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

Protein crystallography data

The structure of 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-Fucosyllactose, PDB code: 6hus was solved by M.Ejby, M.Abou Hachem, L.Lo Leggio, K.Takane, M.Sakanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.74 / 1.41
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.200, 134.200, 59.990, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 16.5

Zinc Binding Sites:

The binding sites of Zinc atom in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-Fucosyllactose (pdb code 6hus). 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 3-Fucosyllactose, PDB code: 6hus:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6hus

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Zinc binding site 1 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-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 3-Fucosyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:11.9
occ:0.76
OD2 A:ASP350 1.9 69.4 1.0
OD2 A:ASP348 2.0 11.5 1.0
O A:HOH977 2.2 11.8 1.0
OD1 A:ASP348 2.6 15.8 1.0
CG A:ASP348 2.6 13.1 1.0
HB2 A:ASP350 2.7 17.2 1.0
CG A:ASP350 2.9 19.1 1.0
H A:ASP350 3.0 15.3 1.0
CB A:ASP350 3.2 14.3 1.0
HE1 A:TRP344 3.4 16.6 1.0
N A:ASP350 3.8 12.8 1.0
HB3 A:ASP350 4.0 17.2 1.0
NE1 A:TRP344 4.0 13.8 1.0
HZ2 A:TRP344 4.0 17.9 1.0
OD1 A:ASP350 4.0 23.1 1.0
O A:HOH966 4.1 28.3 1.0
CA A:ASP350 4.2 12.2 1.0
CB A:ASP348 4.2 13.2 1.0
HB3 A:ASP348 4.4 15.8 1.0
HE3 A:LYS74 4.4 27.0 1.0
H A:ALA351 4.4 14.1 1.0
H A:LYS349 4.4 14.6 1.0
CZ2 A:TRP344 4.6 14.9 1.0
CE2 A:TRP344 4.6 13.1 1.0
HB2 A:ASP348 4.6 15.8 1.0
N A:LYS349 4.7 12.2 1.0
HA A:ASP350 4.8 14.6 1.0
HB2 A:LYS349 4.9 17.2 1.0
C A:ASP348 5.0 11.8 1.0
C A:LYS349 5.0 12.3 1.0

Zinc binding site 2 out of 5 in 6hus

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Zinc binding site 2 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-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 3-Fucosyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:21.2
occ:0.66
OE2 A:GLU134 2.0 19.1 1.0
NE2 A:HIS150 2.1 23.2 1.0
OE1 A:GLU134 2.1 33.2 1.0
CD A:GLU134 2.2 28.6 1.0
CD2 A:HIS150 2.9 24.4 1.0
HD2 A:HIS150 3.0 29.2 1.0
CE1 A:HIS150 3.1 21.9 1.0
HE1 A:HIS150 3.4 26.3 1.0
CG A:GLU134 3.5 32.8 1.0
HG3 A:GLU134 3.5 39.3 1.0
HE1 A:TRP146 3.9 21.4 1.0
HG2 A:GLU134 4.0 39.3 1.0
CG A:HIS150 4.1 19.1 1.0
ND1 A:HIS150 4.2 17.8 1.0
HB3 A:GLU134 4.4 22.7 1.0
NE1 A:TRP146 4.5 17.8 1.0
CB A:GLU134 4.6 18.9 1.0
HD13 A:LEU155 4.8 22.2 1.0
HB2 A:LEU155 5.0 16.4 1.0
HD1 A:HIS150 5.0 21.3 1.0
HZ2 A:TRP146 5.0 21.1 1.0

