Zinc in PDB 5vmd: Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation

The structure of Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation, PDB code: 5vmd was solved by J.Munoz-Escobar, G.Kozlov, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.72 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.570, 69.200, 82.590, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation (pdb code 5vmd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation, PDB code: 5vmd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:58.8 occ:1.00 NE2 C:HIS848 2.0 42.1 1.0 NE2 A:HIS848 2.1 51.3 1.0 ND1 C:HIS883 2.2 40.0 1.0 ND1 A:HIS883 2.3 46.2 1.0 CE1 C:HIS848 2.3 38.1 1.0 CE1 A:HIS848 2.9 47.4 1.0 CG C:HIS883 3.1 37.8 1.0 CG A:HIS883 3.2 43.8 1.0 CE1 A:HIS883 3.2 42.3 1.0 CE1 C:HIS883 3.3 40.8 1.0 CD2 C:HIS848 3.3 32.9 1.0 CD2 A:HIS848 3.3 43.7 1.0 CB C:HIS883 3.3 39.6 1.0 CB A:HIS883 3.5 32.0 1.0 ND1 C:HIS848 3.6 41.6 1.0 H11 C:EDO1003 4.1 80.4 1.0 ND1 A:HIS848 4.1 36.9 1.0 CG C:HIS848 4.1 39.3 1.0 CE1 C:PHE850 4.3 31.4 1.0 CD2 C:HIS883 4.3 41.6 1.0 CG A:HIS848 4.3 40.3 1.0 NE2 A:HIS883 4.3 39.2 1.0 CD2 A:HIS883 4.3 44.6 1.0 NE2 C:HIS883 4.3 44.6 1.0 CA A:HIS883 4.8 32.2 1.0 CD1 C:PHE850 4.8 34.3 1.0 CA C:HIS883 4.9 38.9 1.0 C1 C:EDO1003 5.0 67.0 1.0 H12 C:EDO1003 5.0 80.4 1.0

Zinc binding site 2 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:45.0 occ:1.00 SG C:CYS888 2.4 29.8 1.0 SG A:CYS868 2.4 35.5 1.0 SG A:CYS865 2.4 31.7 1.0 CB C:CYS888 3.1 30.9 1.0 CB A:CYS868 3.3 33.5 1.0 CB A:CYS865 3.5 30.3 1.0 N C:GLY891 3.9 34.7 1.0 N A:CYS865 4.0 39.5 1.0 CA A:CYS865 4.3 35.1 1.0 N A:CYS868 4.4 36.9 1.0 CA C:GLY891 4.4 32.0 1.0 ZN A:ZN1003 4.4 51.4 1.0 CA A:CYS868 4.4 38.8 1.0 CB C:CYS890 4.5 29.7 1.0 CA C:CYS888 4.6 29.0 1.0 C C:CYS890 4.9 43.3 1.0 O A:CYS865 5.0 37.0 1.0 C A:CYS865 5.0 37.1 1.0

Zinc binding site 3 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:51.4 occ:1.00 SG C:CYS890 2.3 33.0 1.0 SG C:CYS899 2.4 40.5 1.0 SG A:CYS868 2.4 35.5 1.0 SG A:CYS872 2.5 45.0 1.0 CB C:CYS899 3.1 40.0 1.0 CB A:CYS868 3.2 33.5 1.0 CB C:CYS890 3.3 29.7 1.0 CB A:CYS872 3.4 38.0 1.0 CA C:CYS899 3.5 45.0 1.0 CA A:CYS868 4.0 38.8 1.0 N C:THR900 4.0 50.1 1.0 C C:CYS890 4.1 43.3 1.0 N C:GLY891 4.1 34.7 1.0 C C:CYS899 4.2 49.3 1.0 CA C:CYS890 4.3 39.6 1.0 ZN A:ZN1002 4.4 45.0 1.0 O C:CYS890 4.5 43.5 1.0 N C:LEU901 4.6 43.0 1.0 CA C:GLY891 4.7 32.0 1.0 CG C:LEU901 4.7 47.4 1.0 N C:CYS899 4.8 50.9 1.0 CD1 C:LEU901 4.8 41.7 1.0 CA A:CYS872 4.8 40.9 1.0 CB C:LEU901 4.8 48.3 1.0 O A:CYS868 4.8 41.7 1.0 C A:CYS868 4.9 36.1 1.0

