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

Protein crystallography data

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

Other elements in 3ubf:

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

Calcium (Ca) 1 atom

Zinc Binding Sites:

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 3ubf

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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 3ubf

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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 3ubf

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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 3ubf

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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 3ubf

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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 3ubf

Go back to Zinc Binding Sites List in 3ubf
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 3ubf

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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 3ubf

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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 3ubf

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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 3ubf

Go back to Zinc Binding Sites List in 3ubf
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

Reference:

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
Page generated: Wed Dec 16 04:53:58 2020

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