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Zinc in PDB 3eyv: Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions

Protein crystallography data

The structure of Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions, PDB code: 3eyv was solved by W.Farrugia, A.M.Scott, P.A.Ramsland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.65 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.752, 101.467, 114.998, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions (pdb code 3eyv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions, PDB code: 3eyv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3eyv

Go back to Zinc Binding Sites List in 3eyv
Zinc binding site 1 out of 4 in the Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn220

b:26.6
occ:1.00
NE2 H:HIS170 2.2 12.0 1.0
OE1 B:GLU1 2.2 25.4 1.0
ND2 L:ASN142 2.2 19.9 1.0
ND2 L:ASN143 2.3 36.5 1.0
CD2 H:HIS170 2.8 12.1 1.0
CD B:GLU1 3.0 23.1 1.0
CG L:ASN142 3.1 18.1 1.0
OE2 B:GLU1 3.1 18.2 1.0
CG L:ASN143 3.1 37.9 1.0
OD1 L:ASN142 3.2 18.6 1.0
CE1 H:HIS170 3.4 13.2 1.0
OD1 L:ASN143 3.4 42.6 1.0
OG L:SER179 4.0 18.9 1.0
CG H:HIS170 4.0 16.1 1.0
O H:GLY168 4.3 17.9 1.0
ND1 H:HIS170 4.3 14.9 1.0
CG B:GLU1 4.4 24.5 1.0
N L:ASN143 4.4 26.7 1.0
CB L:ASN143 4.4 31.4 1.0
CB L:ASN142 4.5 17.1 1.0
OG1 H:THR189 4.5 15.8 1.0
CA H:GLY168 4.6 18.3 1.0
C H:GLY168 4.6 17.7 1.0
CG2 H:THR189 4.8 12.9 1.0
O L:HOH222 4.8 17.0 1.0
CA L:ASN143 4.9 28.0 1.0

Zinc binding site 2 out of 4 in 3eyv

Go back to Zinc Binding Sites List in 3eyv
Zinc binding site 2 out of 4 in the Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn221

b:59.5
occ:1.00
NE2 L:HIS194 2.2 44.5 1.0
OD1 L:ASP190 2.4 48.4 1.0
CE1 L:HIS194 3.2 45.6 1.0
CD2 L:HIS194 3.2 45.1 1.0
CG L:ASP190 3.4 46.8 1.0
OD2 L:ASP190 3.7 47.8 1.0
ND1 L:HIS194 4.3 45.3 1.0
CG L:HIS194 4.4 44.2 1.0
O L:ASP190 4.4 42.1 1.0
CB L:ASP190 4.7 44.7 1.0
C L:ASP190 5.0 42.4 1.0
CB L:LYS193 5.0 47.1 1.0

Zinc binding site 3 out of 4 in 3eyv

Go back to Zinc Binding Sites List in 3eyv
Zinc binding site 3 out of 4 in the Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn220

b:24.1
occ:1.00
O H:HOH227 2.0 4.4 1.0
NE2 B:HIS170 2.1 17.8 1.0
ND2 A:ASN142 2.2 20.1 1.0
OE2 H:GLU1 2.2 24.7 1.0
ND2 A:ASN143 2.3 33.6 1.0
OD1 A:ASN143 2.6 32.6 1.0
CG A:ASN143 2.7 31.3 1.0
CD H:GLU1 2.8 23.8 1.0
OE1 H:GLU1 2.9 22.6 1.0
CD2 B:HIS170 3.0 19.5 1.0
CG A:ASN142 3.1 18.8 1.0
CE1 B:HIS170 3.2 17.0 1.0
OD1 A:ASN142 3.3 16.9 1.0
OG A:SER179 4.1 18.5 1.0
CB A:ASN143 4.1 28.1 1.0
CG H:GLU1 4.2 22.7 1.0
CG B:HIS170 4.2 18.8 1.0
ND1 B:HIS170 4.2 19.0 1.0
N A:ASN143 4.4 22.2 1.0
OG1 B:THR189 4.4 12.5 1.0
O B:GLY168 4.5 23.7 1.0
CB A:ASN142 4.5 18.0 1.0
CB H:GLU1 4.7 22.3 1.0
CA A:ASN143 4.8 23.3 1.0
CA B:GLY168 4.8 21.4 1.0
C B:GLY168 4.9 20.2 1.0
CG2 B:THR189 4.9 15.3 1.0

Zinc binding site 4 out of 4 in 3eyv

Go back to Zinc Binding Sites List in 3eyv
Zinc binding site 4 out of 4 in the Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Anti-Lewis Y Fab Fragment with Lewis Y Antigen in the Presence of Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn221

b:72.5
occ:1.00
NE2 A:HIS194 2.7 27.8 1.0
CD2 A:HIS194 3.2 29.2 1.0
O A:ASP190 3.6 32.8 1.0
CB A:ASP190 3.8 38.2 1.0
OD2 A:ASP190 3.8 46.6 1.0
CE1 A:HIS194 3.9 30.9 1.0
O A:HOH236 4.2 40.3 1.0
C A:ASP190 4.3 32.7 1.0
CA A:ASP190 4.3 34.5 1.0
CG A:ASP190 4.3 43.5 1.0
CG A:HIS194 4.5 28.9 1.0
CB A:LYS193 4.8 36.7 1.0
ND1 A:HIS194 4.9 30.1 1.0
CD A:LYS193 4.9 43.4 1.0

Reference:

W.Farrugia, A.M.Scott, P.A.Ramsland. A Possible Role For Metallic Ions in the Carbohydrate Cluster Recognition Displayed By A Lewis Y Specific Antibody. Plos One V. 4 E7777 2009.
ISSN: ESSN 1932-6203
PubMed: 19901987
DOI: 10.1371/JOURNAL.PONE.0007777
Page generated: Wed Dec 16 04:17:16 2020

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