Zinc binding site 4 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:50.5 occ:1.00 ND1 A:HIS873 2.0 35.7 1.0 ND1 A:HIS876 2.1 44.9 1.0 SG A:CYS853 2.3 36.8 1.0 SG A:CYS856 2.5 43.1 1.0 CE1 A:HIS876 3.0 41.7 1.0 CE1 A:HIS873 3.0 37.9 1.0 CG A:HIS873 3.0 40.8 1.0 CG A:HIS876 3.3 41.1 1.0 CB A:CYS853 3.4 34.5 1.0 CB A:HIS873 3.4 37.9 1.0 CB A:CYS856 3.4 42.0 1.0 CB A:HIS876 3.7 40.4 1.0 N A:CYS856 3.8 45.5 1.0 NE2 A:HIS873 4.1 39.6 1.0 NE2 A:HIS876 4.2 40.9 1.0 CD2 A:HIS873 4.2 40.0 1.0 CB A:THR855 4.2 44.9 1.0 CA A:HIS873 4.2 41.5 1.0 CA A:CYS856 4.3 47.4 1.0 CD2 A:HIS876 4.3 39.7 1.0 C A:THR855 4.7 48.2 1.0 CG2 A:THR855 4.7 40.0 1.0 CA A:CYS853 4.8 37.7 1.0 CA A:THR855 4.9 45.5 1.0 O A:CYS872 4.9 41.1 1.0

Zinc binding site 5 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:53.4 occ:1.00 SG A:CYS890 2.3 42.3 1.0 SG C:CYS872 2.4 43.0 1.0 SG C:CYS868 2.4 36.7 1.0 SG A:CYS899 2.6 42.5 1.0 CB C:CYS868 3.1 32.3 1.0 CB C:CYS872 3.2 38.9 1.0 CB A:CYS899 3.3 42.5 1.0 CB A:CYS890 3.3 34.6 1.0 CA A:CYS899 3.6 50.5 1.0 CA C:CYS868 3.8 33.7 1.0 N A:THR900 4.0 54.1 1.0 C A:CYS890 4.2 37.0 1.0 N A:GLY891 4.3 38.4 1.0 C A:CYS899 4.3 56.6 1.0 CA A:CYS890 4.4 37.7 1.0 ZN C:ZN1001 4.4 49.9 1.0 N A:LEU901 4.5 53.2 1.0 CG A:LEU901 4.6 50.4 1.0 O A:CYS890 4.6 39.0 1.0 CA C:CYS872 4.7 43.3 1.0 CD1 A:LEU901 4.7 46.4 1.0 CB A:LEU901 4.7 50.7 1.0 C C:CYS868 4.7 34.5 1.0 O C:CYS868 4.7 36.8 1.0 N A:CYS899 4.8 52.7 1.0 CA A:GLY891 4.9 39.4 1.0 NE2 C:HIS873 4.9 38.2 1.0 N C:CYS868 4.9 36.6 1.0

Zinc binding site 6 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:70.2 occ:1.00 NE2 B:HIS848 2.2 40.0 1.0 NE2 D:HIS848 2.3 54.2 1.0 ND1 B:HIS883 2.3 67.6 1.0 CE1 B:HIS848 2.4 39.5 1.0 ND1 D:HIS883 2.6 45.0 1.0 HO1 B:EDO1006 2.7 78.2 1.0 CE1 D:HIS848 2.8 45.5 1.0 CG B:HIS883 3.2 59.4 1.0 CG D:HIS883 3.3 47.5 1.0 CE1 B:HIS883 3.4 69.1 1.0 CB B:HIS883 3.4 50.3 1.0 CB D:HIS883 3.4 39.9 1.0 CD2 B:HIS848 3.5 40.2 1.0 CD2 D:HIS848 3.5 44.9 1.0 O1 B:EDO1006 3.6 65.1 1.0 CE1 D:HIS883 3.6 41.6 1.0 ND1 B:HIS848 3.7 36.7 1.0 ND1 D:HIS848 4.1 47.6 1.0 CG B:HIS848 4.2 39.7 1.0 CD2 B:HIS883 4.4 64.9 1.0 CG D:HIS848 4.4 46.2 1.0 NE2 B:HIS883 4.4 67.4 1.0 CD2 D:HIS883 4.5 46.0 1.0 CE1 B:PHE850 4.5 32.4 1.0 NE2 D:HIS883 4.6 43.6 1.0 C1 B:EDO1006 4.7 63.4 1.0 CA D:HIS883 4.8 35.5 1.0 H11 B:EDO1006 4.8 76.1 1.0 CA B:HIS883 4.9 41.0 1.0 CE1 D:PHE850 4.9 38.3 1.0 H12 B:EDO1006 4.9 76.1 1.0 C D:HIS883 5.0 35.0 1.0

Zinc binding site 7 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:83.6 occ:1.00 ND1 B:HIS876 2.1 70.6 1.0 ND1 B:HIS873 2.2 55.7 1.0 SG B:CYS853 2.3 60.5 1.0 SG B:CYS856 2.4 66.1 1.0 CE1 B:HIS876 2.9 72.2 1.0 CE1 B:HIS873 3.1 52.5 1.0 CG B:HIS876 3.2 71.8 1.0 CG B:HIS873 3.3 54.1 1.0 CB B:CYS853 3.5 46.1 1.0 CB B:CYS856 3.6 68.2 1.0 CB B:HIS876 3.7 66.8 1.0 CB B:HIS873 3.7 54.3 1.0 N B:CYS856 3.9 72.3 1.0 NE2 B:HIS876 4.1 76.1 1.0 CB B:THR855 4.2 65.3 1.0 NE2 B:HIS873 4.3 51.2 1.0 CD2 B:HIS876 4.3 76.5 1.0 CD2 B:HIS873 4.4 53.3 1.0 CA B:CYS856 4.4 74.9 1.0 CA B:HIS873 4.4 59.4 1.0 CG2 B:THR855 4.7 68.7 1.0 C B:THR855 4.7 74.3 1.0 CA B:CYS853 4.8 47.4 1.0 CA B:THR855 4.9 69.6 1.0 O B:CYS872 5.0 65.6 1.0

