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

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

The binding sites of Zinc atom in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer Without A Ligand (pdb code 9hfq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer Without A Ligand, PDB code: 9hfq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer 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): Trimer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:74.0 occ:1.00 OE1 A:GLU157 2.0 15.8 1.0 ND1 A:HIS109 2.0 9.1 1.0 SG A:CYS137 2.3 3.6 1.0 SG A:CYS134 2.3 7.4 1.0 CE1 A:HIS109 2.9 6.6 1.0 CD A:GLU157 3.0 7.9 1.0 CG A:HIS109 3.1 9.1 1.0 CB A:CYS137 3.4 3.6 1.0 CB A:CYS134 3.4 4.5 1.0 OE2 A:GLU157 3.5 15.5 1.0 CB A:HIS109 3.5 10.8 1.0 N A:CYS134 3.9 10.1 1.0 NE2 A:HIS109 4.0 8.0 1.0 N A:CYS137 4.1 9.1 1.0 CG A:GLU157 4.1 11.3 1.0 CD2 A:HIS109 4.2 4.0 1.0 CA A:CYS134 4.2 8.3 1.0 NE2 A:GLN112 4.3 6.7 1.0 CA A:CYS137 4.3 4.5 1.0 CD A:GLN112 4.8 8.8 1.0 C A:CYS134 4.8 8.6 1.0 CB A:GLU157 4.9 14.6 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer 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): Trimer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:124.8 occ:1.00 ND1 A:HIS398 2.0 16.2 1.0 O A:HOH701 2.1 5.7 1.0 SG A:CYS426 2.3 6.3 1.0 SG A:CYS429 2.3 4.3 1.0 CE1 A:HIS398 3.0 8.8 1.0 CG A:HIS398 3.0 9.1 1.0 CB A:CYS426 3.2 13.2 1.0 CB A:HIS398 3.4 14.0 1.0 N A:CYS426 3.6 5.7 1.0 CB A:CYS429 3.7 6.2 1.0 CA A:CYS426 4.0 11.1 1.0 NE2 A:HIS398 4.1 9.7 1.0 CD2 A:HIS398 4.1 14.1 1.0 CD1 A:ILE455 4.6 39.4 1.0 C A:PRO425 4.7 9.9 1.0 N A:CYS429 4.7 9.3 1.0 CA A:HIS398 4.8 15.7 1.0 C A:CYS426 4.8 9.3 1.0 CA A:CYS429 4.8 7.3 1.0 CA A:PRO425 4.8 7.3 1.0 CG A:GLU428 5.0 21.5 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer 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): Trimer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:85.1 occ:1.00 OE1 B:GLU157 2.0 9.2 1.0 ND1 B:HIS109 2.0 8.5 1.0 SG B:CYS137 2.3 18.5 1.0 SG B:CYS134 2.3 7.6 1.0 CE1 B:HIS109 2.9 6.5 1.0 CG B:HIS109 3.1 10.1 1.0 CD B:GLU157 3.1 8.4 1.0 CB B:CYS134 3.4 9.0 1.0 CB B:HIS109 3.5 7.6 1.0 CB B:CYS137 3.6 20.3 1.0 OE2 B:GLU157 3.7 15.1 1.0 N B:CYS134 3.8 16.8 1.0 NE2 B:HIS109 4.0 5.5 1.0 CD2 B:HIS109 4.1 11.0 1.0 CA B:CYS134 4.2 9.7 1.0 NE2 B:GLN112 4.2 10.7 1.0 N B:CYS137 4.3 19.0 1.0 CG B:GLU157 4.3 15.0 1.0 CB B:GLU157 4.4 6.9 1.0 CA B:CYS137 4.6 18.7 1.0 C B:CYS134 4.8 8.5 1.0 CD B:GLN112 4.9 5.7 1.0 C B:PRO133 4.9 6.1 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer 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): Trimer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:113.9 occ:1.00 ND1 B:HIS398 2.0 2.1 1.0 O B:HOH701 2.1 1.6 1.0 SG B:CYS426 2.3 7.7 1.0 SG B:CYS429 2.3 2.3 1.0 CE1 B:HIS398 3.0 3.0 1.0 CG B:HIS398 3.0 4.6 1.0 CB B:CYS426 3.2 9.0 1.0 CB B:HIS398 3.4 7.4 1.0 CB B:CYS429 3.4 8.0 1.0 N B:CYS426 3.7 11.2 1.0 CA B:CYS426 4.0 11.9 1.0 NE2 B:HIS398 4.1 1.3 1.0 CD2 B:HIS398 4.1 6.8 1.0 N B:CYS429 4.3 5.8 1.0 CA B:CYS429 4.5 5.5 1.0 CD1 B:ILE455 4.6 46.5 1.0 NE2 B:GLN401 4.8 3.2 1.0 C B:CYS426 4.8 11.2 1.0 C B:PRO425 4.8 13.8 1.0 CA B:HIS398 4.8 5.1 1.0 O B:CYS426 5.0 14.0 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer 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): Trimer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:79.9 occ:1.00 OE1 C:GLU157 2.0 9.9 1.0 ND1 C:HIS109 2.0 12.0 1.0 SG C:CYS137 2.3 12.3 1.0 SG C:CYS134 2.3 13.6 1.0 CE1 C:HIS109 2.9 14.3 1.0 CG C:HIS109 3.1 17.8 1.0 CD C:GLU157 3.1 13.8 1.0 CB C:CYS137 3.4 18.2 1.0 CB C:HIS109 3.5 18.9 1.0 CB C:CYS134 3.5 12.0 1.0 OE2 C:GLU157 3.6 15.5 1.0 N C:CYS134 3.8 13.5 1.0 NE2 C:HIS109 4.1 10.4 1.0 CD2 C:HIS109 4.1 10.6 1.0 N C:CYS137 4.2 15.4 1.0 CA C:CYS134 4.2 8.2 1.0 NE2 C:GLN112 4.2 7.7 1.0 CG C:GLU157 4.4 8.9 1.0 CA C:CYS137 4.4 16.2 1.0 CB C:GLU157 4.5 8.8 1.0 CD C:GLN112 4.8 3.6 1.0 C C:CYS134 4.9 9.5 1.0 C C:PRO133 5.0 5.4 1.0 CA C:HIS109 5.0 13.8 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer 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): Trimer Without A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:100.5 occ:1.00 ND1 C:HIS398 2.0 8.8 1.0 O C:HOH701 2.2 6.4 1.0 SG C:CYS426 2.3 20.6 1.0 SG C:CYS429 2.3 4.2 1.0 CG C:HIS398 3.0 7.0 1.0 CE1 C:HIS398 3.0 11.2 1.0 CB C:CYS429 3.2 8.6 1.0 CB C:HIS398 3.3 8.7 1.0 CB C:CYS426 3.4 24.4 1.0 N C:CYS426 3.8 21.3 1.0 N C:CYS429 4.1 11.4 1.0 NE2 C:HIS398 4.1 4.4 1.0 CA C:CYS426 4.1 15.9 1.0 CD2 C:HIS398 4.1 5.0 1.0 CA C:CYS429 4.2 4.7 1.0 NE2 C:GLN401 4.6 7.8 1.0 CA C:HIS398 4.8 12.0 1.0 C C:CYS426 4.8 17.9 1.0 CD1 C:ILE455 4.9 39.0 1.0 C C:GLU428 4.9 14.3 1.0 C C:PRO425 4.9 10.7 1.0 O C:CYS426 4.9 18.8 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.