Zinc in PDB 3phd: Crystal Structure of Human HDAC6 in Complex with Ubiquitin

All present enzymatic activity of Crystal Structure of Human HDAC6 in Complex with Ubiquitin:
3.5.1.98;

The structure of Crystal Structure of Human HDAC6 in Complex with Ubiquitin, PDB code: 3phd was solved by A.Dong, W.Qui, M.Ravichandran, A.Schuetz, P.Loppnau, F.Li, F.Mackenzie, I.Kozieradzki, H.Ouyang, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.72 / 3.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	133.748, 133.748, 118.768, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin (pdb code 3phd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin, PDB code: 3phd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:57.8 occ:1.00 ND1 A:HIS62 1.9 62.4 1.0 NE2 A:HIS56 2.0 54.1 1.0 SG A:CYS37 2.2 51.6 1.0 SG A:CYS40 2.3 59.8 1.0 CE1 A:HIS62 2.8 61.2 1.0 CE1 A:HIS56 3.0 54.1 1.0 CG A:HIS62 3.0 60.7 1.0 CD2 A:HIS56 3.0 54.1 1.0 CB A:CYS37 3.3 48.0 1.0 CB A:CYS40 3.4 55.6 1.0 CB A:HIS62 3.4 57.8 1.0 N A:CYS40 3.8 55.7 1.0 NE2 A:HIS62 4.0 61.1 1.0 OG A:SER60 4.1 53.3 1.0 CD2 A:HIS62 4.1 61.5 1.0 ND1 A:HIS56 4.1 54.9 1.0 CA A:CYS40 4.1 55.3 1.0 CG A:HIS56 4.1 52.7 1.0 CB A:SER60 4.5 50.3 1.0 CB A:SER39 4.6 55.8 1.0 CA A:CYS37 4.7 49.0 1.0 C A:SER39 4.8 58.3 1.0 C A:CYS40 4.8 60.5 1.0 N A:TYR41 5.0 53.9 1.0 CA A:HIS62 5.0 57.5 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:66.1 occ:1.00 ND1 A:HIS52 2.1 73.3 1.0 SG A:CYS45 2.3 61.9 1.0 SG A:CYS28 2.3 70.7 1.0 SG A:CYS25 2.4 65.4 1.0 CE1 A:HIS52 2.9 72.9 1.0 CG A:HIS52 3.2 71.0 1.0 CB A:CYS25 3.2 61.7 1.0 CB A:CYS45 3.4 57.5 1.0 CB A:CYS28 3.5 66.6 1.0 CB A:HIS52 3.6 66.6 1.0 N A:CYS28 3.9 66.0 1.0 CB A:ASN50 4.0 61.2 1.0 CG2 A:THR30 4.0 74.0 1.0 N A:CYS45 4.0 56.2 1.0 NE2 A:HIS52 4.1 73.2 1.0 ND2 A:ASN50 4.1 60.2 1.0 CD2 A:HIS52 4.2 73.1 1.0 CA A:CYS28 4.2 66.4 1.0 CA A:CYS45 4.3 56.5 1.0 N A:HIS52 4.4 65.0 1.0 CG A:ASN50 4.6 69.8 1.0 CA A:HIS52 4.6 65.0 1.0 CA A:CYS25 4.7 61.5 1.0 CB A:ASP27 4.7 65.0 1.0 CA A:ASN50 4.8 64.4 1.0 C A:ASP27 4.9 67.2 1.0 N