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Zinc in PDB 3n1f: Crystal Structure of Ihhn Bound to CDOFN3

Protein crystallography data

The structure of Crystal Structure of Ihhn Bound to CDOFN3, PDB code: 3n1f was solved by J.M.Kavran, D.J.Leahy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.31 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.758, 98.198, 144.105, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.9

Other elements in 3n1f:

The structure of Crystal Structure of Ihhn Bound to CDOFN3 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ihhn Bound to CDOFN3 (pdb code 3n1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ihhn Bound to CDOFN3, PDB code: 3n1f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3n1f

Go back to Zinc Binding Sites List in 3n1f
Zinc binding site 1 out of 2 in the Crystal Structure of Ihhn Bound to CDOFN3


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 Ihhn Bound to CDOFN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:20.0
occ:1.00
OD1 A:ASP152 1.9 17.8 1.0
NE2 A:HIS145 2.0 18.4 1.0
O A:HOH20 2.0 21.0 1.0
ND1 A:HIS187 2.0 17.8 1.0
CG A:ASP152 2.7 17.6 1.0
OD2 A:ASP152 2.9 20.1 1.0
CE1 A:HIS187 2.9 18.2 1.0
HB2 A:HIS187 3.0 23.4 1.0
CE1 A:HIS145 3.0 19.5 1.0
CD2 A:HIS145 3.0 18.9 1.0
HE1 A:HIS187 3.1 21.9 1.0
CG A:HIS187 3.1 18.0 1.0
HE1 A:HIS145 3.2 23.4 1.0
HD2 A:HIS145 3.2 22.6 1.0
CB A:HIS187 3.5 19.4 1.0
OE1 A:GLU181 3.8 21.3 1.0
HA A:HIS187 3.8 18.2 1.0
HE1 A:HIS139 4.0 24.8 1.0
NE2 A:HIS187 4.1 16.2 1.0
HB1 A:ALA150 4.1 25.4 1.0
ND1 A:HIS145 4.1 19.5 1.0
CB A:ASP152 4.1 18.0 1.0
CG A:HIS145 4.1 18.0 1.0
HE2 A:HIS185 4.2 26.9 1.0
CD2 A:HIS187 4.2 19.7 1.0
CA A:HIS187 4.2 15.2 1.0
O A:HOH219 4.3 24.5 1.0
O A:VAL151 4.3 19.1 1.0
HA A:ASP152 4.3 23.7 1.0
HB3 A:HIS187 4.3 23.4 1.0
ND1 A:HIS139 4.3 20.1 1.0
CE1 A:HIS139 4.4 20.6 1.0
O A:HOH292 4.4 51.6 1.0
N A:ASP152 4.4 17.0 1.0
O A:HOH394 4.5 39.3 1.0
CA A:ASP152 4.5 19.7 1.0
C A:VAL151 4.5 18.3 1.0
HB3 A:ASP152 4.6 21.6 1.0
HB2 A:ASP152 4.6 21.6 1.0
H A:ASP152 4.7 20.5 1.0
NE2 A:HIS185 4.7 22.4 1.0
HB3 A:ALA150 4.8 25.4 1.0
HD2 A:HIS185 4.8 24.2 1.0
HE2 A:HIS187 4.9 19.5 1.0
CD A:GLU181 4.9 28.1 1.0
CB A:ALA150 4.9 21.1 1.0
HD1 A:HIS145 4.9 23.4 1.0
H A:CYS188 4.9 24.2 1.0
HB2 A:GLU131 5.0 23.4 1.0

Zinc binding site 2 out of 2 in 3n1f

Go back to Zinc Binding Sites List in 3n1f
Zinc binding site 2 out of 2 in the Crystal Structure of Ihhn Bound to CDOFN3


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 Ihhn Bound to CDOFN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:19.9
occ:1.00
O B:HOH328 1.9 20.6 1.0
OD1 B:ASP152 1.9 17.6 1.0
NE2 B:HIS145 2.0 17.9 1.0
ND1 B:HIS187 2.1 16.1 1.0
CG B:ASP152 2.7 19.0 1.0
OD2 B:ASP152 2.9 19.9 1.0
CE1 B:HIS187 2.9 19.3 1.0
CE1 B:HIS145 3.0 18.4 1.0
CD2 B:HIS145 3.0 19.1 1.0
HB2 B:HIS187 3.0 20.6 1.0
HE1 B:HIS187 3.1 23.2 1.0
CG B:HIS187 3.1 18.7 1.0
HE1 B:HIS145 3.2 22.1 1.0
HD2 B:HIS145 3.2 22.9 1.0
CB B:HIS187 3.5 17.2 1.0
OE1 B:GLU181 3.7 25.2 1.0
HA B:HIS187 3.8 23.8 1.0
HE1 B:HIS139 3.8 24.4 1.0
NE2 B:HIS187 4.1 18.6 1.0
CB B:ASP152 4.1 19.6 1.0
ND1 B:HIS145 4.1 19.0 1.0
HE2 B:HIS185 4.2 26.7 1.0
CG B:HIS145 4.2 18.3 1.0
O B:HOH664 4.2 23.4 1.0
ND1 B:HIS139 4.2 19.9 1.0
CE1 B:HIS139 4.2 20.4 1.0
CD2 B:HIS187 4.2 17.1 1.0
HB1 B:ALA150 4.2 23.7 1.0
CA B:HIS187 4.2 19.8 1.0
O B:VAL151 4.2 19.7 1.0
HA B:ASP152 4.3 19.2 1.0
HB3 B:HIS187 4.4 20.6 1.0
N B:ASP152 4.4 15.2 1.0
C B:VAL151 4.5 19.0 1.0
CA B:ASP152 4.5 16.0 1.0
HB2 B:ASP152 4.6 23.6 1.0
HB3 B:ASP152 4.6 23.6 1.0
O B:HOH241 4.7 33.6 1.0
H B:ASP152 4.7 18.3 1.0
NE2 B:HIS185 4.7 22.3 1.0
CD B:GLU181 4.8 34.0 1.0
HD2 B:HIS185 4.8 24.7 1.0
H B:CYS188 4.9 20.6 1.0
HE2 B:HIS187 4.9 22.4 1.0
HB3 B:ALA150 4.9 23.7 1.0
HD1 B:HIS145 4.9 22.8 1.0
HB2 B:GLU131 4.9 21.2 1.0
CB B:ALA150 5.0 19.7 1.0

Reference:

J.M.Kavran, M.D.Ward, O.O.Oladosu, S.Mulepati, D.J.Leahy. All Mammalian Hedgehog Proteins Interact with Cell Adhesion Molecule, Down-Regulated By Oncogenes (Cdo) and Brother of Cdo (Boc) in A Conserved Manner. J.Biol.Chem. V. 285 24584 2010.
ISSN: ISSN 0021-9258
PubMed: 20519495
DOI: 10.1074/JBC.M110.131680
Page generated: Wed Dec 16 04:36:26 2020

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