Zinc in PDB 6hur: 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose

The structure of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose, PDB code: 6hur was solved by M.Ejby, M.Abou Hachem, L.Lo Leggio, T.Katayama, M.Sakanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.61 / 1.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	134.000, 134.000, 59.700, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 17.1

The binding sites of Zinc atom in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose (pdb code 6hur). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose, PDB code: 6hur:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:25.3 occ:0.68 OE1 A:GLU134 2.0 30.7 1.0 OE2 A:GLU134 2.0 26.5 1.0 NE2 A:HIS150 2.1 30.1 1.0 CD A:GLU134 2.1 27.3 1.0 CD2 A:HIS150 2.9 24.8 1.0 HD2 A:HIS150 3.1 29.8 1.0 CE1 A:HIS150 3.1 24.3 1.0 HE1 A:HIS150 3.4 29.2 1.0 CG A:GLU134 3.5 36.9 1.0 HG2 A:GLU134 3.5 44.3 1.0 HE1 A:TRP146 3.7 23.7 1.0 HG3 A:GLU134 4.0 44.3 1.0 O A:HOH608 4.0 35.9 1.0 CG A:HIS150 4.1 22.1 1.0 ND1 A:HIS150 4.1 19.6 1.0 NE1 A:TRP146 4.4 19.7 1.0 HB2 A:GLU134 4.4 29.0 1.0 CB A:GLU134 4.6 24.1 1.0 HD13 A:LEU155 4.8 25.0 1.0 HZ2 A:TRP146 4.8 23.7 1.0 HD1 A:HIS150 4.9 23.5 1.0 HB2 A:LEU155 4.9 19.3 1.0 HD22 A:LEU155 5.0 26.5 1.0

Zinc binding site 2 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:16.4 occ:0.88 OD2 A:ASP348 2.0 13.8 1.0 OD2 A:ASP350 2.0 21.2 1.0 O A:HOH998 2.2 14.1 1.0 OD1 A:ASP348 2.6 18.7 1.0 HB2 A:ASP350 2.6 20.6 1.0 CG A:ASP348 2.6 16.1 1.0 CG A:ASP350 2.9 18.7 1.0 H A:ASP350 3.0 17.1 1.0 CB A:ASP350 3.2 17.1 1.0 HE1 A:TRP344 3.4 18.8 1.0 N A:ASP350 3.8 14.2 1.0 HB3 A:ASP350 3.9 20.6 1.0 HZ2 A:TRP344 4.0 19.3 1.0 O A:HOH962 4.0 28.4 1.0 NE1 A:TRP344 4.0 15.7 1.0 CA A:ASP350 4.1 15.3 1.0 OD1 A:ASP350 4.1 24.8 1.0 CB A:ASP348 4.1 14.5 1.0 HB3 A:ASP348 4.4 17.4 1.0 HE3 A:LYS74 4.4 32.7 1.0 H A:ALA351 4.4 16.0 1.0 H A:LYS349 4.4 17.5 1.0 CZ2 A:TRP344 4.6 16.1 1.0 CE2 A:TRP344 4.6 14.6 1.0 HB2 A:ASP348 4.6 17.4 1.0 N A:LYS349 4.7 14.6 1.0 HA A:ASP350 4.8 18.4 1.0 HB2 A:LYS349 4.8 18.6 1.0 C A:ASP348 4.9 13.4 1.0 C A:LYS349 5.0 14.9 1.0 HG2 A:LYS74 5.0 20.2 1.0 N A:ALA351 5.0 13.4 1.0 CA A:ASP348 5.0 13.3 1.0

Zinc binding site 3 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:18.6 occ:0.60 O A:HOH969 2.0 29.9 1.0 NE2 A:HIS177 2.0 17.8 1.0 OD2 A:ASP199 2.1 28.2 1.0 O A:HOH1009 2.2 15.4 1.0 HB2 A:ASP199 2.9 25.5 1.0 CE1 A:HIS177 3.0 22.6 1.0 CD2 A:HIS177 3.1 18.3 1.0 CG A:ASP199 3.1 26.8 1.0 HE1 A:HIS177 3.1 27.1 1.0 HD2 A:HIS177 3.3 22.0 1.0 CB A:ASP199 3.4 21.2 1.0 HD2 A:LYS202 3.4 22.2 1.0 HB3 A:ASP199 3.6 25.5 1.0 HG2 A:GLU176 3.6 30.9 1.0 HE2 A:LYS202 3.9 24.4 1.0 HG23 A:ILE173 4.1 19.7 1.0 ND1 A:HIS177 4.1 20.6 1.0 HG3 A:GLU176 4.1 30.9 1.0 HE3 A:LYS202 4.2 24.4 1.0 CG A:HIS177 4.2 16.1 1.0 OD1 A:ASP199 4.2 24.7 1.0 CD A:LYS202 4.2 18.5 1.0 CE A:LYS202 4.3 20.3 1.0 CG A:GLU176 4.3 25.7 1.0 O A:HOH1034 4.4 42.0 1.0 HD11 A:LEU195 4.4 20.0 1.0 HD12 A:LEU195 4.4 20.0 1.0 HB3 A:GLU176 4.7 25.9 1.0 CA A:ASP199 4.8 17.0 1.0 CD1 A:LEU195 4.8 16.7 1.0 HD3 A:LYS202 4.8 22.2 1.0 HD1 A:HIS177 4.9 24.7 1.0 HG3 A:LYS202 4.9 21.4 1.0 CG2 A:ILE173 5.0 16.4 1.0

