Zinc in PDB 7ufu: Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A

The binding sites of Zinc atom in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A (pdb code 7ufu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A, PDB code: 7ufu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


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 BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:79.2 occ:1.00 OD1 A:ASP277 2.0 56.0 1.0 NE2 A:HIS597 2.1 54.5 1.0 O2 A:MAN1102 2.2 60.7 1.0 O3 A:MAN1102 2.2 60.7 1.0 NE2 A:HIS275 2.3 53.6 1.0 CE1 A:HIS597 2.6 54.5 1.0 C2 A:MAN1102 2.9 60.7 1.0 CG A:ASP277 3.1 56.0 1.0 C3 A:MAN1102 3.1 60.7 1.0 CE1 A:HIS275 3.2 53.6 1.0 CD2 A:HIS275 3.2 53.6 1.0 CD2 A:HIS597 3.3 54.5 1.0 OD2 A:ASP277 3.5 56.0 1.0 ND1 A:HIS597 3.9 54.5 1.0 OD2 A:ASP598 3.9 55.1 1.0 C4 A:MAN1102 4.0 60.7 1.0 CB A:ALA387 4.1 53.3 1.0 CG A:HIS597 4.2 54.5 1.0 ND1 A:HIS275 4.3 53.6 1.0 CB A:ASP277 4.4 56.0 1.0 CG A:HIS275 4.4 53.6 1.0 C1 A:MAN1102 4.4 60.7 1.0 OH A:TYR445 4.8 51.7 1.0 O4 A:MAN1102 4.8 60.7 1.0 CG A:ASP598 4.9 55.1 1.0 CA A:ASP277 4.9 56.0 1.0 CZ A:PHE596 4.9 53.4 1.0 CE2 A:PHE596 5.0 53.4 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


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 BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:79.5 occ:1.00 OD1 B:ASP277 2.0 55.9 1.0 NE2 B:HIS597 2.1 54.3 1.0 O2 B:MAN1102 2.2 60.5 1.0 O3 B:MAN1102 2.2 60.5 1.0 NE2 B:HIS275 2.3 53.5 1.0 CE1 B:HIS597 2.6 54.3 1.0 C2 B:MAN1102 2.9 60.5 1.0 CG B:ASP277 3.1 55.9 1.0 C3 B:MAN1102 3.1 60.5 1.0 CE1 B:HIS275 3.2 53.5 1.0 CD2 B:HIS275 3.2 53.5 1.0 CD2 B:HIS597 3.3 54.3 1.0 OD2 B:ASP277 3.5 55.9 1.0 ND1 B:HIS597 3.9 54.3 1.0 OD2 B:ASP598 3.9 55.0 1.0 C4 B:MAN1102 4.0 60.5 1.0 CB B:ALA387 4.1 53.3 1.0 CG B:HIS597 4.2 54.3 1.0 ND1 B:HIS275 4.3 53.5 1.0 CB B:ASP277 4.4 55.9 1.0 CG B:HIS275 4.4 53.5 1.0 C1 B:MAN1102 4.4 60.5 1.0 OH B:TYR445 4.8 51.6 1.0 O4 B:MAN1102 4.8 60.5 1.0 CG B:ASP598 4.9 55.0 1.0 CA B:ASP277 4.9 55.9 1.0 CZ B:PHE596 4.9 53.2 1.0 CE2 B:PHE596 5.0 53.2 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


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 BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:79.6 occ:1.00 OD1 C:ASP277 2.0 56.2 1.0 NE2 C:HIS597 2.1 54.5 1.0 O2 C:MAN1102 2.2 60.9 1.0 O3 C:MAN1102 2.2 60.9 1.0 NE2 C:HIS275 2.3 53.7 1.0 CE1 C:HIS597 2.6 54.5 1.0 C2 C:MAN1102 2.9 60.9 1.0 CG C:ASP277 3.1 56.2 1.0 C3 C:MAN1102 3.1 60.9 1.0 CE1 C:HIS275 3.2 53.7 1.0 CD2 C:HIS275 3.2 53.7 1.0 CD2 C:HIS597 3.3 54.5 1.0 OD2 C:ASP277 3.5 56.2 1.0 ND1 C:HIS597 3.9 54.5 1.0 OD2 C:ASP598 3.9 55.3 1.0 C4 C:MAN1102 4.0 60.9 1.0 CB C:ALA387 4.1 53.2 1.0 CG C:HIS597 4.2 54.5 1.0 ND1 C:HIS275 4.3 53.7 1.0 CB C:ASP277 4.4 56.2 1.0 CG C:HIS275 4.4 53.7 1.0 C1 C:MAN1102 4.4 60.9 1.0 OH C:TYR445 4.8 51.6 1.0 O4 C:MAN1102 4.8 60.9 1.0 CG C:ASP598 4.9 55.3 1.0 CA C:ASP277 4.9 56.2 1.0 CZ C:PHE596 4.9 53.5 1.0 CE2 C:PHE596 5.0 53.5 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


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 BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1101 b:79.6 occ:1.00 OD1 D:ASP277 2.0 56.1 1.0 NE2 D:HIS597 2.1 54.5 1.0 O2 D:MAN1102 2.2 60.7 1.0 O3 D:MAN1102 2.2 60.7 1.0 NE2 D:HIS275 2.3 53.8 1.0 CE1 D:HIS597 2.6 54.5 1.0 C2 D:MAN1102 2.9 60.7 1.0 CG D:ASP277 3.1 56.1 1.0 C3 D:MAN1102 3.1 60.7 1.0 CE1 D:HIS275 3.2 53.8 1.0 CD2 D:HIS275 3.2 53.8 1.0 CD2 D:HIS597 3.3 54.5 1.0 OD2 D:ASP277 3.5 56.1 1.0 ND1 D:HIS597 3.9 54.5 1.0 OD2 D:ASP598 3.9 55.1 1.0 C4 D:MAN1102 4.0 60.7 1.0 CB D:ALA387 4.1 53.5 1.0 CG D:HIS597 4.2 54.5 1.0 ND1 D:HIS275 4.3 53.8 1.0 CB D:ASP277 4.4 56.1 1.0 CG D:HIS275 4.4 53.8 1.0 C1 D:MAN1102 4.4 60.7 1.0 OH D:TYR445 4.8 51.6 1.0 O4 D:MAN1102 4.8 60.7 1.0 CG D:ASP598 4.9 55.1 1.0 CA D:ASP277 4.9 56.1 1.0 CZ D:PHE596 4.9 53.3 1.0 CE2 D:PHE596 5.0 53.3 1.0

C.R.Santos, R.L.Cordeiro, M.N.Domingues, A.C.Borges, M.A.De Farias, M.Van Heel, M.T.Murakami, R.V.Portugal. Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A Nat.Chem.Biol. 2022.
ISSN: ESSN 1552-4469