Zinc in PDB 3hcs: Crystal Structure of the N-Terminal Domain of TRAF6

The structure of Crystal Structure of the N-Terminal Domain of TRAF6, PDB code: 3hcs 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)	30.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.663, 80.757, 50.723, 90.00, 91.36, 90.00
R / Rfree (%)	22.9 / 27.1

The binding sites of Zinc atom in the Crystal Structure of the N-Terminal Domain of TRAF6 (pdb code 3hcs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the N-Terminal Domain of TRAF6, PDB code: 3hcs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:54.6 occ:1.00 SG A:CYS93 2.5 56.2 1.0 SG A:CYS73 2.5 51.5 1.0 SG A:CYS70 2.5 45.4 1.0 SG A:CYS90 2.6 45.8 1.0 CB A:CYS70 3.0 45.8 1.0 CB A:CYS73 3.1 53.1 1.0 CB A:CYS93 3.3 52.6 1.0 CB A:CYS90 3.3 45.8 1.0 N A:CYS73 3.6 54.4 1.0 CA A:CYS73 4.0 55.6 1.0 N A:CYS90 4.0 44.0 1.0 N A:GLY55 4.3 62.6 1.0 CA A:CYS90 4.3 44.7 1.0 CA A:CYS70 4.4 48.0 1.0 N A:GLN54 4.5 69.0 1.0 CB A:ILE72 4.5 51.7 1.0 CA A:CYS93 4.7 52.2 1.0 CA A:GLY55 4.7 59.8 1.0 C A:ILE72 4.7 53.7 1.0 C A:CYS73 4.8 57.6 1.0 N A:LEU74 4.9 58.6 1.0 C A:CYS70 4.9 48.5 1.0 O A:CYS70 5.0 49.0 1.0 N A:CYS93 5.0 51.0 1.0 CA A:ILE72 5.0 52.2 1.0 N A:ILE72 5.0 51.6 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:65.6 occ:1.00 SG A:CYS105 2.3 43.8 1.0 ND1 A:HIS87 2.4 47.9 1.0 SG A:CYS85 2.4 42.6 1.0 OD1 A:ASP108 2.7 61.0 1.0 OD2 A:ASP108 2.8 62.0 1.0 CE1 A:HIS87 3.0 49.2 1.0 CG A:ASP108 3.0 62.7 1.0 CG A:HIS87 3.2 46.8 1.0 CB A:CYS105 3.2 50.9 1.0 CG2 A:VAL107 3.2 58.1 1.0 CB A:CYS85 3.3 38.8 1.0 CB A:HIS87 3.7 43.4 1.0 NE2 A:HIS87 3.9 50.2 1.0 O A:CYS85 4.0 41.2 1.0 OG1 A:THR83 4.0 42.1 1.0 CD2 A:HIS87 4.0 48.1 1.0 C A:CYS85 4.3 41.4 1.0 CB A:ASP108 4.4 61.5 1.0 CA A:CYS85 4.4 41.1 1.0 N A:ASP108 4.5 60.1 1.0 CA A:CYS105 4.6 52.4 1.0 N A:HIS87 4.7 42.4 1.0 CB A:VAL107 4.7 56.8 1.0 CA A:HIS87 4.8 42.4 1.0 CB A:GLU110 4.9 62.4 1.0 CB A:THR83 5.0 41.7 1.0 CG A:GLU110 5.0 66.0 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:51.3 occ:1.00 NE2 A:HIS151 2.2 38.3 1.0 SG A:CYS139 2.3 36.0 1.0 SG A:CYS155 2.4 38.7 1.0 SG A:CYS134 2.5 36.7 1.0 CB A:CYS139 3.1 36.6 1.0 CB A:CYS134 3.2 35.9 1.0 CE1 A:HIS151 3.2 40.2 1.0 CD2 A:HIS151 3.2 37.7 1.0 CB A:CYS155 3.4 41.4 1.0 O A:HOH419 3.6 43.7 1.0 ND2 A:ASN136 3.9 43.6 1.0 ND1 A:HIS151 4.3 41.0 1.0 CG A:HIS151 4.3 40.0 1.0 CA A:CYS155 4.5 42.7 1.0 CB A:ASN136 4.5 44.2 1.0 CD2 A:HIS141 4.6 44.5 1.0 CA A:CYS139 4.6 38.8 1.0 CB A:HIS141 