Atomistry » Zinc » PDB 3czn-3d7g » 3d1m
Atomistry »
  Zinc »
    PDB 3czn-3d7g »
      3d1m »

Zinc in PDB 3d1m: Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo

Protein crystallography data

The structure of Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo, PDB code: 3d1m was solved by J.S.Mclellan, D.J.Leahy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.56 / 1.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.179, 98.582, 144.047, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.9

Other elements in 3d1m:

The structure of Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo (pdb code 3d1m). 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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo, PDB code: 3d1m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3d1m

Go back to Zinc Binding Sites List in 3d1m
Zinc binding site 1 out of 2 in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo


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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:25.5
occ:0.50
OD1 A:ASP148 2.1 31.6 1.0
O A:HOH268 2.2 24.0 1.0
NE2 A:HIS141 2.2 34.0 1.0
O A:HOH241 2.3 25.1 1.0
ND1 A:HIS183 2.3 31.2 1.0
OE1 A:GLU177 2.4 34.3 1.0
CG A:ASP148 3.0 32.0 1.0
CE1 A:HIS183 3.2 31.2 1.0
OD2 A:ASP148 3.2 32.6 1.0
CD2 A:HIS141 3.2 36.7 1.0
CE1 A:HIS141 3.2 34.7 1.0
CG A:HIS183 3.3 31.2 1.0
CD A:GLU177 3.4 32.5 1.0
CB A:HIS183 3.7 29.6 1.0
OE2 A:GLU177 3.7 35.6 1.0
NE2 A:HIS181 4.1 30.0 1.0
O A:HOH209 4.2 31.2 1.0
NE2 A:HIS183 4.3 30.4 1.0
ND1 A:HIS141 4.3 34.1 1.0
CG A:HIS141 4.4 33.2 1.0
CB A:ASP148 4.4 30.0 1.0
CD2 A:HIS183 4.4 29.2 1.0
CA A:HIS183 4.5 30.4 1.0
O A:HOH192 4.5 24.7 1.0
O A:HOH293 4.6 24.0 1.0
CD2 A:HIS181 4.6 31.9 1.0
CE1 A:HIS135 4.7 33.6 1.0
CG A:GLU177 4.8 32.5 1.0
CA A:ASP148 4.8 30.1 1.0
ND1 A:HIS135 4.8 32.3 1.0
N A:ASP148 4.8 30.2 1.0
O A:VAL147 4.9 30.4 1.0
CE1 A:HIS181 5.0 32.8 1.0

Zinc binding site 2 out of 2 in 3d1m

Go back to Zinc Binding Sites List in 3d1m
Zinc binding site 2 out of 2 in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo


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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:26.4
occ:0.50
OD1 B:ASP148 2.1 30.8 1.0
O B:HOH265 2.1 32.3 1.0
NE2 B:HIS141 2.1 28.4 1.0
O B:HOH210 2.2 25.2 1.0
ND1 B:HIS183 2.2 31.0 1.0
OD2 B:ASP148 2.6 30.1 1.0
CG B:ASP148 2.6 29.5 1.0
CD2 B:HIS141 3.1 29.6 1.0
CE1 B:HIS183 3.1 30.5 1.0
CE1 B:HIS141 3.2 27.7 1.0
CG B:HIS183 3.3 30.8 1.0
CB B:HIS183 3.7 29.6 1.0
CB B:ASP148 4.1 29.5 1.0
OE1 B:GLU177 4.2 45.5 1.0
ND1 B:HIS135 4.2 28.4 1.0
CG B:HIS141 4.2 30.2 1.0
ND1 B:HIS141 4.2 30.1 1.0
CE1 B:HIS135 4.2 30.7 1.0
NE2 B:HIS183 4.3 28.5 1.0
O B:HOH298 4.3 42.5 1.0
NE2 B:HIS181 4.3 32.0 1.0
CD2 B:HIS183 4.4 27.4 1.0
CA B:HIS183 4.5 29.2 1.0
O B:HOH193 4.6 21.8 1.0
CA B:ASP148 4.7 29.1 1.0
N B:ASP148 4.7 28.5 1.0
O B:VAL147 4.8 27.8 1.0
CD2 B:HIS181 4.8 30.6 1.0
O B:HOH229 4.9 23.5 1.0
C B:VAL147 4.9 28.6 1.0

Reference:

J.S.Mclellan, X.Zheng, G.Hauk, R.Ghirlando, P.A.Beachy, D.J.Leahy. The Mode of Hedgehog Binding to Ihog Homologues Is Not Conserved Across Different Phyla. Nature V. 455 979 2008.
ISSN: ISSN 0028-0836
PubMed: 18794898
DOI: 10.1038/NATURE07358
Page generated: Wed Dec 16 04:11:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy