Zinc in PDB 3rtr: A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases

The structure of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases, PDB code: 3rtr was solved by M.F.Calabrese, D.C.Scott, D.M.Duda, C.R.Grace, I.Kurinov, R.W.Kriwacki, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 3.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.475, 119.796, 231.861, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 28.2

Pages:

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

Binding sites:

The binding sites of Zinc atom in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases (pdb code 3rtr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases, PDB code: 3rtr:
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 A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn204 b:66.7 occ:1.00 ND1 F:HIS80 2.1 59.2 1.0 SG F:CYS45 2.3 76.1 1.0 SG F:CYS83 2.3 80.2 1.0 SG F:CYS42 2.3 70.6 1.0 CE1 F:HIS80 3.0 59.5 1.0 CB F:CYS42 3.0 68.9 1.0 CG F:HIS80 3.1 73.3 1.0 CB F:CYS83 3.3 62.5 1.0 CB F:CYS45 3.4 75.0 1.0 CB F:HIS80 3.5 61.1 1.0 CB F:CYS53 3.9 73.2 1.0 N F:CYS45 3.9 70.5 1.0 NE2 F:HIS80 4.1 70.8 1.0 CD2 F:HIS80 4.2 60.9 1.0 CA F:CYS45 4.2 71.9 1.0 N F:HIS80 4.3 63.1 1.0 CA F:CYS53 4.3 72.4 1.0 CA F:CYS42 4.5 68.5 1.0 CA F:HIS80 4.5 64.8 1.0 CA F:CYS83 4.7 60.5 1.0 OD1 F:ASN47 4.7 79.1 1.0 CB F:ILE44 4.9 60.6 1.0 O F:CYS42 4.9 61.3 1.0 C F:CYS42 5.0 64.0 1.0 C F:ILE44 5.0 67.5 1.0

Zinc binding site 2 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn208 b:71.7 occ:1.00 ND1 F:HIS77 2.1 71.9 1.0 SG F:CYS75 2.2 0.8 1.0 SG F:CYS94 2.3 79.8 1.0 OD2 F:ASP97 2.4 73.8 1.0 CB F:CYS75 2.8 70.4 1.0 CE1 F:HIS77 3.0 71.5 1.0 CG F:HIS77 3.1 70.4 1.0 CG F:ASP97 3.1 74.2 1.0 CB F:HIS77 3.4 68.6 1.0 OD1 F:ASP97 3.4 75.2 1.0 CB F:CYS94 3.4 78.8 1.0 NE2 F:HIS77 4.2 72.6 1.0 CD2 F:HIS77 4.2 71.0 1.0 CA F:CYS75 4.2 74.0 1.0 CB F:ASP97 4.3 74.1 1.0 CE3 F:TRP101 4.5 78.5 1.0 CZ3 F:TRP101 4.5 78.8 1.0 N F:HIS77 4.5 75.6 1.0 CA F:HIS77 4.5 70.1 1.0 C F:CYS75 4.6 74.0 1.0 O F:CYS75 4.8 71.0 1.0 N F:ASP97 4.8 87.4 1.0 N F:CYS75 4.8 76.5 1.0 CA F:CYS94 4.9 80.8 1.0 CB F:LEU96 5.0 75.7 1.0 C F:LEU96 5.0 83.8 1.0

Zinc binding site 3 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn212 b:74.5 occ:1.00 ND1 F:HIS82 2.1 68.7 1.0 SG F:CYS56 2.3 77.2 1.0 SG F:CYS53 2.3 71.8 1.0 SG F:CYS68 2.3 92.1 1.0 CE1 F:HIS82 3.0 67.8 1.0 CG F:HIS82 3.1 64.7 1.0 CB F:CYS68 3.2 99.7 1.0 CB F:CYS56 3.4 77.2 1.0 CB F:HIS82 3.4 62.3 1.0 CB F:CYS53 3.6 73.2 1.0 CA F:CYS68 4.0 0.3 1.0 NE2 F:HIS82 4.1 64.1 1.0 CD2 F:HIS82 4.1 62.1 1.0 N F:CYS53 4.1 75.0 1.0 N F:CYS56 4.3 70.1 1.0 CA F:CYS56 4.4 74.5 1.0 CA F:CYS53 4.5 72.4 1.0 N F:CYS68 4.8 0.9 1.0 CA F:HIS82 4.9 61.1 1.0

