 64.3 1.0
CG1 A:VAL107 4.8 59.5 1.0
CG2 A:VAL107 4.8 61.5 1.0
C A:VAL107 4.8 65.4 1.0
CA A:VAL107 4.8 62.0 1.0
N A:VAL107 4.9 60.0 1.0
CA A:HIS87 5.0 53.5 1.0

Zinc binding site 3 out of 6 in 3hcu

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Zinc binding site 3 out of 6 in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group


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 TRAF6 in Complex with UBC13 in the C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:85.0
occ:1.00
 NE2 A:HIS151 2.4 74.8 1.0
SG A:CYS134 2.4 78.3 1.0
SG A:CYS155 2.5 75.0 1.0
SG A:CYS139 2.6 86.5 1.0
CB A:CYS134 3.1 72.8 1.0
CB A:CYS139 3.2 80.7 1.0
CD2 A:HIS151 3.2 75.2 1.0
CE1 A:HIS151 3.4 77.0 1.0
CB A:CYS155 3.7 80.1 1.0
ND2 A:ASN136 3.8 82.8 1.0
CB A:HIS141 4.2 80.8 1.0
CA A:CYS155 4.4 80.0 1.0
CG A:HIS151 4.4 75.8 1.0
ND1 A:HIS151 4.5 76.8 1.0
CA A:CYS134 4.5 72.8 1.0
CD2 A:HIS141 4.6 82.9 1.0
CA A:CYS139 4.6 78.7 1.0
CB A:ASN136 4.7 83.0 1.0
CG A:HIS141 4.7 83.9 1.0
CG A:ASN136 4.8 83.2 1.0

Zinc binding site 4 out of 6 in 3hcu

Go back to Zinc Binding Sites List in 3hcu
Zinc binding site 4 out of 6 in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group


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 TRAF6 in Complex with UBC13 in the C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:84.3
occ:1.00
 SG C:CYS93 2.7 67.8 1.0
SG C:CYS90 2.7 77.2 1.0
CB C:CYS73 2.7 90.7 1.0
SG C:CYS70 2.7 72.9 1.0
SG C:CYS73 2.8 0.1 1.0
CB C:CYS70 2.8 73.8 1.0
N C:GLY55 3.6 0.5 1.0
CA C:CYS73 3.7 86.8 1.0
N C:CYS73 3.7 84.0 1.0
CA C:GLY55 3.8 0.2 1.0
CB C:CYS90 3.9 75.6 1.0
CB C:MET75 3.9 87.7 1.0
O C:MET75 4.0 88.4 1.0
C C:GLN54 4.1 0.8 1.0
CB C:CYS93 4.2 76.9 1.0
C C:CYS73 4.2 86.2 1.0
CA C:CYS70 4.3 75.1 1.0
N C:GLN54 4.3 0.7 1.0
N C:MET75 4.3 86.9 1.0
CA C:MET75 4.5 87.4 1.0
C C:MET75 4.5 87.3 1.0
O C:CYS70 4.6 76.1 1.0
CA C:GLN54 4.6 0.5 1.0
O C:GLN54 4.7 0.2 1.0
O C:CYS73 4.7 85.3 1.0
C C:ILE72 4.7 81.7 1.0
O C:ALA76 4.7 85.0 1.0
C C:CYS70 4.7 75.7 1.0
CB C:GLN54 4.7 0.8 1.0
N C:LEU74 4.8 86.8 1.0
N C:CYS70 4.9 74.4 1.0

Zinc binding site 5 out of 6 in 3hcu

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Zinc binding site 5 out of 6 in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group


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 TRAF6 in Complex with UBC13 in the C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn305

b:75.2
occ:1.00
 OD1 C:ASP108 2.5 81.2 1.0
SG C:CYS105 2.5 80.5 1.0
OD2 C:ASP108 2.7 80.5 1.0
CG C:ASP108 2.7 80.7 1.0
SG C:CYS85 2.8 74.4 1.0
ND1 C:HIS87 2.9 69.7 1.0
CG C:HIS87 3.0 67.6 1.0
CB C:CYS85 3.3 69.6 1.0
CE1 C:HIS87 3.3 67.5 1.0
CB C:CYS105 3.4 83.0 1.0
CD2 C:HIS87 3.4 68.4 1.0
NE2 C:HIS87 3.6 67.0 1.0
CB C:HIS87 3.6 67.0 1.0
OG1 C:THR83 3.8 74.5 1.0
CB C:ASP108 3.9 79.8 1.0
N C:ASP108 4.0 77.6 1.0
O C:CYS85 4.2 70.5 1.0
CA C:CYS85 4.4 70.4 1.0
C C:CYS85 4.4 70.0 1.0
CA C:ASP108 4.6 78.7 1.0
CB C:VAL107 4.6 74.8 1.0
N C:HIS87 4.7 67.6 1.0
CA C:HIS87 4.8 65.7 1.0
CA C:CYS105 4.8 84.1 1.0
CB C:THR83 5.0 74.5 1.0
C C:VAL107 5.0 76.2 1.0
N C:VAL107 5.0 77.3 1.0
N C:CYS85 5.0 70.8 1.0

Zinc binding site 6 out of 6 in 3hcu

Go back to Zinc Binding Sites List in 3hcu
Zinc binding site 6 out of 6 in the Crystal Structure of TRAF6 in Complex with UBC13 in the C2 Space Group


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 TRAF6 in Complex with UBC13 in the C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn306

b:0.5
occ:1.00
 SG C:CYS139 2.6 0.9 1.0
SG C:CYS134 3.0 0.3 1.0
SG C:CYS155 3.2 0.1 1.0
N C:CYS139 3.2 0.6 1.0
CB C:CYS139 3.5 0.0 1.0
OE2 C:GLU156 3.9 0.7 1.0
CA C:CYS139 4.0 0.6 1.0
CA C:GLY138 4.0 0.6 1.0
CB C:CYS155 4.0 0.7 1.0
O C:HIS151 4.0 0.3 1.0
C C:GLY138 4.1 0.8 1.0
CD2 C:HIS151 4.2 0.1 1.0
NE2 C:HIS151 4.3 1.0 1.0
CB C:CYS134 4.4 0.4 1.0
CD1 C:PHE157 4.6 0.3 1.0
CA C:CYS155 4.6 0.8 1.0
O C:CYS139 4.7 0.9 1.0
C C:CYS139 4.8 0.9 1.0
CE1 C:PHE157 4.9 0.6 1.0
CG C:HIS151 4.9 0.4 1.0

Reference:

Q.Yin, S.C.Lin, B.Lamothe, M.Lu, Y.C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, H.Wu. E2 Interaction and Dimerization in the Crystal Structure of TRAF6. Nat.Struct.Mol.Biol. V. 16 658 2009.
ISSN: ISSN 1545-9993
PubMed: 19465916
DOI: 10.1038/NSMB.1605
Page generated: Wed Aug 20 10:03:29 2025

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