Zinc binding site 3 out of 5 in 6hus

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Zinc binding site 3 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-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 3-Fucosyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:16.9
occ:0.69
NE2 A:HIS177 2.0 15.4 1.0
O A:HOH945 2.0 26.7 1.0
OD2 A:ASP199 2.1 25.4 1.0
O A:HOH991 2.3 12.1 1.0
CE1 A:HIS177 3.0 22.6 1.0
HB2 A:ASP199 3.0 20.6 1.0
CD2 A:HIS177 3.1 16.8 1.0
CG A:ASP199 3.1 24.7 1.0
HE1 A:HIS177 3.1 27.1 1.0
HD2 A:HIS177 3.3 20.1 1.0
CB A:ASP199 3.4 17.1 1.0
HD2 A:LYS202 3.5 20.4 1.0
HB3 A:ASP199 3.6 20.6 1.0
HG2 A:GLU176 3.7 24.8 1.0
HE2 A:LYS202 3.9 24.3 1.0
HE3 A:LYS202 4.1 24.3 1.0
ND1 A:HIS177 4.1 18.6 1.0
O A:HOH1009 4.1 41.4 1.0
HG23 A:ILE173 4.1 17.7 1.0
CG A:HIS177 4.2 14.6 1.0
HG3 A:GLU176 4.2 24.8 1.0
OD1 A:ASP199 4.2 21.6 1.0
CE A:LYS202 4.3 20.2 1.0
CD A:LYS202 4.3 17.0 1.0
CG A:GLU176 4.4 20.7 1.0
HD11 A:LEU195 4.5 19.4 1.0
HD12 A:LEU195 4.5 19.4 1.0
HB3 A:GLU176 4.8 22.8 1.0
HD1 A:HIS177 4.9 22.4 1.0
CA A:ASP199 4.9 16.1 1.0
HG3 A:LYS202 4.9 20.0 1.0
CD1 A:LEU195 4.9 16.1 1.0
HD3 A:LYS202 5.0 20.4 1.0

Zinc binding site 4 out of 5 in 6hus

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Zinc binding site 4 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-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 3-Fucosyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:13.0
occ:0.78
NE2 A:HIS196 2.0 12.9 1.0
CD2 A:HIS196 3.0 12.4 1.0
CE1 A:HIS196 3.0 14.7 1.0
HD2 A:HIS196 3.2 14.9 1.0
HE1 A:HIS196 3.3 17.6 1.0
OH A:TYR203 3.8 20.4 1.0
O A:HOH915 3.9 27.8 1.0
HB2 A:SER200 4.1 23.4 1.0
HH A:TYR203 4.1 24.5 1.0
ND1 A:HIS196 4.1 15.1 1.0
CG A:HIS196 4.2 12.3 1.0
HE2 A:TYR203 4.3 18.5 1.0
O A:HOH729 4.4 15.7 1.0
CZ A:TYR203 4.5 16.1 1.0
CE2 A:TYR203 4.7 15.4 1.0
HA3 A:GLY257 4.7 13.2 1.0
O A:SER200 4.8 17.3 1.0
HA A:SER200 4.8 18.8 1.0
CB A:SER200 4.9 19.5 1.0
HB3 A:SER200 4.9 23.4 1.0
HD1 A:HIS196 4.9 18.1 1.0

Zinc binding site 5 out of 5 in 6hus

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Zinc binding site 5 out of 5 in the 2'-Fucosyllactose and 3-Fucosyllactose Binding Protein From Bifidobacterium Longum Infantis, Bound with 3-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 3-Fucosyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:23.8
occ:0.09
OD1 A:ASP267 1.8 15.7 1.0
OE1 A:GLU268 1.9 42.6 1.0
OD2 A:ASP267 2.1 16.1 1.0
CG A:ASP267 2.2 12.8 1.0
OE2 A:GLU268 2.3 16.9 1.0
CD A:GLU268 2.3 19.4 1.0
O A:HOH968 2.6 19.4 1.0
H A:GLU268 3.3 14.5 1.0
CB A:ASP267 3.6 12.8 1.0
HH12 A:ARG271 3.7 21.1 1.0
CG A:GLU268 3.8 14.6 1.0
N A:GLU268 3.8 12.1 1.0
H A:ASP267 4.0 14.5 1.0
HG3 A:GLU268 4.0 17.5 1.0
HB3 A:ASP267 4.1 15.3 1.0
O A:HOH623 4.1 20.4 1.0
HH22 A:ARG271 4.1 23.6 1.0
HB2 A:ASP267 4.1 15.3 1.0
CA A:ASP267 4.3 11.4 1.0
C A:ASP267 4.3 11.9 1.0
HG2 A:GLU268 4.3 17.5 1.0
N A:ASP267 4.4 12.1 1.0
HB A:THR266 4.4 13.8 1.0
NH1 A:ARG271 4.5 17.6 1.0
CB A:GLU268 4.6 14.1 1.0
CA A:GLU268 4.6 11.8 1.0
HA A:GLU268 4.6 14.2 1.0
HB2 A:GLU268 4.7 16.9 1.0
O A:HOH774 4.8 19.9 1.0
NH2 A:ARG271 4.9 19.6 1.0

Reference:

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
Page generated: Mon Oct 28 23:23:01 2024

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