Zinc in PDB 5zi6: The Ring Domain Structure of Mex-3C

All present enzymatic activity of The Ring Domain Structure of Mex-3C:
2.3.2.27;

The structure of The Ring Domain Structure of Mex-3C, PDB code: 5zi6 was solved by S.A.Moududee, Y.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.38 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.135, 44.567, 67.157, 92.43, 90.50, 91.39
R / Rfree (%)	20.7 / 24.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the The Ring Domain Structure of Mex-3C (pdb code 5zi6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the The Ring Domain Structure of Mex-3C, PDB code: 5zi6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:44.7 occ:1.00 SG A:CYS629 2.1 40.1 1.0 SG A:CYS632 2.3 50.0 1.0 SG A:CYS611 2.3 52.3 1.0 SG A:CYS608 2.4 46.6 1.0 CB A:CYS632 3.1 49.2 1.0 CB A:CYS608 3.1 46.9 1.0 CB A:CYS629 3.4 42.8 1.0 CB A:CYS611 3.4 50.1 1.0 N A:CYS611 3.8 51.3 1.0 N A:CYS629 4.0 42.4 1.0 N A:CYS632 4.2 53.6 1.0 CA A:CYS611 4.2 52.5 1.0 CA A:CYS629 4.3 43.9 1.0 CA A:CYS632 4.3 51.7 1.0 ND2 A:ASN614 4.5 69.0 1.0 CA A:CYS608 4.6 44.6 1.0 CB A:ILE610 4.6 49.9 1.0 CB A:ASN614 4.7 63.7 1.0 C A:ILE610 4.9 44.5 1.0 C A:CYS629 4.9 48.3 1.0 CG A:ASN614 5.0 66.6 1.0 O A:CYS629 5.0 50.0 1.0 N A:ASN614 5.0 57.3 1.0 N A:ILE610 5.0 45.6 1.0

Zinc binding site 2 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:40.6 occ:1.00 ND1 A:HIS625 2.1 43.8 1.0 SG A:CYS623 2.2 34.5 1.0 SG A:CYS644 2.3 39.5 1.0 SG A:CYS647 2.5 36.3 1.0 CE1 A:HIS625 3.0 46.2 1.0 CB A:CYS644 3.0 38.9 1.0 CG A:HIS625 3.1 39.6 1.0 CB A:CYS623 3.1 38.2 1.0 CB A:HIS625 3.4 37.4 1.0 CB A:CYS647 3.7 41.7 1.0 N A:CYS647 4.0 43.7 1.0 NE2 A:HIS625 4.2 44.2 1.0 CD2 A:HIS625 4.2 41.1 1.0 CA A:CYS647 4.4 45.5 1.0 N A:HIS625 4.4 36.2 1.0 CA A:CYS623 4.5 39.1 1.0 CA A:CYS644 4.5 39.3 1.0 CA A:HIS625 4.5 38.4 1.0 C A:CYS623 4.7 41.5 1.0 CB A:VAL646 4.7 49.8 1.0 CB A:THR649 4.9 41.3 1.0 O A:CYS623 4.9 36.2 1.0 C A:VAL646 5.0 45.9 1.0 OG1 A:THR649 5.0 42.3 1.0

Zinc binding site 3 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:42.6 occ:1.00 SG B:CYS632 2.2 44.2 1.0 SG B:CYS629 2.3 40.1 1.0 SG B:CYS608 2.3 39.8 1.0 SG B:CYS611 2.4 40.2 1.0 CB B:CYS632 3.1 44.0 1.0 CB B:CYS608 3.3 45.9 1.0 CB B:CYS611 3.4 39.5 1.0 CB B:CYS629 3.6 41.3 1.0 N B:CYS611 3.7 45.5 1.0 N B:CYS629 4.0 40.0 1.0 CA B:CYS611 4.2 43.9 1.0 N B:CYS632 4.2 47.0 1.0 CA B:CYS632 4.3 44.1 1.0 CB B:ILE610 4.3 48.4 1.0 CA B:CYS629 4.4 42.2 1.0 ND2 B:ASN614 4.6 48.4 1.0 CA B:CYS608 4.7 46.1 1.0 C B:ILE610 4.7 46.1 1.0 CB B:ASN614 4.7 49.7 1.0 N B:ILE610 4.9 46.9 1.0 CA B:ILE610 4.9 47.7 1.0 C B:CYS629 4.9 46.8 1.0 O B:CYS629 5.0 43.4 1.0 CG2 B:ILE610 5.0 49.7 1.0

