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Zinc in PDB 2fut: Crystal Structure of Heparinase II Complexed with A Disaccharide Product

Protein crystallography data

The structure of Crystal Structure of Heparinase II Complexed with A Disaccharide Product, PDB code: 2fut was solved by D.Shaya, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.67 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.100, 163.300, 95.300, 90.00, 105.50, 90.00
R / Rfree (%) 17.6 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Heparinase II Complexed with A Disaccharide Product (pdb code 2fut). 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 Heparinase II Complexed with A Disaccharide Product, PDB code: 2fut:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2fut

Go back to Zinc Binding Sites List in 2fut
Zinc binding site 1 out of 2 in the Crystal Structure of Heparinase II Complexed with A Disaccharide Product


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 Heparinase II Complexed with A Disaccharide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:10.1
occ:1.00
O A:HOH1275 2.0 2.0 1.0
NE2 A:HIS451 2.1 2.0 1.0
OD1 A:ASP425 2.2 3.3 1.0
O A:HOH893 2.2 2.0 1.0
ND1 A:HIS408 2.2 4.2 1.0
O A:HOH1101 2.2 2.0 1.0
CE1 A:HIS408 3.0 4.8 1.0
CD2 A:HIS451 3.0 2.0 1.0
CE1 A:HIS451 3.1 2.0 1.0
CG A:ASP425 3.1 3.6 1.0
CG A:HIS408 3.3 5.0 1.0
OD2 A:ASP425 3.4 2.1 1.0
CB A:HIS408 3.8 5.4 1.0
O A:PHE445 3.9 2.9 1.0
O A:HOH902 4.1 2.0 1.0
CG A:HIS451 4.1 2.0 1.0
NE2 A:HIS408 4.2 5.1 1.0
ND1 A:HIS451 4.2 2.0 1.0
O A:GLY306 4.3 5.7 1.0
N A:GLY306 4.3 5.8 1.0
CD2 A:HIS408 4.4 4.8 1.0
OD2 A:ASP410 4.4 7.1 1.0
CB A:ASP425 4.5 4.8 1.0
O A:ALA426 4.7 6.0 1.0
CE1 A:PHE445 4.7 2.0 1.0
CA A:GLY306 4.8 5.6 1.0
C A:GLY306 4.9 5.8 1.0
O A:HOH934 4.9 2.3 1.0
C A:ASP425 5.0 5.2 1.0

Zinc binding site 2 out of 2 in 2fut

Go back to Zinc Binding Sites List in 2fut
Zinc binding site 2 out of 2 in the Crystal Structure of Heparinase II Complexed with A Disaccharide Product


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 Heparinase II Complexed with A Disaccharide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:37.2
occ:1.00
ND1 B:HIS408 1.9 24.9 1.0
NE2 B:HIS451 2.0 25.9 1.0
OD1 B:ASP425 2.2 21.1 1.0
O B:HOH1006 2.5 21.9 1.0
O B:HOH992 2.5 23.3 1.0
O B:HOH900 2.6 28.1 1.0
CE1 B:HIS408 2.7 23.6 1.0
OD2 B:ASP425 2.8 22.9 1.0
CG B:ASP425 2.9 24.4 1.0
CD2 B:HIS451 2.9 24.7 1.0
CG B:HIS408 3.1 24.5 1.0
CE1 B:HIS451 3.1 25.3 1.0
CB B:HIS408 3.6 24.5 1.0
O B:PHE445 3.8 27.3 1.0
NE2 B:HIS408 3.9 24.2 1.0
CD2 B:HIS408 4.1 24.1 1.0
CG B:HIS451 4.1 24.8 1.0
ND1 B:HIS451 4.1 25.0 1.0
N B:GLY306 4.3 25.5 1.0
CB B:ASP425 4.4 25.9 1.0
OD2 B:ASP410 4.5 23.9 1.0
O B:GLY306 4.5 25.9 1.0
O B:HOH994 4.7 19.4 1.0
CA B:GLY306 4.7 25.8 1.0
CE1 B:PHE445 4.7 26.4 1.0
O B:ALA426 4.8 28.0 1.0
C B:GLY306 4.9 25.9 1.0
C B:PHE445 5.0 27.4 1.0
C B:ASP425 5.0 26.9 1.0

Reference:

D.Shaya, A.Tocilj, Y.Li, J.Myette, G.Venkataraman, R.Sasisekharan, M.Cygler. Crystal Structure of Heparinase II From Pedobacter Heparinus and Its Complex with A Disaccharide Product. J.Biol.Chem. V. 281 15525 2006.
ISSN: ISSN 0021-9258
PubMed: 16565082
DOI: 10.1074/JBC.M512055200
Page generated: Wed Dec 16 03:28:39 2020

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