Zinc in PDB 5ysb: Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form

The structure of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form, PDB code: 5ysb was solved by K.Abe, M.Nakajima, H.Taguchi, T.Arakawa, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.24 / 2.20
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	74.925, 74.925, 120.844, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form (pdb code 5ysb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form, PDB code: 5ysb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


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 Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:40.0 occ:1.00 OE2 A:GLU100 1.8 48.0 1.0 NE2 A:HIS75 1.8 35.7 1.0 ND1 A:HIS418 1.9 63.7 1.0 NE2 B:HIS417 2.3 69.8 1.0 CE1 A:HIS418 2.5 58.6 1.0 CE1 A:HIS75 2.6 40.7 1.0 CD A:GLU100 2.7 37.2 1.0 OE1 A:GLU100 2.9 32.5 1.0 CD2 A:HIS75 3.1 41.1 1.0 CE1 B:HIS417 3.1 69.8 1.0 CG A:HIS418 3.1 62.6 1.0 CD2 B:HIS417 3.4 65.5 1.0 CA A:HIS418 3.6 58.5 1.0 NE2 A:HIS418 3.7 65.6 1.0 CB A:HIS418 3.7 58.5 1.0 ND1 A:HIS75 3.8 38.2 1.0 N A:HIS418 4.0 56.8 1.0 CG A:HIS75 4.1 42.0 1.0 CD2 A:HIS418 4.1 65.5 1.0 CG A:GLU100 4.1 41.4 1.0 CD1 A:LEU79 4.3 54.8 1.0 ND1 B:HIS417 4.3 67.3 1.0 CG B:HIS417 4.4 66.2 1.0 NE2 A:HIS420 4.6 59.6 1.0 C A:HIS418 4.7 54.5 1.0 O A:HIS418 5.0 64.7 1.0

Zinc binding site 2 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


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 Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:49.6 occ:1.00 OE1 A:GLU51 2.1 64.9 1.0 OD2 A:ASP335 2.1 76.5 1.0 CG A:ASP335 2.6 50.5 1.0 CD A:GLU51 2.7 60.1 1.0 OD1 A:ASP335 2.8 48.5 1.0 OE2 A:GLU51 2.8 55.6 1.0 CB A:ASP335 3.9 54.2 1.0 CG A:GLU51 4.2 67.0 1.0 CD1 A:LEU52 4.3 67.4 1.0 CB A:GLU51 4.7 67.1 1.0

Zinc binding site 3 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


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 Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:73.5 occ:1.00 O B:HOH708 2.4 61.1 1.0 NE2 A:HIS418 2.5 65.6 1.0 CD2 A:HIS418 3.3 65.5 1.0 OD1 B:ASP76 3.4 59.3 1.0 CE1 A:HIS418 3.5 58.6 1.0 OD2 B:ASP76 3.9 72.1 1.0 CG B:ASP76 4.0 60.1 1.0 CG A:HIS418 4.5 62.6 1.0 CE1 B:HIS75 4.5 38.0 1.0 ND1 A:HIS418 4.6 63.7 1.0 ND1 B:HIS75 4.6 37.0 1.0 CG A:GLU378 4.6 53.6 1.0 CB A:HIS417 4.7 60.8 1.0 CG A:HIS417 4.8 67.1 1.0 CD2 A:HIS417 4.8 68.1 1.0 OE1 A:GLU378 5.0 80.8 1.0

Zinc binding site 4 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


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 Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:66.3 occ:1.00 OE1 B:GLU416 1.8 62.9 1.0 ND1 A:HIS420 2.1 64.9 1.0 OE2 B:GLU416 2.3 63.5 1.0 CD B:GLU416 2.3 67.2 1.0 O B:HOH703 2.4 56.1 1.0 O B:HOH605 2.4 55.4 1.0 CE1 A:HIS420 2.9 65.3 1.0 CG A:HIS420 3.2 56.2 1.0 CB A:HIS420 3.7 57.8 1.0 CG B:GLU416 3.8 69.1 1.0 CE B:LYS414 4.0 90.7 1.0 NE2 A:HIS420 4.1 59.6 1.0 CD2 A:HIS420 4.3 60.4 1.0 CA A:HIS420 4.4 62.1 1.0 CB B:GLU416 4.6 75.1 1.0 O A:HIS419 4.9 63.2 1.0 CD B:LYS414 4.9 88.5 1.0