Zinc binding site 4 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:42.2 occ:1.00 ND1 B:HIS625 2.2 44.5 1.0 SG B:CYS623 2.3 45.6 1.0 SG B:CYS644 2.3 40.7 1.0 SG B:CYS647 2.4 53.6 1.0 CB B:CYS644 3.0 45.9 1.0 CE1 B:HIS625 3.1 48.2 1.0 CG B:HIS625 3.2 40.2 1.0 CB B:CYS623 3.2 40.5 1.0 CB B:HIS625 3.5 40.1 1.0 CB B:CYS647 3.6 46.8 1.0 N B:CYS647 4.0 48.1 1.0 NE2 B:HIS625 4.2 46.8 1.0 CD2 B:HIS625 4.3 42.5 1.0 CA B:CYS647 4.3 47.7 1.0 CA B:CYS644 4.4 44.6 1.0 N B:HIS625 4.5 34.8 1.0 CA B:CYS623 4.6 39.3 1.0 CA B:HIS625 4.6 38.1 1.0 CB B:VAL646 4.6 48.2 1.0 C B:CYS623 4.8 38.3 1.0 CB B:THR649 4.9 49.0 1.0 C B:CYS647 4.9 44.0 1.0 O B:CYS623 5.0 39.0 1.0

Zinc binding site 5 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:42.2 occ:1.00 SG C:CYS632 2.3 48.0 1.0 SG C:CYS608 2.3 46.4 1.0 SG C:CYS629 2.4 42.9 1.0 SG C:CYS611 2.4 48.0 1.0 CB C:CYS608 3.1 46.5 1.0 CB C:CYS632 3.2 45.0 1.0 CB C:CYS611 3.5 47.4 1.0 CB C:CYS629 3.5 43.5 1.0 N C:CYS611 3.9 51.3 1.0 N C:CYS629 4.0 37.2 1.0 N C:CYS632 4.3 44.9 1.0 CA C:CYS629 4.3 37.8 1.0 CA C:CYS632 4.3 44.5 1.0 CA C:CYS611 4.3 50.3 1.0 CA C:CYS608 4.5 45.0 1.0 CB C:ILE610 4.7 48.7 1.0 CB C:ASN614 4.8 52.6 1.0 ND2 C:ASN614 4.9 52.4 1.0 C C:CYS629 4.9 36.9 1.0 C C:CYS608 4.9 43.9 1.0 O C:CYS629 5.0 32.8 1.0

Zinc binding site 6 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:41.5 occ:1.00 ND1 C:HIS625 2.1 32.8 1.0 SG C:CYS644 2.3 45.8 1.0 SG C:CYS623 2.3 37.2 1.0 SG C:CYS647 2.3 47.5 1.0 CE1 C:HIS625 3.0 35.3 1.0 CB C:CYS644 3.1 41.5 1.0 CG C:HIS625 3.1 33.0 1.0 CB C:CYS623 3.1 35.2 1.0 CB C:HIS625 3.5 33.1 1.0 CB C:CYS647 3.5 46.5 1.0 N C:CYS647 3.9 51.7 1.0 NE2 C:HIS625 4.1 34.2 1.0 CD2 C:HIS625 4.2 35.1 1.0 CA C:CYS647 4.3 50.0 1.0 N C:HIS625 4.5 34.5 1.0 CA C:CYS623 4.5 34.8 1.0 CA C:CYS644 4.5 43.4 1.0 CA C:HIS625 4.6 35.1 1.0 CB C:VAL646 4.7 50.3 1.0 C C:CYS623 4.7 37.2 1.0 C C:CYS647 4.9 46.3 1.0 CB C:THR649 4.9 43.4 1.0 C C:VAL646 4.9 55.0 1.0 O C:CYS623 4.9 42.2 1.0

Zinc binding site 7 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:49.0 occ:1.00 SG D:CYS632 2.2 44.1 1.0 SG D:CYS629 2.3 47.6 1.0 SG D:CYS608 2.4 50.2 1.0 SG D:CYS611 2.4 58.4 1.0 CB D:CYS632 3.1 47.5 1.0 CB D:CYS608 3.3 51.8 1.0 CB D:CYS629 3.4 42.7 1.0 CB D:CYS611 3.4 58.9 1.0 N D:CYS611 3.8 56.8 1.0 N D:CYS629 3.8 41.8 1.0 N D:CYS632 4.1 45.1 1.0 CA D:CYS629 4.2 41.5 1.0 CA D:CYS632 4.2 45.4 1.0 CA D:CYS611 4.2 61.0 1.0 CB D:ILE610 4.6 55.4 1.0 CA D:CYS608 4.7 49.9 1.0 C D:CYS629 4.7 39.7 1.0 CB D:ASN614 4.8 60.0 1.0 O D:CYS629 4.8 44.1 1.0 ND2 D:ASN614 4.8 63.0 1.0 C D:ILE610 4.9 54.0 1.0

