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Zinc in PDB 4f0a: Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8

Protein crystallography data

The structure of Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8, PDB code: 4f0a was solved by C.Y.Janda, D.Waghray, A.M.Levin, C.Thomas, K.C.Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.64 / 3.25
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 110.070, 110.070, 82.820, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8 (pdb code 4f0a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8, PDB code: 4f0a:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4f0a

Go back to Zinc Binding Sites List in 4f0a
Zinc binding site 1 out of 3 in the Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8


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 XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn410

b:84.8
occ:1.00
OE2 B:GLU152 2.4 0.9 1.0
NE2 B:HIS90 2.5 71.6 1.0
NE2 B:HIS76 2.5 94.2 1.0
CE1 B:HIS76 2.7 98.1 1.0
OE1 B:GLU152 2.7 86.7 1.0
CD B:GLU152 2.8 97.6 1.0
CD2 B:HIS90 2.9 67.4 1.0
CD2 B:HIS76 3.6 98.3 1.0
CE1 B:HIS90 3.6 78.8 1.0
O B:LEU73 3.7 94.8 1.0
ND1 B:HIS76 3.8 0.1 1.0
ND2 B:ASN162 3.9 77.7 1.0
CG B:HIS90 4.1 71.8 1.0
CG B:GLU152 4.2 97.1 1.0
CG B:HIS76 4.2 0.2 1.0
ND1 B:HIS90 4.4 78.4 1.0
CG B:ASN162 4.5 83.6 1.0
C B:LEU73 4.6 95.0 1.0
CB B:LEU73 4.6 83.3 1.0
CB B:ASN162 4.6 83.7 1.0
CA B:LEU73 4.7 94.6 1.0
CD1 B:LEU79 4.9 90.7 1.0

Zinc binding site 2 out of 3 in 4f0a

Go back to Zinc Binding Sites List in 4f0a
Zinc binding site 2 out of 3 in the Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8


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 XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn411

b:68.3
occ:1.00
NE2 B:HIS335 2.3 67.7 1.0
OE2 B:GLU304 2.4 68.1 1.0
CE1 B:HIS335 2.9 70.4 1.0
CD B:GLU304 3.2 75.2 1.0
CD2 B:HIS335 3.5 76.7 1.0
CG B:GLU304 3.6 73.0 1.0
OE1 B:GLU304 4.1 79.2 1.0
ND1 B:HIS335 4.2 72.1 1.0
CG B:GLN278 4.4 97.0 1.0
CG B:HIS335 4.5 70.5 1.0
CB B:GLN278 4.8 93.2 1.0

Zinc binding site 3 out of 3 in 4f0a

Go back to Zinc Binding Sites List in 4f0a
Zinc binding site 3 out of 3 in the Crystal Structure of XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8


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 XWNT8 in Complex with the Cysteine-Rich Domain of Frizzled 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn412

b:74.2
occ:1.00
ND1 B:HIS208 2.6 78.5 1.0
CG B:HIS208 3.0 73.9 1.0
CE1 B:HIS208 3.2 76.7 1.0
CB B:HIS208 3.4 66.2 1.0
CD2 B:HIS208 3.7 64.4 1.0
NE2 B:HIS208 3.8 66.5 1.0
CA B:HIS208 4.1 58.1 1.0
CG2 B:THR176 4.8 62.1 1.0
O B:ASP204 5.0 67.0 1.0
N B:HIS208 5.0 57.8 1.0

Reference:

C.Y.Janda, D.Waghray, A.M.Levin, C.Thomas, K.C.Garcia. Structural Basis of Wnt Recognition By Frizzled. Science V. 337 59 2012.
ISSN: ISSN 0036-8075
PubMed: 22653731
DOI: 10.1126/SCIENCE.1222879
Page generated: Wed Dec 16 05:16:36 2020

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