Zinc in PDB 3hm3: The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin

The structure of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin, PDB code: 3hm3 was solved by A.B.Datta, G.L.Hura, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.68 / 1.96
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	105.882, 105.882, 105.882, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.6

Pages:

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

Binding sites:

The binding sites of Zinc atom in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin (pdb code 3hm3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin, PDB code: 3hm3:
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 The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:42.9 occ:0.50 ZN A:ZN600 0.0 42.9 0.5 OE2 A:GLU64 1.8 55.5 1.0 ZN A:ZN600 2.3 65.6 0.5 CD A:GLU64 2.7 48.0 1.0 OE1 A:GLU64 3.0 51.2 1.0 CG A:GLU64 4.1 45.9 1.0 CB A:GLU64 4.6 48.8 1.0

Zinc binding site 2 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:65.6 occ:0.50 ZN A:ZN600 0.0 65.6 0.5 OE1 A:GLU64 2.1 51.2 1.0 ZN A:ZN600 2.3 42.9 0.5 CD A:GLU64 2.8 48.0 1.0 OE2 A:GLU64 2.9 55.5 1.0 O B:HOH151 3.5 74.3 1.0 CE A:LYS63 4.1 58.2 1.0 CG A:GLU64 4.1 45.9 1.0 NZ A:LYS63 4.7 59.5 1.0 O B:GLY76 4.8 59.5 1.0 CD1 B:LEU73 4.8 55.4 1.0 CG A:LYS63 4.9 49.1 1.0 C B:GLY76 4.9 58.7 1.0 CD A:LYS63 5.0 53.0 1.0

Zinc binding site 3 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:32.4 occ:0.50 ZN A:ZN700 0.0 32.4 0.5 ZN A:ZN700 1.6 59.0 0.5 O A:HOH88 1.9 55.9 1.0 OD2 A:ASP21 2.0 53.2 1.0 CG A:ASP21 2.8 51.8 1.0 OD1 A:ASP21 2.9 48.6 1.0 NZ A:LYS29 3.9 54.7 1.0 OD1 A:ASN25 3.9 52.3 1.0 CE A:LYS29 4.0 53.5 1.0 CB A:ASP21 4.2 48.7 1.0 OE1 A:GLU18 4.2 57.1 1.0 CG A:GLU18 4.5 54.8 1.0 CG A:ASN25 4.7 49.4 1.0 CA A:ASP21 4.7 49.4 1.0 CB A:GLU18 4.7 49.1 1.0 CB A:ASN25 4.8 50.1 1.0 N A:GLU18 4.9 50.5 1.0 CD A:GLU18 4.9 51.2 1.0

Zinc binding site 4 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:59.0 occ:0.50 ZN A:ZN700 0.0 59.0 0.5 ZN A:ZN700 1.6 32.4 0.5 OD2 A:ASP21 2.7 53.2 1.0 O A:HOH88 2.7 55.9 1.0 OE1 A:GLU18 2.8 57.1 1.0 CG A:ASP21 3.4 51.8 1.0 OD1 A:ASP21 3.6 48.6 1.0 CG A:GLU18 3.7 54.8 1.0 CD A:GLU18 3.7 51.2 1.0 CB A:GLU18 3.9 49.1 1.0 OG A:SER20 4.4 45.1 0.5 OD1 A:ASN25 4.5 52.3 1.0 CB A:ASP21 4.6 48.7 1.0 CA A:ASP21 4.7 49.4 1.0 N A:GLU18 4.8 50.5 1.0 OE2 A:GLU18 4.9 54.0 1.0 N A:ASP21 5.0 48.5 1.0

Zinc binding site 5 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:56.9 occ:0.50 ZN B:ZN400 0.0 56.9 0.5 ZN B:ZN400 1.0 51.4 0.5 O B:HOH91 2.2 71.8 1.0 OD1 B:ASP21 2.6 55.3 1.0 OD2 B:ASP21 2.9 49.6 1.0 CG B:ASP21 3.1 52.4 1.0 NZ B:LYS29 3.7 49.3 1.0 CE B:LYS29 3.8 51.9 1.0 OE1 B:GLU18 4.3 54.6 1.0 ND2 B:ASN25 4.4 42.8 1.0 CB B:ASP21 4.6 51.1 1.0 N B:GLU18 4.9 49.5 1.0 CG B:GLU18 5.0 50.9 1.0