Zinc binding site 4 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:17.1 occ:0.89 OE1 A:GLU268 2.0 20.4 1.0 OD2 A:ASP267 2.0 20.0 1.0 O A:HOH964 2.0 22.0 1.0 OD1 A:ASP267 2.4 19.9 1.0 CG A:ASP267 2.6 15.9 1.0 OE2 A:GLU268 2.6 19.5 1.0 CD A:GLU268 2.7 18.7 1.0 H A:GLU268 4.0 17.4 1.0 CB A:ASP267 4.1 13.8 1.0 HH12 A:ARG271 4.1 22.1 1.0 O A:HOH663 4.1 20.7 1.0 CG A:GLU268 4.1 16.8 1.0 HG3 A:GLU268 4.3 20.1 1.0 HB3 A:ASP267 4.4 16.6 1.0 H A:ASP267 4.4 16.7 1.0 N A:GLU268 4.5 14.5 1.0 HH22 A:ARG271 4.5 23.2 1.0 HB2 A:ASP267 4.5 16.6 1.0 HG2 A:GLU268 4.6 20.1 1.0 CA A:ASP267 4.8 13.7 1.0 HB A:THR266 4.8 19.2 1.0 N A:ASP267 4.9 13.9 1.0 NH1 A:ARG271 4.9 18.4 1.0 C A:ASP267 4.9 13.9 1.0 O A:HOH744 5.0 22.4 1.0

Zinc binding site 5 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 2'-Fucosyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:0.1 occ:0.39 OE1 A:GLU53 2.0 33.7 1.0 O A:HOH656 2.1 26.4 1.0 O A:HOH996 2.6 35.4 1.0 HB2 A:ASN81 3.2 18.8 1.0 CD A:GLU53 3.2 35.2 1.0 HB3 A:LYS79 3.4 25.7 1.0 HB3 A:GLU53 3.5 26.2 1.0 HB2 A:LYS79 3.9 25.7 1.0 OE2 A:GLU53 3.9 35.5 1.0 HD3 A:LYS79 4.0 50.5 1.0 CB A:LYS79 4.1 21.4 1.0 CB A:ASN81 4.1 15.7 1.0 CB A:GLU53 4.3 21.8 1.0 CG A:GLU53 4.3 24.2 1.0 HA A:GLU53 4.4 23.3 1.0 HB3 A:ASN81 4.4 18.8 1.0 H A:ASN81 4.5 16.9 1.0 N A:ASN81 4.5 14.1 1.0 O A:LYS79 4.6 20.6 1.0 HA A:ASN81 4.6 18.0 1.0 CA A:ASN81 4.7 15.0 1.0 HG3 A:GLU53 4.7 29.0 1.0 HD2 A:LYS79 4.7 50.5 1.0 C A:LYS79 4.7 17.0 1.0 CD A:LYS79 4.7 42.1 1.0 O A:HOH983 4.8 47.8 1.0 C A:ILE80 4.8 17.4 1.0 CA A:GLU53 4.9 19.4 1.0 O A:HOH613 5.0 38.0 1.0

M.Sakanaka, M.E.Hansen, A.Gotoh, T.Katoh, K.Yoshida, T.Odamaki, H.Yachi, Y.Sugiyama, S.Kurihara, J.Hirose, T.Urashima, J.Z.Xiao, M.Kitaoka, S.Fukiya, A.Yokota, L.Lo Leggio, M.Abou Hachem, T.Katayama. Evolutionary Adaptation in Fucosyllactose Uptake Systems Supports Bifidobacteria-Infant Symbiosis. Sci Adv V. 5 W7696 2019.
ISSN: ESSN 2375-2548
PubMed: 31489370
DOI: 10.1126/SCIADV.AAW7696