Zinc in PDB 3ubf: Crystal Structure of Drosophila N-Cadherin EC1-3, I

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, I, PDB code: 3ubf was solved by X.Jin, M.A.Walker, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.289, 96.289, 148.196, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 27.9

The structure of Crystal Structure of Drosophila N-Cadherin EC1-3, I also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Drosophila N-Cadherin EC1-3, I (pdb code 3ubf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Crystal Structure of Drosophila N-Cadherin EC1-3, I, PDB code: 3ubf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:45.2 occ:1.00 O A:HOH165 1.6 2.0 1.0 OE2 A:GLU498 1.9 46.9 1.0 OD2 A:ASP573 2.0 49.5 1.0 OD2 A:ASP535 2.0 56.2 1.0 OD1 A:ASP535 2.6 53.7 1.0 CG A:ASP535 2.6 54.4 1.0 CG A:ASP573 2.8 49.0 1.0 CD A:GLU498 2.8 48.0 1.0 OD1 A:ASP573 3.0 51.4 1.0 OE1 A:GLU498 3.1 45.3 1.0 CA A:CA754 3.3 51.4 1.0 ZN A:ZN19 3.5 95.0 1.0 NE2 A:HIS576 3.6 44.1 1.0 OE1 A:GLU450 3.8 53.0 1.0 CD2 A:HIS576 3.9 44.8 1.0 CB A:ASP535 4.1 53.9 1.0 CG A:GLU498 4.2 52.3 1.0 CB A:ASP573 4.2 46.3 1.0 CB A:ASP575 4.3 53.1 1.0 OE2 A:GLU450 4.4 55.2 1.0 CD A:GLU450 4.5 53.5 1.0 CB A:ASN537 4.6 58.2 1.0 CE1 A:HIS576 4.6 42.2 1.0 CD2 A:TYR497 4.7 47.9 1.0 CB A:TYR497 4.8 45.4 1.0 CG A:ASN537 5.0 61.9 1.0 OD2 A:ASP575 5.0 61.2 1.0

Zinc binding site 2 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:51.5 occ:1.00 OE1 A:GLU595 2.0 48.0 1.0 ND1 A:HIS579 2.2 47.2 1.0 CD A:GLU595 3.0 46.2 1.0 CG A:HIS579 3.1 43.7 1.0 CE1 A:HIS579 3.2 49.2 1.0 OE2 A:GLU595 3.3 46.3 1.0 CB A:HIS579 3.3 40.4 1.0 CD2 A:HIS579 4.2 46.8 1.0 NE2 A:HIS579 4.2 48.7 1.0 CG A:GLU595 4.3 42.2 1.0 NE2 A:GLN623 4.6 55.6 1.0 CB A:GLU595 4.6 40.3 1.0 OE1 A:GLN623 4.6 60.8 1.0 CA A:HIS579 4.8 39.2 1.0 CD A:GLN623 4.9 58.1 1.0

Zinc binding site 3 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:45.6 occ:1.00 OD2 A:ASP594 1.8 43.9 1.0 CG A:ASP594 2.8 38.3 1.0 OD1 A:ASP594 3.1 40.6 1.0 O A:HOH37 3.4 15.4 1.0 OG A:SER597 4.0 36.2 1.0 NH1 A:ARG596 4.1 58.3 1.0 CB A:ASP594 4.1 37.0 1.0 NH1 A:ARG601 4.4 38.9 1.0 CB A:SER597 4.6 38.4 1.0 CB A:ARG596 4.8 44.3 1.0 N A:SER597 4.9 39.6 1.0 NH2 A:ARG601 5.0 38.0 1.0

Zinc binding site 4 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:0.0 occ:1.00 O A:HOH24 2.1 23.9 1.0 OD2 A:ASP680 2.6 66.5 1.0 O A:HOH138 2.7 6.0 1.0 O A:HOH167 3.1 69.5 1.0 CG A:ASP680 3.5 61.4 1.0 OD1 A:ASP680 3.7 60.7 1.0 CB A:ASP680 4.9 58.5 1.0

Zinc binding site 5 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:97.6 occ:1.00 OD1 A:ASP741 2.7 47.8 1.0 OD2 A:ASP741 2.8 49.6 1.0 CG A:ASP741 3.1 43.8 1.0 CB A:ASP741 4.5 39.4 1.0 O A:HOH121 4.7 38.4 1.0

