Zinc in PDB 3h7s: Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture

The structure of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture, PDB code: 3h7s was solved by S.D.Weeks, K.C.Grasty, L.Hernandez-Cuebas, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.82 / 2.30
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.320, 105.320, 105.320, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.3

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture (pdb code 3h7s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture, PDB code: 3h7s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:0.0 occ:0.85 N A:MET1 2.4 47.7 1.0 O A:HOH220 2.6 66.9 1.0 OE2 A:GLU16 2.6 79.5 1.0 CA A:MET1 3.1 44.9 1.0 CD A:GLU16 3.4 77.9 1.0 OE1 A:GLU16 3.5 75.7 1.0 C A:MET1 3.5 44.8 1.0 NH2 A:ARG63 3.7 65.4 0.3 NZ A:ARG63 3.9 64.4 0.7 O A:MET1 4.0 52.3 1.0 N A:GLN2 4.1 47.9 1.0 NH1 A:ARG63 4.2 63.0 0.3 CZ A:ARG63 4.3 65.9 0.3 CB A:MET1 4.5 49.5 1.0 CG A:GLU16 4.9 72.2 1.0 CB A:GLN2 4.9 64.3 1.0 CA A:GLN2 5.0 52.6 1.0

Zinc binding site 2 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:62.0 occ:1.00 O A:HOH203 2.2 39.0 1.0 OE1 A:GLU18 2.3 52.0 1.0 OE2 A:GLU18 2.7 49.3 1.0 CD A:GLU18 2.8 48.2 1.0 CG A:GLU18 4.2 48.7 1.0

Zinc binding site 3 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:0.3 occ:0.44 OD2 A:ASP52 2.4 66.1 1.0 O A:HOH208 2.6 59.4 1.0 O A:HOH216 2.7 70.0 1.0 CG A:ASP52 3.5 57.5 1.0 OE2 A:GLU24 3.7 82.9 1.0 CG A:GLU24 3.7 61.4 1.0 CD A:GLU24 3.8 77.4 1.0 CB A:ASP52 4.1 49.9 1.0 OD1 A:ASP52 4.4 57.0 1.0 OE1 A:GLU24 4.6 77.4 1.0 O A:HOH214 4.6 50.3 1.0 CB A:GLU24 4.6 44.7 1.0

Zinc binding site 4 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:65.3 occ:0.48 ZN A:ZN104 0.0 65.3 0.5 OE1 A:GLU64 2.1 55.3 1.0 CD A:GLU64 2.8 50.5 1.0 OE2 A:GLU64 2.8 58.8 1.0 ZN A:ZN104 3.9 70.8 0.5 CG A:GLU64 4.3 48.2 1.0 CB A:GLU64 4.8 43.9 1.0

Zinc binding site 5 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:70.8 occ:0.52 ZN A:ZN104 0.0 70.8 0.5 OE2 A:GLU64 2.2 58.8 1.0 CD A:GLU64 3.4 50.5 1.0 ZN A:ZN104 3.9 65.3 0.5 NE A:ARG63 4.1 67.6 0.3 OE1 A:GLU64 4.2 55.3 1.0 CE A:ARG63 4.3 68.1 0.7 CG A:GLU64 4.4 48.2 1.0 CD A:ARG63 4.6 64.8 0.3 CD A:ARG63 4.8 65.3 0.7

Zinc binding site 6 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:0.5 occ:1.00 CD A:ARG74 3.7 0.2 1.0 NH1 A:ARG74 4.2 0.8 1.0 CB A:ARG74 4.3 0.6 1.0 O B:HOH208 4.6 59.2 1.0 CG A:ARG74 4.7 0.6 1.0 NE A:ARG74 4.8 0.2 1.0

Zinc binding site 7 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn106 b:0.7 occ:0.93 ZN B:ZN104 3.4 0.5 0.7 C A:GLY75 4.6 1.0 1.0 CG B:GLN2 4.7 70.0 1.0 CA B:MET1 4.9 60.8 1.0 O A:GLY75 5.0 97.1 1.0

Zinc binding site 8 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:75.0 occ:1.00 OE2 B:GLU18 2.3 70.5 1.0 O B:HOH201 2.4 59.3 1.0 OE1 B:GLU18 2.9 60.9 1.0 CD B:GLU18 2.9 62.9 1.0 CG B:GLU18 4.4 59.1 1.0

Zinc binding site 9 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:93.3 occ:0.47 OD2 B:ASP52 2.6 74.2 1.0 OE1 B:GLU24 2.6 96.2 1.0 O B:HOH214 3.1 79.5 1.0 CG B:ASP52 3.4 63.4 1.0 CD B:GLU24 3.7 88.5 1.0 OD1 B:ASP52 4.0 60.6 1.0 OD2 B:ASP39 4.0 90.5 1.0 OE2 B:GLU24 4.1 91.8 1.0 CB B:ASP52 4.4 56.7 1.0 CB B:PRO38 4.4 53.1 1.0 O B:PRO38 4.5 56.4 1.0 C B:PRO38 4.6 54.5 1.0 CD B:LYS27 4.8 50.6 1.0 N B:ASP39 4.9 54.8 1.0 NZ B:LYS27 4.9 51.5 1.0 CG B:GLU24 4.9 70.1 1.0 CA B:ASP39 5.0 57.9 1.0

Zinc binding site 10 out of 11 in the Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structures of K63-Linked Di- and Tri-Ubiquitin Reveal A Highly Extended Chain Architecture within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:0.7 occ:1.00 OE1 B:GLU64 3.2 94.8 1.0 CD B:GLU64 4.0 91.9 1.0 CE2 B:PHE4 4.0 58.3 1.0 O B:HOH219 4.2 73.8 1.0 CZ B:PHE4 4.3 58.9 1.0 CG B:GLU64 4.6 76.3 1.0 CB B:GLU64 4.7 66.9 1.0 OE2 B:GLU64 4.7 0.7 1.0

S.D.Weeks, K.C.Grasty, L.Hernandez-Cuebas, P.J.Loll. Crystal Structures of Lys-63-Linked Tri- and Di-Ubiquitin Reveal A Highly Extended Chain Architecture. Proteins V. 77 753 2009.
ISSN: ISSN 0887-3585
PubMed: 19731378
DOI: 10.1002/PROT.22568