Zinc binding site 6 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:51.4 occ:0.50 ZN B:ZN400 0.0 51.4 0.5 ZN B:ZN400 1.0 56.9 0.5 OD1 B:ASP21 2.0 55.3 1.0 CG B:ASP21 2.8 52.4 1.0 OD2 B:ASP21 3.0 49.6 1.0 O B:HOH91 3.1 71.8 1.0 ND2 B:ASN25 3.6 42.8 1.0 OE1 B:GLU18 4.0 54.6 1.0 CB B:ASP21 4.2 51.1 1.0 CG B:ASN25 4.5 49.2 1.0 CE B:LYS29 4.5 51.9 1.0 NZ B:LYS29 4.6 49.3 1.0 CB B:ASN25 4.6 48.6 1.0 CA B:ASP21 4.6 51.7 1.0 CB B:GLU18 4.9 48.4 1.0

Zinc binding site 7 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn100 b:43.7 occ:0.50 ZN C:ZN100 0.0 43.7 0.5 OE2 C:GLU64 1.7 52.3 1.0 ZN C:ZN100 2.6 73.5 0.5 CD C:GLU64 2.7 47.3 1.0 OE1 C:GLU64 3.1 49.6 1.0 CG C:GLU64 4.1 46.5 1.0 CB C:GLU64 4.6 48.7 1.0

Zinc binding site 8 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn100 b:73.5 occ:0.50 ZN C:ZN100 0.0 73.5 0.5 OE1 C:GLU64 2.0 49.6 1.0 ZN C:ZN100 2.6 43.7 0.5 CD C:GLU64 2.8 47.3 1.0 OE2 C:GLU64 3.0 52.3 1.0 O D:HOH95 3.5 75.3 1.0 CG C:GLU64 4.1 46.5 1.0 CD C:LYS63 4.3 54.1 1.0 NZ C:LYS63 4.5 56.8 1.0 CG C:LYS63 4.7 49.0 1.0 CD2 D:LEU73 4.9 60.3 1.0

Zinc binding site 9 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn200 b:40.6 occ:0.50 ZN C:ZN200 0.0 40.6 0.5 ZN C:ZN200 0.9 45.5 0.5 O C:HOH85 1.8 48.8 1.0 OD2 C:ASP21 2.1 50.1 1.0 OD1 C:ASP21 2.7 49.0 1.0 CG C:ASP21 2.7 52.4 1.0 NZ C:LYS29 3.6 56.2 1.0 CE C:LYS29 3.7 54.8 1.0 OD1 C:ASN25 4.0 52.0 1.0 CB C:ASP21 4.2 48.4 1.0 OE1 C:GLU18 4.4 55.1 1.0 CG C:GLU18 4.5 52.9 1.0 CB C:ASN25 4.7 50.1 1.0 CG C:ASN25 4.7 50.3 1.0 CA C:ASP21 4.8 49.6 1.0 N C:GLU18 4.8 50.3 1.0 CB C:GLU18 4.9 48.5 1.0

Zinc binding site 10 out of 12 in the The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure and Conformation of Lys-63 Linked Tetra-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn200 b:45.5 occ:0.50 ZN C:ZN200 0.0 45.5 0.5 ZN C:ZN200 0.9 40.6 0.5 OD2 C:ASP21 2.1 50.1 1.0 O C:HOH85 2.4 48.8 1.0 CG C:ASP21 2.9 52.4 1.0 OD1 C:ASP21 3.1 49.0 1.0 OE1 C:GLU18 3.8 55.1 1.0 OD1 C:ASN25 3.9 52.0 1.0 CB C:ASP21 4.3 48.4 1.0 CG C:GLU18 4.3 52.9 1.0 NZ C:LYS29 4.4 56.2 1.0 CD C:GLU18 4.6 50.2 1.0 CA C:ASP21 4.6 49.6 1.0 CB C:GLU18 4.6 48.5 1.0 CE C:LYS29 4.6 54.8 1.0 CG C:ASN25 4.8 50.3 1.0 CB C:ASN25 5.0 50.1 1.0

A.B.Datta, G.L.Hura, C.Wolberger. The Structure and Conformation of LYS63-Linked Tetraubiquitin. J.Mol.Biol. V. 392 1117 2009.
ISSN: ISSN 0022-2836
PubMed: 19664638
DOI: 10.1016/J.JMB.2009.07.090