Zinc in PDB 9hfr: Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand

All present enzymatic activity of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand:
3.5.4.5;

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand (pdb code 9hfr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand, PDB code: 9hfr:
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 Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:70.7 occ:1.00 ND1 A:HIS109 2.0 22.3 1.0 SG A:CYS137 2.3 32.0 1.0 OE1 A:GLU157 2.3 25.4 1.0 SG A:CYS134 2.3 22.1 1.0 CD A:GLU157 2.4 30.3 1.0 OE2 A:GLU157 2.5 37.3 1.0 CG A:HIS109 2.8 22.2 1.0 CE1 A:HIS109 2.9 21.6 1.0 CB A:HIS109 3.2 14.2 1.0 CG A:GLU157 3.6 24.9 1.0 CB A:CYS134 3.7 17.9 1.0 CB A:CYS137 3.7 12.9 1.0 CD2 A:HIS109 3.8 24.6 1.0 NE2 A:HIS109 3.8 20.6 1.0 N A:CYS134 3.9 23.9 1.0 CB A:GLU157 4.3 23.4 1.0 CA A:CYS134 4.4 20.6 1.0 CA A:HIS109 4.7 13.6 1.0 N A:CYS137 4.9 24.6 1.0 CA A:CYS137 4.9 18.6 1.0 C A:PRO133 4.9 22.1 1.0 CA A:PRO133 5.0 17.0 1.0

Zinc binding site 2 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:84.5 occ:1.00 ND1 A:HIS398 2.0 25.4 1.0 O A:HOH701 2.1 26.9 1.0 SG A:CYS426 2.3 27.6 1.0 SG A:CYS429 2.3 31.1 1.0 CG A:HIS398 2.8 16.7 1.0 CB A:HIS398 3.0 14.2 1.0 CE1 A:HIS398 3.1 24.4 1.0 CB A:CYS426 3.6 26.7 1.0 CB A:CYS429 3.8 16.2 1.0 N A:CYS426 3.8 31.0 1.0 CD2 A:HIS398 3.9 18.6 1.0 NE2 A:HIS398 4.0 21.2 1.0 CA A:CYS426 4.3 30.4 1.0 CA A:HIS398 4.4 15.8 1.0 N A:CYS429 4.8 24.5 1.0 CD1 A:ILE455 4.8 48.6 1.0 C A:PRO425 4.8 31.8 1.0 CA A:CYS429 4.9 13.7 1.0 CA A:PRO425 4.9 25.2 1.0 NE2 A:GLN401 5.0 20.5 1.0

Zinc binding site 3 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:70.7 occ:1.00 OE1 B:GLU157 2.0 31.3 1.0 ND1 B:HIS109 2.0 21.4 1.0 SG B:CYS137 2.3 37.7 1.0 SG B:CYS134 2.3 27.3 1.0 CD B:GLU157 2.6 30.5 1.0 CE1 B:HIS109 2.9 22.2 1.0 CG B:HIS109 3.0 25.0 1.0 OE2 B:GLU157 3.1 37.5 1.0 CB B:CYS137 3.4 15.3 1.0 CB B:HIS109 3.4 12.4 1.0 CB B:CYS134 3.5 16.6 1.0 CG B:GLU157 3.6 25.1 1.0 N B:CYS134 3.7 30.1 1.0 NE2 B:HIS109 4.0 26.1 1.0 CD2 B:HIS109 4.0 30.1 1.0 CB B:GLU157 4.2 23.0 1.0 CA B:CYS134 4.2 21.7 1.0 CA B:CYS137 4.7 20.4 1.0 N B:CYS137 4.7 30.2 1.0 C B:PRO133 4.8 27.5 1.0 CA B:HIS109 4.8 11.0 1.0 CA B:PRO133 4.9 17.0 1.0

