Zinc in PDB 4pfb: Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate, PDB code: 4pfb was solved by M.W.Vetting, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, M.Stead, J.D.Attonito, A.Scott Glenn, S.Chowdhury, B.Evans, B.Hillerich, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative(Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.15 / 2.70
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.574, 113.574, 79.937, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.4

The binding sites of Zinc atom in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate (pdb code 4pfb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate, PDB code: 4pfb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate


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 A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.8 occ:1.00 OD2 A:ASP35 1.9 38.7 1.0 N3 A:IMD405 2.1 54.2 1.0 N3 A:IMD406 2.2 34.6 1.0 C2 A:IMD405 2.3 54.9 1.0 C2 A:IMD406 2.7 32.8 1.0 CG A:ASP35 2.7 34.7 1.0 OD1 A:ASP35 2.9 30.1 1.0 C4 A:IMD405 3.4 55.6 1.0 C4 A:IMD406 3.5 34.4 1.0 N1 A:IMD405 3.6 56.8 1.0 N1 A:IMD406 4.0 34.2 1.0 OG1 A:THR64 4.1 20.2 1.0 CB A:ASP35 4.1 24.3 1.0 C5 A:IMD405 4.1 56.0 1.0 C5 A:IMD406 4.4 35.2 1.0 O A:HOH504 4.6 23.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate


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 A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:63.1 occ:1.00 OE2 A:GLU48 2.0 99.1 1.0 OE1 A:GLU48 2.1 94.3 1.0 CD A:GLU48 2.4 96.3 1.0 O A:HOH513 3.6 30.4 1.0 CG A:GLU48 3.9 25.2 1.0 CB A:GLU48 4.8 24.4 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate


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 A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:90.3 occ:1.00 OD2 A:ASP305 2.1 75.2 1.0 OD1 A:ASP305 2.1 73.9 1.0 CG A:ASP305 2.5 75.4 1.0 CB A:ASP305 4.0 54.9 1.0 O A:HOH515 4.5 30.8 0.5 O A:ALA301 4.7 54.5 1.0 N A:ASP305 4.7 53.1 1.0 CA A:ASP305 4.8 53.7 1.0 C A:TYR304 4.8 54.5 1.0 CB A:TYR304 4.9 51.2 1.0 O A:TYR304 5.0 55.6 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate


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 A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:95.7 occ:1.00 ND1 A:HIS289 2.1 68.4 1.0 CE1 A:HIS289 2.9 68.6 1.0 CG A:HIS289 3.2 63.6 1.0 CB A:HIS289 3.7 61.3 1.0 CA A:HIS289 4.0 45.2 1.0 NE2 A:HIS289 4.1 65.8 1.0 CD2 A:HIS289 4.2 62.7 1.0 O A:PHE288 4.5 43.9 1.0 CB A:PRO155 4.6 46.2 1.0 CG A:PRO155 4.8 48.2 1.0 N A:HIS289 5.0 43.6 1.0 N A:GLU290 5.0 56.2 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate


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 A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatun (FN1258, Target Efi-510120) with Bound Sn- Glycerol-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:78.7 occ:1.00 OE2 A:GLU113 2.0 79.8 1.0 OE1 A:GLU113 2.2 75.2 1.0 CD A:GLU113 2.3 73.2 1.0 CG A:GLU113 3.7 61.5 1.0 NE A:ARG117 4.2 40.0 1.0 NH2 A:ARG117 4.2 39.3 1.0 CZ A:ARG117 4.7 41.4 1.0 CB A:GLU113 4.9 49.7 1.0 CG A:ARG117 5.0 33.6 1.0

M.W.Vetting, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, M.Stead, J.D.Attonito, A.Scott Glenn, S.Chowdhury, B.Evans, B.Hillerich, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Trap Periplasmic Solute Binding Protein From Fusobacterium Nucleatum (FN1258, Target Efi-510120) with Bound Sn-Glycerol-3-Phosphate To Be Published.