4.6 41.2 1.0 CA A:CYS134 4.6 38.4 1.0 CG A:ASN136 4.7 44.5 1.0 CG A:HIS141 5.0 44.6 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:54.5 occ:1.00 NE2 A:HIS177 2.3 33.4 1.0 SG A:CYS162 2.3 41.9 1.0 SG A:CYS182 2.5 37.4 1.0 SG A:CYS165 2.5 43.0 1.0 CD2 A:HIS177 2.9 32.0 1.0 CB A:CYS162 3.0 44.6 1.0 CB A:CYS182 3.2 37.0 1.0 CB A:CYS165 3.4 47.2 1.0 CE1 A:HIS177 3.4 35.1 1.0 N A:CYS165 3.6 47.1 1.0 CA A:CYS165 4.1 47.6 1.0 CA A:CYS182 4.1 39.9 1.0 CG A:HIS177 4.2 35.1 1.0 ND1 A:HIS177 4.4 34.6 1.0 CA A:CYS162 4.5 47.8 1.0 CB A:GLN164 4.5 49.6 1.0 C A:GLN164 4.6 48.5 1.0 C A:CYS165 4.8 48.8 1.0 N A:GLN164 4.8 49.8 1.0 CA A:GLN164 4.9 49.0 1.0 CE2 A:PHE169 4.9 35.0 1.0 C A:CYS162 4.9 48.2 1.0 N A:GLN166 5.0 49.0 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:65.8 occ:1.00 NE2 A:HIS204 2.2 51.4 1.0 SG A:CYS192 2.4 55.6 1.0 SG A:CYS189 2.5 52.5 1.0 SG A:CYS208 2.6 69.9 1.0 CE1 A:HIS204 3.0 50.1 1.0 CB A:CYS189 3.2 49.4 1.0 CB A:CYS192 3.3 55.5 1.0 CD2 A:HIS204 3.4 49.7 1.0 N A:CYS192 3.6 55.6 1.0 CB A:CYS208 3.7 69.8 1.0 CA A:CYS192 4.0 55.2 1.0 ND1 A:HIS204 4.2 51.2 1.0 CG A:HIS204 4.4 51.2 1.0 CB A:ALA194 4.5 49.2 1.0 CD A:PRO209 4.5 76.4 1.0 CB A:ASN191 4.6 58.0 1.0 CA A:CYS208 4.6 70.3 1.0 C A:ASN191 4.7 56.0 1.0 C A:CYS192 4.7 55.1 1.0 CA A:CYS189 4.7 48.8 1.0 N A:ALA194 4.9 51.9 1.0 N A:ALA193 5.0 54.2 1.0 CE A:MET196 5.0 50.0 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn306 b:59.8 occ:1.00 SG B:CYS73 2.3 46.1 1.0 SG B:CYS93 2.4 51.2 1.0 SG B:CYS90 2.5 43.9 1.0 SG B:CYS70 2.5 48.4 1.0 CB B:CYS70 3.1 49.5 1.0 CB B:CYS73 3.1 52.2 1.0 CB B:CYS90 3.2 43.7 1.0 CB B:CYS93 3.4 51.4 1.0 N B:CYS73 3.7 52.5 1.0 CA B:CYS73 4.0 53.0 1.0 N B:GLY55 4.0 62.6 1.0 N B:CYS90 4.1 42.4 1.0 N B:GLN54 4.2 66.8 1.0 CA B:CYS90 4.3 43.0 1.0 CA B:GLY55 4.4 60.9 1.0 CA B:CYS70 4.6 49.1 1.0 CB B:ILE72 4.7 51.2 1.0 C B:GLN54 4.8 64.6 1.0 CA B:CYS93 4.8 51.0 1.0 C B:CYS73 4.8 54.7 1.0 C B:ILE72 4.9 52.0 1.0 N B:LEU74 5.0 55.0 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn307 b:62.6 occ:1.00 ND1 B:HIS87 2.3 45.7 1.0 OD2 B:ASP108 2.4 53.4 1.0 SG B:CYS105 2.4 46.0 1.0 SG B:CYS85 2.4 43.7 1.0 OD1 B:ASP108 2.8 51.5 1.0 CG B:ASP108 2.9 54.4 1.0 CE1 B:HIS87 3.1 45.7 1.0 CB B:CYS105 3.2 50.4 1.0 CG B:HIS87 3.2 45.0 1.0 CB B:CYS85 3.6 39.4 1.0 CB B:HIS87 3.7 42.5 1.0 O B:CYS85 4.1 42.5 1.0 OG1 B:THR83 4.1 43.3 1.0 NE2 B:HIS87 4.2 45.3 1.0 CD2 B:HIS87 4.2 45.4 1.0 CB B:ASP108 4.3 54.6 1.0 CB B:VAL107 4.3 53.9 1.0 N B:ASP108 4.3 55.1 1.0 C B:CYS85 4.5 42.2 1.0 O B:HOH454 4.6 65.2 1.0 CA B:CYS85 4.6 40.6 1.0 CA B:CYS105 4.7 51.9 1.0 N B:HIS87 4.7 41.8 1.0 CA B:HIS87 4.8 41.3 1.0 CA B:ASP108 4.9 55.9 1.0 N B:VAL107 5.0 53.3 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