A:ASN50 4.9 64.1 1.0 C A:ASN50 4.9 71.8 1.0 C A:CYS28 4.9 71.3 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:57.9 occ:1.00 ND1 A:HIS7 2.0 63.8 1.0 SG A:CYS78 2.2 56.5 1.0 SG A:CYS75 2.3 57.3 1.0 SG A:CYS5 2.3 55.1 1.0 CE1 A:HIS7 3.0 63.5 1.0 CG A:HIS7 3.0 61.4 1.0 CB A:CYS5 3.2 51.4 1.0 CB A:CYS75 3.3 53.5 1.0 CB A:CYS78 3.3 52.1 1.0 CB A:HIS7 3.4 57.6 1.0 N A:HIS7 3.8 57.4 1.0 N A:CYS78 4.0 51.8 1.0 CD A:PRO6 4.1 58.5 1.0 NE2 A:HIS7 4.2 63.6 1.0 CD2 A:HIS7 4.2 63.4 1.0 CA A:HIS7 4.2 56.8 1.0 N A:PRO6 4.3 56.9 1.0 CA A:CYS78 4.3 51.8 1.0 CA A:CYS5 4.3 51.8 1.0 C A:CYS5 4.4 59.2 1.0 CG A:PRO6 4.7 62.5 1.0 CA A:CYS75 4.7 54.0 1.0 CB A:TYR77 4.8 49.2 1.0 C A:PRO6 4.8 61.3 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:55.5 occ:1.00 ND1 B:HIS62 2.0 59.0 1.0 NE2 B:HIS56 2.0 49.4 1.0 SG B:CYS37 2.2 59.9 1.0 SG B:CYS40 2.2 59.4 1.0 CE1 B:HIS62 2.9 58.5 1.0 CE1 B:HIS56 3.0 49.3 1.0 CG B:HIS62 3.1 57.0 1.0 CD2 B:HIS56 3.1 49.7 1.0 CB B:CYS37 3.2 56.0 1.0 CB B:CYS40 3.3 56.0 1.0 CB B:HIS62 3.5 53.4 1.0 N B:CYS40 3.7 56.6 1.0 CA B:CYS40 4.0 56.6 1.0 NE2 B:HIS62 4.0 58.8 1.0 CD2 B:HIS62 4.2 59.0 1.0 ND1 B:HIS56 4.2 50.5 1.0 CG B:HIS56 4.2 48.2 1.0 OG B:SER60 4.2 64.4 1.0 CB B:SER39 4.6 57.8 1.0 CA B:CYS37 4.6 56.1 1.0 CB B:SER60 4.6 57.2 1.0 C B:CYS40 4.7 63.1 1.0 C B:SER39 4.7 59.4 1.0 N B:TYR41 4.8 59.0 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:62.9 occ:1.00 ND1 B:HIS52 2.0 62.5 1.0 SG B:CYS45 2.2 60.8 1.0 SG B:CYS25 2.2 65.4 1.0 SG B:CYS28 2.4 61.1 1.0 CE1 B:HIS52 3.0 61.7 1.0 CB B:CYS25 3.1 61.9 1.0 CG B:HIS52 3.1 60.8 1.0 CB B:CYS45 3.3 57.5 1.0 CB B:HIS52 3.5 57.4 1.0 CB B:CYS28 3.6 58.1 1.0 N B:CYS45 3.8 56.3 1.0 N B:CYS28 3.8 60.0 1.0 CA B:CYS45 4.1 57.0 1.0 NE2 B:HIS52 4.2 61.8 1.0 CB B:ASN50 4.2 58.1 1.0 CG2 B:THR30 4.2 71.3 1.0 CA B:CYS28 4.2 59.0 1.0 CD2 B:HIS52 4.2 62.0 1.0 ND2 B:ASN50 4.3 47.4 1.0 N B:HIS52 4.6 57.3 1.0 CA B:CYS25 4.6 61.8 1.0 CB B:ASP27 4.6 63.3 1.0 CA B:HIS52 4.7 56.6 1.0 C B:ASP27 4.8 64.8 1.0 CG B:ASN50 4.8 63.4 1.0 C B:TYR44 4.9 58.3 1.0 C B:CYS28 