Zinc binding site 4 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:65.6 occ:1.00 ND1 D:HIS80 2.0 61.9 1.0 SG D:CYS83 2.3 93.3 1.0 SG D:CYS45 2.3 68.2 1.0 SG D:CYS42 2.4 57.2 1.0 CB D:CYS42 3.0 54.5 1.0 CE1 D:HIS80 3.0 60.4 1.0 CG D:HIS80 3.0 58.7 1.0 CB D:CYS83 3.3 65.0 1.0 CB D:HIS80 3.4 56.3 1.0 CB D:CYS45 3.5 0.9 1.0 N D:CYS45 3.9 72.9 1.0 CB D:CYS53 4.1 77.3 1.0 NE2 D:HIS80 4.1 60.3 1.0 CD2 D:HIS80 4.2 59.6 1.0 CA D:CYS45 4.3 81.6 1.0 N D:HIS80 4.3 50.1 1.0 CA D:CYS42 4.4 55.5 1.0 CA D:HIS80 4.5 54.8 1.0 CA D:CYS53 4.6 77.4 1.0 OD1 D:ASN47 4.7 72.4 1.0 CA D:CYS83 4.7 67.8 1.0 O D:CYS42 4.7 56.2 1.0 CB D:ILE44 4.7 58.4 1.0 C D:CYS45 4.8 76.8 1.0 C D:CYS42 4.9 56.2 1.0 N D:ARG46 4.9 72.0 1.0 C D:ILE44 4.9 66.8 1.0

Zinc binding site 5 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn205 b:68.4 occ:1.00 ND1 D:HIS77 2.1 74.6 1.0 SG D:CYS94 2.3 56.0 1.0 OD2 D:ASP97 2.3 63.7 1.0 SG D:CYS75 2.4 69.0 1.0 CE1 D:HIS77 2.8 75.5 1.0 CB D:CYS75 2.8 66.7 1.0 CG D:ASP97 2.9 63.1 1.0 OD1 D:ASP97 3.1 63.7 1.0 CB D:CYS94 3.2 72.9 1.0 CG D:HIS77 3.2 70.2 1.0 CB D:HIS77 3.8 64.1 1.0 NE2 D:HIS77 4.0 75.5 1.0 CB D:ASP97 4.0 64.8 1.0 CD2 D:HIS77 4.2 71.8 1.0 CA D:CYS75 4.3 66.0 1.0 N D:ASP97 4.4 64.4 1.0 C D:LEU96 4.6 61.0 1.0 CA D:CYS94 4.6 71.6 1.0 C D:CYS75 4.7 68.0 1.0 N D:HIS77 4.7 62.3 1.0 CZ3 D:TRP101 4.7 69.4 1.0 CB D:LEU96 4.7 54.4 1.0 CA D:ASP97 4.8 68.4 1.0 O D:CYS75 4.8 68.6 1.0 CA D:HIS77 4.9 60.6 1.0 CE3 D:TRP101 4.9 74.1 1.0 O D:LEU96 4.9 62.1 1.0 N D:LEU96 5.0 59.2 1.0

Zinc binding site 6 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn209 b:75.3 occ:1.00 ND1 D:HIS82 2.1 69.4 1.0 SG D:CYS56 2.3 89.8 1.0 SG D:CYS53 2.3 72.8 1.0 SG D:CYS68 2.3 71.9 1.0 CE1 D:HIS82 2.8 71.8 1.0 CG D:HIS82 3.2 67.6 1.0 CB D:CYS68 3.3 91.8 1.0 CB D:CYS56 3.4 90.6 1.0 CB D:CYS53 3.7 77.3 1.0 CB D:HIS82 3.7 67.8 1.0 CA D:CYS68 3.9 90.2 1.0 NE2 D:HIS82 3.9 72.5 1.0 CD2 D:HIS82 4.1 69.3 1.0 N D:CYS53 4.2 77.8 1.0 N D:CYS56 4.4 92.1 1.0 CA D:CYS56 4.5 93.1 1.0 CA D:CYS53 4.6 77.4 1.0 N D:CYS68 4.7 0.2 1.0

Zinc binding site 7 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:74.6 occ:1.00 ND1 B:HIS80 2.0 65.1 1.0 SG B:CYS83 2.3 80.3 1.0 SG B:CYS42 2.3 88.1 1.0 SG B:CYS45 2.3 90.1 1.0 CB B:CYS42 2.8 63.7 1.0 CE1 B:HIS80 3.0 64.1 1.0 CG B:HIS80 3.1 66.8 1.0 CB B:CYS83 3.3 73.1 1.0 CB B:CYS45 3.4 81.7 1.0 CB B:HIS80 3.4 70.1 1.0 N B:CYS45 4.0 78.5 1.0 NE2 B:HIS80 4.1 65.2 1.0 N B:HIS80 4.2 74.4 1.0 CD2 B:HIS80 4.2 66.3 1.0 CB B:CYS53 4.2 86.6 1.0 CA B:CYS45 4.3 79.7 1.0 CA B:CYS42 4.3 63.5 1.0 CA B:HIS80 4.4 74.8 1.0 O B:CYS42 4.6 67.7 1.0 OD1 B:ASN47 4.7 81.0 1.0 CA B:CYS53 4.7 87.5 1.0 CA B:CYS83 4.7 74.5 1.0 C B:CYS42 4.7 66.3 1.0 CB B:ILE44 4.9 70.1 1.0