Zinc binding site 6 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn6 b:49.5 occ:1.00 OD2 A:ASP571 1.7 40.6 1.0 OD2 A:ASP622 1.7 48.6 1.0 ND1 A:HIS576 2.0 42.0 1.0 CG A:ASP571 2.5 40.9 1.0 CG A:ASP622 2.7 52.5 1.0 OD1 A:ASP571 2.7 41.5 1.0 CE1 A:HIS576 2.8 42.2 1.0 CG A:HIS576 3.1 43.8 1.0 OD1 A:ASP622 3.3 58.3 1.0 CB A:HIS576 3.6 42.9 1.0 CB A:ASP622 3.8 51.5 1.0 OE1 A:GLN633 3.9 52.0 1.0 CB A:ASP571 4.0 40.1 1.0 NE2 A:HIS576 4.0 44.1 1.0 O A:GLU539 4.0 44.5 1.0 OD1 A:ASP538 4.0 55.4 1.0 CD2 A:HIS576 4.1 44.8 1.0 N A:GLY625 4.3 61.9 1.0 CD A:PRO541 4.4 37.3 1.0 C A:GLY625 4.4 60.5 1.0 CB A:ASP573 4.5 46.3 1.0 CA A:GLY625 4.5 62.0 1.0 C A:GLU539 4.9 45.3 1.0 CA A:ASP622 4.9 50.5 1.0 N A:PRO541 5.0 37.5 1.0 CA A:ASP571 5.0 39.8 1.0

Zinc binding site 7 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7 b:64.6 occ:1.00 O A:HOH108 1.8 6.4 1.0 O A:HOH107 2.1 8.1 1.0 OD2 A:ASP496 2.1 58.9 1.0 OD2 A:ASP575 2.2 61.2 1.0 CG A:ASP496 2.8 55.4 1.0 OD1 A:ASP496 2.9 57.6 1.0 CG A:ASP575 2.9 56.9 1.0 OD1 A:ASP575 3.0 58.0 1.0 OE2 A:GLU499 4.0 71.2 1.0 CB A:ASP496 4.2 51.9 1.0 CA A:CA754 4.3 51.4 1.0 CB A:ASP575 4.4 53.1 1.0 O A:HOH115 4.5 9.1 1.0 CB A:GLU498 4.7 54.0 1.0 CD A:GLU499 4.7 68.3 1.0 OE1 A:GLU498 4.8 45.3 1.0 CG A:GLU499 4.9 63.6 1.0

Zinc binding site 8 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn8 b:84.3 occ:0.48 OE2 A:GLU539 2.6 55.5 1.0 O A:HOH136 2.8 47.0 1.0 CD A:GLU539 3.4 55.2 1.0 OE1 A:GLU539 3.6 56.0 1.0 CG A:GLU539 4.9 51.6 1.0

Zinc binding site 9 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9 b:90.9 occ:1.00 OE2 A:GLU637 2.2 44.5 1.0 O A:HOH116 2.5 42.9 1.0 CD A:GLU637 2.9 40.7 1.0 OE1 A:GLU637 3.0 41.0 1.0 CG A:GLU637 4.2 36.9 1.0 O A:HOH125 4.6 20.7 1.0 NZ A:LYS619 4.9 51.8 1.0

Zinc binding site 10 out of 18 in the Crystal Structure of Drosophila N-Cadherin EC1-3, I


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 Drosophila N-Cadherin EC1-3, I within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn10 b:77.9 occ:1.00 OD2 A:ASP606 2.0 48.5 1.0 O A:HOH170 2.0 40.1 1.0 CG A:ASP606 3.0 48.0 1.0 OD1 A:ASP606 3.3 49.4 1.0 CB A:ASP606 4.4 45.8 1.0 O A:HOH56 4.8 22.5 1.0

X.Jin, M.A.Walker, K.Felsovalyi, J.Vendome, F.Bahna, S.Mannepalli, F.Cosmanescu, G.Ahlsen, B.Honig, L.Shapiro. Crystal Structures of Drosophila N-Cadherin Ectodomain Regions Reveal A Widely Used Class of CA2+-Free Interdomain Linkers. Proc.Natl.Acad.Sci.Usa V. 109 E127 2012.
ISSN: ISSN 0027-8424
PubMed: 22171007
DOI: 10.1073/PNAS.1117538108