4.9 66.0 1.0 CA B:ASN50 5.0 59.7 1.0 N B:ASP27 5.0 62.8 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:62.9 occ:1.00 ND1 B:HIS7 2.0 52.7 1.0 SG B:CYS78 2.2 59.6 1.0 SG B:CYS75 2.2 58.5 1.0 SG B:CYS5 2.4 65.8 1.0 CE1 B:HIS7 3.0 51.8 1.0 CG B:HIS7 3.0 51.0 1.0 CB B:CYS78 3.3 55.4 1.0 CB B:CYS5 3.3 61.2 1.0 CB B:HIS7 3.3 48.9 1.0 CB B:CYS75 3.3 55.1 1.0 N B:CYS78 3.9 53.9 1.0 N B:HIS7 3.9 51.6 1.0 NE2 B:HIS7 4.1 51.8 1.0 CD2 B:HIS7 4.1 51.7 1.0 CA B:CYS78 4.2 54.8 1.0 CD B:PRO6 4.2 52.2 1.0 CA B:HIS7 4.2 50.0 1.0 N B:PRO6 4.3 52.0 1.0 CA B:CYS5 4.4 59.5 1.0 C B:CYS5 4.5 58.5 1.0 CB B:TYR77 4.7 48.3 1.0 CA B:CYS75 4.7 54.5 1.0 CG B:PRO6 4.8 55.8 1.0 C B:PRO6 4.9 55.4 1.0 C B:TYR77 4.9 55.3 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2000 b:56.4 occ:1.00 ND1 C:HIS62 2.0 57.6 1.0 NE2 C:HIS56 2.0 53.4 1.0 SG C:CYS37 2.1 50.4 1.0 SG C:CYS40 2.3 58.2 1.0 CE1 C:HIS62 2.9 56.0 1.0 CE1 C:HIS56 3.0 53.2 1.0 CD2 C:HIS56 3.1 53.7 1.0 CG C:HIS62 3.1 56.2 1.0 CB C:CYS37 3.1 47.4 1.0 CB C:CYS40 3.3 54.1 1.0 CB C:HIS62 3.5 53.7 1.0 N C:CYS40 3.7 54.4 1.0 CA C:CYS40 4.0 54.3 1.0 NE2 C:HIS62 4.1 55.7 1.0 CG C:HIS56 4.2 52.0 1.0 OG C:SER60 4.2 51.7 1.0 ND1 C:HIS56 4.2 53.9 1.0 CD2 C:HIS62 4.2 56.4 1.0 CB C:SER39 4.5 57.5 1.0 CA C:CYS37 4.6 48.6 1.0 C C:SER39 4.6 59.0 1.0 CB C:SER60 4.6 53.1 1.0 C C:CYS40 4.7 59.4 1.0 N C:TYR41 4.9 54.3 1.0 N C:SER39 4.9 55.5 1.0 CA C:SER39 4.9 54.5 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2001 b:57.5 occ:1.00 ND1 C:HIS52 1.9 59.7 1.0 SG C:CYS45 2.3 59.0 1.0 SG C:CYS25 2.3 56.8 1.0 SG C:CYS28 2.4 58.2 1.0 CE1 C:HIS52 2.9 58.8 1.0 CG C:HIS52 3.0 58.5 1.0 CB C:CYS25 3.3 53.0 1.0 CB C:CYS45 3.4 54.3 1.0 CB C:HIS52 3.4 55.9 1.0 CB C:CYS28 3.5 54.9 1.0 N C:CYS28 3.8 57.4 1.0 CB C:ASN50 4.0 60.6 1.0 N C:CYS45 4.0 50.6 1.0 NE2 C:HIS52 4.0 58.9 1.0 CD2 C:HIS52 4.1 59.0 1.0 CA C:CYS28 4.2 56.0 1.0 CA C:CYS45 4.3 52.8 1.0 OG1 C:THR30 4.3 79.9 1.0 OD1 C:ASN50 4.4 61.7 1.0 N C:HIS52 4.5 55.9 1.0 CB C:ASP27 4.6 58.5 1.0 CA C:HIS52 4.6 55.1 1.0 CG C:ASN50 4.7 70.4 1.0 