Zinc binding site 8 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:60.0 occ:1.00 ND1 B:HIS77 2.1 65.3 1.0 SG B:CYS75 2.3 81.6 1.0 SG B:CYS94 2.3 57.7 1.0 OD2 B:ASP97 2.4 61.4 1.0 CB B:CYS75 3.0 56.5 1.0 CG B:HIS77 3.0 66.7 1.0 CE1 B:HIS77 3.1 64.9 1.0 CG B:ASP97 3.2 63.5 1.0 CB B:HIS77 3.2 68.5 1.0 CB B:CYS94 3.3 65.8 1.0 OD1 B:ASP97 3.6 66.7 1.0 CD2 B:HIS77 4.1 65.7 1.0 NE2 B:HIS77 4.2 65.4 1.0 CB B:ASP97 4.4 62.8 1.0 CA B:CYS75 4.4 61.5 1.0 CA B:HIS77 4.5 70.7 1.0 N B:HIS77 4.5 72.2 1.0 O B:CYS75 4.7 69.3 1.0 C B:CYS75 4.7 66.9 1.0 CA B:CYS94 4.7 68.0 1.0 N B:ASP97 4.8 65.3 1.0 C B:LEU96 4.8 65.5 1.0 CB B:LEU96 4.8 65.3 1.0 CE3 B:TRP101 4.9 66.1 1.0

Zinc binding site 9 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn210 b:88.2 occ:1.00 ND1 B:HIS82 2.0 89.5 1.0 SG B:CYS56 2.3 0.5 1.0 SG B:CYS68 2.3 79.8 1.0 SG B:CYS53 2.3 91.4 1.0 CE1 B:HIS82 2.8 92.8 1.0 CB B:CYS56 3.1 95.6 1.0 CG B:HIS82 3.1 86.1 1.0 CB B:CYS68 3.2 0.7 1.0 CB B:CYS53 3.4 86.6 1.0 CB B:HIS82 3.6 83.5 1.0 NE2 B:HIS82 4.0 90.7 1.0 N B:CYS56 4.0 96.5 1.0 CA B:CYS56 4.1 97.5 1.0 N B:CYS53 4.1 89.9 1.0 CD2 B:HIS82 4.2 86.0 1.0 CA B:CYS68 4.2 0.4 1.0 CA B:CYS53 4.3 87.5 1.0 O B:CYS53 4.7 91.2 1.0 C B:CYS53 4.8 89.3 1.0

Zinc binding site 10 out of 12 in the A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn203 b:98.2 occ:1.00 ND1 H:HIS80 2.1 1.0 1.0 SG H:CYS83 2.3 0.9 1.0 SG H:CYS42 2.3 94.5 1.0 SG H:CYS45 2.3 80.6 1.0 CB H:CYS42 2.9 95.8 1.0 CE1 H:HIS80 2.9 0.4 1.0 CG H:HIS80 3.1 0.3 1.0 CB H:CYS45 3.3 88.7 1.0 CB H:CYS83 3.4 0.9 1.0 CB H:HIS80 3.6 0.6 1.0 N H:CYS45 3.8 82.3 1.0 CB H:CYS53 4.0 0.5 1.0 NE2 H:HIS80 4.0 0.0 1.0 CA H:CYS45 4.1 83.6 1.0 CD2 H:HIS80 4.2 0.7 1.0 CA H:CYS42 4.3 94.8 1.0 N H:HIS80 4.4 0.9 1.0 OD1 H:ASN47 4.4 0.1 1.0 CA H:CYS53 4.5 1.0 1.0 CA H:HIS80 4.6 0.5 1.0 C H:CYS42 4.8 88.3 1.0 N H:ARG46 4.8 84.7 1.0 C H:CYS45 4.8 81.9 1.0 CA H:CYS83 4.8 0.3 1.0 C H:ILE44 4.8 79.7 1.0 O H:CYS42 4.8 84.5 1.0 CB H:ILE44 4.9 80.1 1.0 N H:ILE44 5.0 80.2 1.0

M.F.Calabrese, D.C.Scott, D.M.Duda, C.R.Grace, I.Kurinov, R.W.Kriwacki, B.A.Schulman. A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases. Nat.Struct.Mol.Biol. V. 18 947 2011.
ISSN: ISSN 1545-9993
PubMed: 21765416
DOI: 10.1038/NSMB.2086