Zinc binding site 4 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:89.5 occ:1.00 ND1 B:HIS398 2.0 31.1 1.0 O B:HOH701 2.2 28.2 1.0 SG B:CYS426 2.3 32.3 1.0 SG B:CYS429 2.3 28.1 1.0 CG B:HIS398 2.7 22.0 1.0 CB B:HIS398 2.9 19.6 1.0 CE1 B:HIS398 3.1 25.6 1.0 CB B:CYS426 3.6 23.9 1.0 N B:CYS426 3.8 31.7 1.0 CB B:CYS429 3.8 14.7 1.0 CD2 B:HIS398 3.8 21.2 1.0 NE2 B:HIS398 4.0 23.4 1.0 CA B:HIS398 4.3 15.1 1.0 CA B:CYS426 4.3 26.4 1.0 N B:CYS429 4.8 19.2 1.0 N B:ALA399 4.9 18.1 1.0 C B:PRO425 4.9 33.6 1.0 CD1 B:ILE455 4.9 47.0 1.0 CA B:CYS429 5.0 9.9 1.0 CA B:PRO425 5.0 23.6 1.0

Zinc binding site 5 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:74.0 occ:1.00 OE1 C:GLU157 2.0 32.8 1.0 ND1 C:HIS109 2.0 19.5 1.0 SG C:CYS137 2.3 34.2 1.0 SG C:CYS134 2.3 30.3 1.0 CD C:GLU157 2.6 32.6 1.0 CE1 C:HIS109 2.8 21.7 1.0 OE2 C:GLU157 3.1 38.1 1.0 CG C:HIS109 3.1 21.9 1.0 CB C:CYS134 3.3 20.7 1.0 CB C:CYS137 3.4 16.1 1.0 N C:CYS134 3.5 26.9 1.0 CB C:HIS109 3.6 11.9 1.0 CG C:GLU157 3.6 29.5 1.0 NE2 C:HIS109 4.0 23.8 1.0 CA C:CYS134 4.0 19.4 1.0 CD2 C:HIS109 4.1 24.5 1.0 CB C:GLU157 4.2 26.2 1.0 C C:PRO133 4.6 29.1 1.0 CA C:CYS137 4.6 22.2 1.0 N C:CYS137 4.6 24.5 1.0 CA C:PRO133 4.7 20.5 1.0 C C:CYS134 4.9 20.4 1.0

Zinc binding site 6 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:92.7 occ:1.00 ND1 C:HIS398 2.0 34.9 1.0 O C:HOH701 2.2 25.8 1.0 SG C:CYS426 2.3 28.8 1.0 SG C:CYS429 2.3 27.3 1.0 CG C:HIS398 2.7 25.9 1.0 CB C:HIS398 2.9 20.2 1.0 CE1 C:HIS398 3.1 27.8 1.0 CB C:CYS426 3.7 27.0 1.0 CB C:CYS429 3.8 18.6 1.0 CD2 C:HIS398 3.8 25.7 1.0 N C:CYS426 3.9 35.3 1.0 NE2 C:HIS398 4.0 26.9 1.0 CA C:HIS398 4.3 16.9 1.0 CA C:CYS426 4.4 30.6 1.0 N C:CYS429 4.8 28.1 1.0 N C:ALA399 4.9 19.9 1.0 CA C:CYS429 4.9 15.0 1.0 C C:PRO425 4.9 33.7 1.0 C C:HIS398 5.0 23.7 1.0 CA C:PRO425 5.0 28.2 1.0

Zinc binding site 7 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:66.1 occ:1.00 OE1 D:GLU157 2.0 37.5 1.0 ND1 D:HIS109 2.0 22.5 1.0 SG D:CYS137 2.3 33.4 1.0 SG D:CYS134 2.3 22.4 1.0 CG D:HIS109 2.9 24.0 1.0 CD D:GLU157 2.9 32.2 1.0 CE1 D:HIS109 2.9 23.0 1.0 CB D:HIS109 3.3 15.8 1.0 OE2 D:GLU157 3.3 32.6 1.0 CB D:CYS137 3.6 16.5 1.0 CB D:CYS134 3.7 19.3 1.0 NE2 D:HIS109 3.9 24.2 1.0 CD2 D:HIS109 3.9 26.4 1.0 N D:CYS134 3.9 23.0 1.0 CG D:GLU157 4.1 26.3 1.0 CB D:GLU157 4.2 27.6 1.0 CA D:CYS134 4.4 22.5 1.0 N D:CYS137 4.7 26.8 1.0 CA D:HIS109 4.7 16.7 1.0 CA D:CYS137 4.8 22.8 1.0 NE2 D:GLN112 4.9 22.7 1.0