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 the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn308 b:53.9 occ:1.00 NE2 B:HIS151 2.2 35.9 1.0 SG B:CYS155 2.5 34.9 1.0 SG B:CYS139 2.5 38.0 1.0 SG B:CYS134 2.5 39.9 1.0 CD2 B:HIS151 2.9 38.3 1.0 CB B:CYS134 3.1 40.0 1.0 CB B:CYS155 3.3 41.3 1.0 CE1 B:HIS151 3.3 37.0 1.0 CB B:CYS139 3.4 36.2 1.0 O B:HOH448 4.1 37.5 1.0 ND2 B:ASN136 4.1 46.3 1.0 CG B:HIS151 4.2 38.7 1.0 ND1 B:HIS151 4.3 39.4 1.0 CA B:CYS155 4.3 43.2 1.0 CD2 B:HIS141 4.4 45.8 1.0 CA B:CYS134 4.6 41.0 1.0 CB B:HIS141 4.7 40.8 1.0 CB B:ASN136 4.7 46.0 1.0 CA B:CYS139 4.9 39.1 1.0 CG B:ASN136 4.9 48.1 1.0 CG B:HIS141 4.9 44.2 1.0 CD2 B:PHE157 4.9 48.7 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn309 b:56.4 occ:1.00 NE2 B:HIS177 2.3 37.5 1.0 SG B:CYS162 2.4 41.0 1.0 SG B:CYS165 2.4 38.5 1.0 SG B:CYS182 2.4 39.0 1.0 CD2 B:HIS177 3.0 34.0 1.0 CB B:CYS162 3.1 41.6 1.0 CB B:CYS182 3.2 38.4 1.0 CB B:CYS165 3.3 45.1 1.0 CE1 B:HIS177 3.5 36.5 1.0 N B:CYS165 3.7 48.0 1.0 CA B:CYS182 4.0 40.9 1.0 CA B:CYS165 4.1 47.0 1.0 CG B:HIS177 4.2 37.8 1.0 ND1 B:HIS177 4.4 36.9 1.0 CE2 B:PHE169 4.5 39.5 1.0 O B:HOH433 4.5 37.9 1.0 CA B:CYS162 4.6 44.5 1.0 CB B:GLN164 4.6 49.3 1.0 C B:GLN164 4.6 48.9 1.0 C B:CYS165 4.8 47.4 1.0 N B:GLN164 4.9 50.5 1.0 CA B:GLN164 4.9 48.8 1.0 CD B:PRO183 5.0 43.9 1.0 C B:CYS182 5.0 41.4 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of the N-Terminal Domain of TRAF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the N-Terminal Domain of TRAF6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn310 b:62.6 occ:1.00 SG B:CYS192 2.4 44.9 1.0 NE2 B:HIS204 2.5 60.5 1.0 SG B:CYS189 2.5 49.0 1.0 CD2 B:HIS204 3.2 60.5 1.0 CB B:CYS189 3.2 47.0 1.0 SG B:CYS208 3.4 88.7 1.0 CB B:CYS192 3.5 51.0 1.0 CE1 B:HIS204 3.6 60.7 1.0 O B:PRO209 3.6 95.5 1.0 N B:CYS192 3.7 53.3 1.0 CA B:CYS192 4.2 52.9 1.0 CG B:HIS204 4.4 60.9 1.0 CB B:ASN191 4.5 57.0 1.0 CB B:ALA194 4.6 49.3 1.0 ND1 B:HIS204 4.6 61.4 1.0 CA B:CYS189 4.7 47.3 1.0 CB B:CYS208 4.7 90.4 1.0 C B:ASN191 4.7 55.0 1.0 C B:PRO209 4.8 94.7 1.0 C B:CYS192 4.9 53.8 1.0 CA B:ASN191 5.0 55.8 1.0 N B:ASN191 5.0 56.3 1.0

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