Zinc binding site 5 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


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 Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:79.2 occ:1.00 OD1 A:ASN271 2.5 52.1 1.0 OD2 A:ASP275 2.5 56.1 1.0 O A:HOH688 2.8 54.5 1.0 OD1 A:ASP275 3.0 52.1 1.0 CG A:ASP275 3.1 58.2 1.0 CG A:ASN271 3.5 50.0 1.0 ND2 A:ASN271 3.9 48.3 1.0 CB A:ASP275 4.6 59.7 1.0 CB A:ASN271 4.8 46.3 1.0 O A:ASN271 4.8 43.8 1.0

Zinc binding site 6 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:84.7 occ:1.00 OE2 A:GLU388 2.3 60.2 1.0 OE1 A:GLU388 2.7 56.2 1.0 CD A:GLU388 2.8 55.0 1.0 NH2 A:ARG392 3.3 85.4 1.0 NZ B:LYS77 3.3 70.2 1.0 CE B:LYS77 4.0 66.7 1.0 NE2 B:GLN67 4.1 94.1 1.0 CG A:GLU388 4.3 52.8 1.0 CZ A:ARG392 4.4 78.7 1.0 NZ A:LYS385 4.5 55.3 1.0 O A:HOH605 4.8 46.7 1.0 CZ2 B:TRP40 4.9 48.6 1.0

Zinc binding site 7 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:54.1 occ:0.75 OE1 A:GLU347 2.1 67.8 1.0 O A:HOH686 2.3 45.0 1.0 OE2 A:GLU347 2.6 65.2 1.0 CD A:GLU347 2.7 63.2 1.0 CD A:LYS352 4.1 58.5 1.0 CG A:GLU347 4.1 60.0 1.0 NZ A:LYS352 4.5 56.4 1.0 CB A:GLU347 4.7 56.9 1.0 CA A:GLU347 4.9 55.1 1.0 CE A:LYS352 4.9 57.9 1.0

Zinc binding site 8 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:0.3 occ:1.00 OE1 A:GLU293 2.4 63.7 1.0 CD A:GLU293 3.4 57.6 1.0 OE2 A:GLU293 3.6 66.5 1.0 O A:ASN207 4.2 41.4 1.0 CG A:GLU293 4.7 51.1 1.0 CA A:GLY208 4.8 39.0 1.0

Zinc binding site 9 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:85.4 occ:1.00 OG A:SER48 3.8 55.6 1.0 O A:HOH684 3.9 50.6 1.0 N A:SER48 4.2 57.6 1.0 CB A:SER48 4.4 48.8 1.0 N A:LYS47 4.4 69.4 1.0 CB A:LYS47 4.6 78.5 1.0 CG2 A:THR336 4.9 43.4 1.0 CB A:GLU45 4.9 99.9 1.0 CA A:LYS47 4.9 70.7 1.0 CA A:SER48 4.9 56.0 1.0 O A:ASP335 5.0 66.0 1.0

Zinc binding site 10 out of 24 in the Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Beta-1,2-Glucooligosaccharide Binding Protein in Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:0.3 occ:1.00 OD1 A:ASP396 2.0 63.4 1.0 O A:HOH673 2.9 53.9 1.0 CG A:ASP396 3.1 55.2 1.0 OD2 A:ASP396 3.6 52.4 1.0 O A:HOH664 4.2 52.0 1.0 CB A:ASP396 4.4 55.7 1.0

K.Abe, N.Sunagawa, T.Terada, Y.Takahashi, T.Arakawa, K.Igarashi, M.Samejima, H.Nakai, H.Taguchi, M.Nakajima, S.Fushinobu. Structural and Thermodynamic Insights Into Beta-1,2-Glucooligosaccharide Capture By A Solute-Binding Protein Inlisteria Innocua. J. Biol. Chem. V. 293 8812 2018.
ISSN: ESSN 1083-351X
PubMed: 29678880
DOI: 10.1074/JBC.RA117.001536