Zinc binding site 8 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:90.1 occ:1.00 ND1 D:HIS398 2.0 33.6 1.0 O D:HOH701 2.1 29.1 1.0 SG D:CYS426 2.3 34.6 1.0 SG D:CYS429 2.3 27.4 1.0 CG D:HIS398 2.7 25.4 1.0 CB D:HIS398 3.0 22.7 1.0 CE1 D:HIS398 3.0 27.4 1.0 CB D:CYS426 3.6 28.8 1.0 CB D:CYS429 3.8 21.4 1.0 N D:CYS426 3.8 36.2 1.0 CD2 D:HIS398 3.8 24.6 1.0 NE2 D:HIS398 4.0 27.6 1.0 CA D:CYS426 4.3 31.9 1.0 CA D:HIS398 4.4 18.0 1.0 N D:CYS429 4.8 28.6 1.0 C D:PRO425 4.9 35.5 1.0 CA D:CYS429 4.9 17.3 1.0 CD1 D:ILE455 4.9 51.4 1.0 CA D:PRO425 4.9 27.3 1.0

Zinc binding site 9 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:70.6 occ:1.00 OE1 E:GLU157 2.0 35.7 1.0 ND1 E:HIS109 2.0 26.2 1.0 SG E:CYS137 2.3 33.4 1.0 SG E:CYS134 2.3 23.9 1.0 CG E:HIS109 2.8 26.4 1.0 CE1 E:HIS109 2.9 27.0 1.0 CD E:GLU157 3.1 32.6 1.0 CB E:HIS109 3.2 19.0 1.0 CB E:CYS134 3.7 20.6 1.0 OE2 E:GLU157 3.7 32.7 1.0 CD2 E:HIS109 3.7 29.2 1.0 CB E:CYS137 3.8 18.0 1.0 NE2 E:HIS109 3.8 27.9 1.0 N E:CYS134 4.0 27.0 1.0 CG E:GLU157 4.3 28.5 1.0 CB E:GLU157 4.3 25.6 1.0 CA E:CYS134 4.5 23.6 1.0 CA E:HIS109 4.6 18.3 1.0 N E:CYS137 4.7 28.6 1.0 CA E:CYS137 4.8 22.5 1.0 NE2 E:GLN112 4.9 26.9 1.0

Zinc binding site 10 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn602 b:90.6 occ:1.00 ND1 E:HIS398 2.0 31.9 1.0 O E:HOH701 2.2 33.2 1.0 SG E:CYS426 2.3 32.1 1.0 SG E:CYS429 2.3 34.2 1.0 CG E:HIS398 2.7 23.1 1.0 CB E:HIS398 3.0 20.8 1.0 CE1 E:HIS398 3.0 28.2 1.0 CB E:CYS426 3.6 30.1 1.0 CB E:CYS429 3.8 21.0 1.0 CD2 E:HIS398 3.8 23.3 1.0 N E:CYS426 3.9 34.3 1.0 NE2 E:HIS398 3.9 25.6 1.0 CA E:CYS426 4.4 34.2 1.0 CA E:HIS398 4.4 18.7 1.0 N E:CYS429 4.7 31.6 1.0 CD1 E:ILE455 4.8 48.6 1.0 CA E:CYS429 4.9 16.6 1.0 C E:PRO425 5.0 34.5 1.0

A.Slyvka, I.Rathore, R.Yang, T.Kanai, G.Lountos, Z.Wang, K.Skowronek, M.Czarnocki-Cieciura, A.Wlodawer, M.Bochtler. Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer Without A Ligand To Be Published 2025.