Zinc binding site 8 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:60.0 occ:1.00 SG B:CYS868 2.2 57.7 1.0 SG D:CYS888 2.4 38.6 1.0 SG B:CYS865 2.5 42.3 1.0 CB D:CYS888 3.2 32.7 1.0 CB B:CYS868 3.2 48.9 1.0 CB B:CYS865 3.6 39.0 1.0 N B:CYS865 4.0 43.1 1.0 N D:GLY891 4.0 45.5 1.0 CA B:CYS865 4.3 42.5 1.0 N B:CYS868 4.3 48.1 1.0 CA B:CYS868 4.4 48.5 1.0 ZN B:ZN1004 4.4 67.1 1.0 CB D:CYS890 4.5 47.2 1.0 CA D:GLY891 4.5 46.1 1.0 CA D:CYS888 4.7 38.0 1.0 O B:CYS865 4.9 44.0 1.0 C B:CYS865 4.9 42.8 1.0

Zinc binding site 9 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:67.1 occ:1.00 SG D:CYS890 2.2 51.7 1.0 SG B:CYS872 2.4 54.7 1.0 SG D:CYS899 2.5 57.1 1.0 SG B:CYS868 2.5 57.7 1.0 CB B:CYS868 3.2 48.9 1.0 CB D:CYS890 3.2 47.2 1.0 CB D:CYS899 3.2 60.1 1.0 CB B:CYS872 3.4 56.7 1.0 CA D:CYS899 3.6 63.3 1.0 CA B:CYS868 3.9 48.5 1.0 N D:THR900 4.0 64.3 1.0 C D:CYS890 4.1 47.5 1.0 N D:GLY891 4.2 45.5 1.0 CA D:CYS890 4.3 45.5 1.0 C D:CYS899 4.3 64.8 1.0 ZN B:ZN1003 4.4 60.0 1.0 O D:CYS890 4.5 51.6 1.0 N D:LEU901 4.6 70.9 1.0 CG D:LEU901 4.6 66.7 1.0 CD1 D:LEU901 4.7 63.1 1.0 O B:CYS868 4.7 52.8 1.0 C B:CYS868 4.7 48.9 1.0 CA D:GLY891 4.8 46.1 1.0 CA B:CYS872 4.8 60.9 1.0 N D:CYS899 4.8 62.1 1.0 O D:HOH1115 4.9 51.2 1.0 CB D:LEU901 4.9 68.4 1.0 OG1 D:THR900 5.0 74.5 1.0 N B:CYS868 5.0 48.1 1.0 NE2 B:HIS873 5.0 51.2 1.0

Zinc binding site 10 out of 14 in the Crystal Structure of Ubr-Box From UBR6 in A Domain-Swapping Conformation


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 Ubr-Box From UBR6 in A Domain-Swapping Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:60.6 occ:1.00 SG B:CYS890 2.3 41.1 1.0 SG B:CYS899 2.4 52.8 1.0 SG D:CYS868 2.4 44.3 1.0 SG D:CYS872 2.4 49.7 1.0 CB D:CYS868 3.2 39.4 1.0 CB B:CYS899 3.2 50.2 1.0 CB B:CYS890 3.3 43.1 1.0 CB D:CYS872 3.3 47.7 1.0 CA B:CYS899 3.6 49.2 1.0 CA D:CYS868 4.0 48.5 1.0 N B:THR900 4.0 43.0 1.0 C B:CYS890 4.2 42.1 1.0 N B:GLY891 4.2 38.7 1.0 C B:CYS899 4.3 47.3 1.0 CA B:CYS890 4.3 43.1 1.0 ZN D:ZN1001 4.4 60.1 1.0 CG B:LEU901 4.6 52.6 1.0 O B:CYS890 4.6 46.4 1.0 N B:LEU901 4.6 55.0 1.0 CD1 B:LEU901 4.6 54.2 1.0 CB B:LEU901 4.8 52.2 1.0 NE2 D:HIS873 4.8 41.6 1.0 CA D:CYS872 4.8 47.0 1.0 O D:CYS868 4.8 43.5 1.0 CA B:GLY891 4.8 37.9 1.0 C D:CYS868 4.8 44.5 1.0 N B:CYS899 4.9 51.1 1.0

J.Munoz-Escobar, G.Kozlov, K.Gehring. Crystal Structure of the Ubr-Box From UBR6/FBXO11 Reveals Domain Swapping Mediated By Zinc Binding. Protein Sci. V. 26 2092 2017.
ISSN: ESSN 1469-896X
PubMed: 28691247
DOI: 10.1002/PRO.3227