Zinc binding site 8 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:39.7 occ:1.00 ND1 D:HIS625 2.1 38.0 1.0 SG D:CYS647 2.3 47.3 1.0 SG D:CYS623 2.3 37.4 1.0 SG D:CYS644 2.3 44.0 1.0 CB D:CYS644 3.0 45.0 1.0 CE1 D:HIS625 3.1 40.5 1.0 CG D:HIS625 3.1 35.0 1.0 CB D:CYS623 3.1 39.2 1.0 CB D:HIS625 3.4 37.7 1.0 CB D:CYS647 3.6 46.6 1.0 N D:CYS647 4.0 40.1 1.0 NE2 D:HIS625 4.2 37.5 1.0 CD2 D:HIS625 4.2 36.9 1.0 CA D:CYS647 4.3 45.7 1.0 N D:HIS625 4.4 41.5 1.0 CA D:CYS623 4.5 39.3 1.0 CA D:CYS644 4.5 47.6 1.0 CA D:HIS625 4.5 38.5 1.0 CB D:VAL646 4.7 41.7 1.0 C D:CYS623 4.7 36.9 1.0 O D:CYS623 4.9 34.8 1.0 C D:CYS647 5.0 49.8 1.0

Zinc binding site 9 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:39.3 occ:1.00 SG E:CYS629 2.2 35.4 1.0 SG E:CYS632 2.2 43.0 1.0 SG E:CYS611 2.3 47.4 1.0 SG E:CYS608 2.3 40.8 1.0 CB E:CYS608 3.1 43.5 1.0 CB E:CYS632 3.2 39.8 1.0 CB E:CYS611 3.5 43.7 1.0 CB E:CYS629 3.5 39.3 1.0 N E:CYS611 3.9 44.8 1.0 N E:CYS629 4.1 39.1 1.0 N E:CYS632 4.2 41.6 1.0 CA E:CYS632 4.3 38.6 1.0 CA E:CYS611 4.3 45.3 1.0 CA E:CYS629 4.3 38.5 1.0 CA E:CYS608 4.5 41.3 1.0 CB E:ILE610 4.6 42.3 1.0 ND2 E:ASN614 4.7 64.6 1.0 CB E:ASN614 4.8 59.0 1.0 C E:ILE610 4.9 40.7 1.0 C E:CYS629 4.9 40.0 1.0 O E:CYS629 5.0 39.9 1.0 N E:ILE610 5.0 39.0 1.0 N E:ASN614 5.0 50.9 1.0

Zinc binding site 10 out of 16 in the The Ring Domain Structure of Mex-3C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Ring Domain Structure of Mex-3C within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:37.0 occ:1.00 ND1 E:HIS625 2.1 32.8 1.0 SG E:CYS623 2.3 34.1 1.0 SG E:CYS644 2.3 34.2 1.0 SG E:CYS647 2.3 39.4 1.0 CE1 E:HIS625 3.0 34.9 1.0 CB E:CYS644 3.0 36.3 1.0 CG E:HIS625 3.1 32.8 1.0 CB E:CYS623 3.2 35.3 1.0 CB E:HIS625 3.5 34.6 1.0 CB E:CYS647 3.5 38.5 1.0 N E:CYS647 3.9 44.8 1.0 NE2 E:HIS625 4.2 36.6 1.0 CD2 E:HIS625 4.2 32.8 1.0 CA E:CYS647 4.2 46.4 1.0 N E:HIS625 4.5 33.9 1.0 CA E:CYS644 4.5 39.9 1.0 CA E:HIS625 4.6 34.2 1.0 CA E:CYS623 4.6 33.6 1.0 CB E:VAL646 4.6 44.8 1.0 C E:VAL646 4.9 44.0 1.0 C E:CYS623 4.9 38.7 1.0 C E:CYS647 4.9 47.3 1.0 CB E:THR649 4.9 44.7 1.0

S.A.Moududee, Y.Jiang, N.Gilbert, G.Xie, Z.Xu, J.Wu, Q.Gong, Y.Tang, Y.Shi. Structural and Functional Characterization of Hmex-3C Ring Finger Domain As An E3 Ubiquitin Ligase Protein Sci. V. 27 1661 2018.
ISSN: ESSN 1469-896X
PubMed: 30095198
DOI: 10.1002/PRO.3473