CA C:CYS25 4.7 52.9 1.0 C C:ASP27 4.7 61.0 1.0 CA C:ASN50 4.8 58.0 1.0 N C:ASN50 4.9 57.9 1.0 C C:CYS28 4.9 61.3 1.0 C C:ASN50 5.0 61.7 1.0 N C:ASP27 5.0 55.9 1.0 CA C:ASP27 5.0 56.3 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2002 b:67.7 occ:1.00 ND1 C:HIS7 2.1 59.6 1.0 SG C:CYS5 2.2 71.7 1.0 SG C:CYS78 2.2 69.9 1.0 SG C:CYS75 2.3 59.9 1.0 CG C:HIS7 3.1 59.6 1.0 CE1 C:HIS7 3.1 58.4 1.0 CB C:CYS5 3.2 68.4 1.0 CB C:CYS75 3.3 55.8 1.0 CB C:HIS7 3.3 57.8 1.0 CB C:CYS78 3.4 65.5 1.0 N C:HIS7 3.8 59.9 1.0 N C:CYS78 4.1 63.5 1.0 CA C:HIS7 4.2 58.1 1.0 CD C:PRO6 4.2 61.2 1.0 CD2 C:HIS7 4.2 60.1 1.0 N C:PRO6 4.2 60.6 1.0 NE2 C:HIS7 4.3 59.1 1.0 CA C:CYS5 4.3 68.6 1.0 C C:CYS5 4.3 67.2 1.0 CA C:CYS78 4.3 64.7 1.0 CG1 C:VAL82 4.6 77.0 1.0 CA C:CYS75 4.7 56.4 1.0 CG C:PRO6 4.7 64.9 1.0 C C:PRO6 4.8 64.3 1.0 CB C:TYR77 5.0 57.0 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Human HDAC6 in Complex with Ubiquitin


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 Human HDAC6 in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2000 b:66.1 occ:1.00 ND1 D:HIS62 2.0 62.6 1.0 NE2 D:HIS56 2.0 62.0 1.0 SG D:CYS37 2.1 62.2 1.0 SG D:CYS40 2.3 59.9 1.0 CE1 D:HIS62 2.9 61.8 1.0 CE1 D:HIS56 3.0 61.6 1.0 CD2 D:HIS56 3.1 62.5 1.0 CG D:HIS62 3.1 60.9 1.0 CB D:CYS37 3.1 57.9 1.0 CB D:CYS40 3.4 55.7 1.0 CB D:HIS62 3.5 58.0 1.0 N D:CYS40 3.7 54.4 1.0 CA D:CYS40 4.1 55.0 1.0 NE2 D:HIS62 4.1 62.0 1.0 ND1 D:HIS56 4.2 62.5 1.0 CD2 D:HIS62 4.2 62.2 1.0 OG D:SER60 4.2 69.1 1.0 CG D:HIS56 4.2 61.4 1.0 CB D:SER39 4.5 54.2 1.0 CA D:CYS37 4.6 56.8 1.0 C D:SER39 4.6 57.4 1.0 CB D:SER60 4.6 67.3 1.0 C D:CYS40 4.8 59.1 1.0 N D:TYR41 4.9 55.8 1.0 N D:SER39 4.9 52.3 1.0 CA D:SER39 4.9 52.3 1.0 C D:CYS37 5.0 59.6 1.0

H.Ouyang, Y.O.Ali, M.Ravichandran, A.Dong, W.Qiu, F.Mackenzie, S.Dhe-Paganon, C.H.Arrowsmith, R.G.Zhai. Protein Aggregates Are Recruited to Aggresome By Histone Deacetylase 6 Via Unanchored Ubiquitin C Termini. J.Biol.Chem. V. 287 2317 2012.
ISSN: ISSN 0021-9258
PubMed: 22069321
DOI: 10.1074/JBC.M111.273730