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Zinc in PDB 3edi: Crystal Structure of Tolloid-Like Protease 1 (Tll-1) Protease Domain

Protein crystallography data

The structure of Crystal Structure of Tolloid-Like Protease 1 (Tll-1) Protease Domain, PDB code: 3edi was solved by A.Mac Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.281, 58.923, 47.444, 90.00, 104.62, 90.00
R / Rfree (%) 15.4 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Tolloid-Like Protease 1 (Tll-1) Protease Domain (pdb code 3edi). 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 Tolloid-Like Protease 1 (Tll-1) Protease Domain, PDB code: 3edi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3edi

Go back to Zinc Binding Sites List in 3edi
Zinc binding site 1 out of 2 in the Crystal Structure of Tolloid-Like Protease 1 (Tll-1) Protease Domain


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 Tolloid-Like Protease 1 (Tll-1) Protease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:11.1
occ:1.00
NE2 A:HIS102 2.0 11.4 1.0
NE2 A:HIS92 2.0 9.0 1.0
NE2 A:HIS96 2.1 11.1 1.0
SG A:CYS65 2.3 21.5 1.0
CD2 A:HIS102 3.0 10.8 1.0
CE1 A:HIS102 3.0 11.8 1.0
CD2 A:HIS92 3.0 10.6 1.0
CE1 A:HIS92 3.0 9.0 1.0
CE1 A:HIS96 3.0 9.6 1.0
CD2 A:HIS96 3.1 10.0 1.0
CB A:CYS65 3.2 22.1 1.0
O A:HOH491 3.9 22.9 1.0
OE2 A:GLU93 4.0 23.4 1.0
ND1 A:HIS102 4.1 10.8 1.0
CG A:HIS102 4.1 9.6 1.0
ND1 A:HIS92 4.1 9.9 1.0
ND1 A:HIS96 4.2 8.8 1.0
CG A:HIS92 4.2 8.7 1.0
CG A:HIS96 4.2 8.0 1.0
O A:HOH284 4.4 22.9 1.0
CA A:CYS65 4.5 22.6 1.0
O A:HOH403 4.6 30.5 1.0
CE A:MET147 4.7 10.6 1.0
CD A:GLU93 4.8 19.8 1.0
O A:HOH350 4.9 39.2 1.0
OE1 A:GLU93 4.9 18.7 1.0

Zinc binding site 2 out of 2 in 3edi

Go back to Zinc Binding Sites List in 3edi
Zinc binding site 2 out of 2 in the Crystal Structure of Tolloid-Like Protease 1 (Tll-1) Protease Domain


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 Tolloid-Like Protease 1 (Tll-1) Protease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn211

b:8.8
occ:0.50
O A:ACE201 2.3 9.5 1.0
OE1 A:GLN189 2.4 10.1 1.0
O A:HOH247 2.4 11.9 1.0
O A:HOH240 2.4 11.9 1.0
O A:HOH236 2.4 13.3 1.0
OE1 A:GLU103 2.4 12.1 1.0
OE2 A:GLU103 2.5 10.6 1.0
CD A:GLU103 2.8 10.6 1.0
C A:ACE201 3.3 9.6 1.0
CD A:GLN189 3.4 10.3 1.0
NE2 A:GLN189 3.8 10.7 1.0
N A:ALA1 3.9 10.2 1.0
O A:HOH232 4.1 12.9 1.0
CB A:ASP142 4.1 9.3 1.0
NH1 A:ARG106 4.3 10.5 1.0
CG A:GLU103 4.4 8.9 1.0
O A:HOH270 4.5 13.0 1.0
CH3 A:ACE201 4.5 5.5 1.0
OG A:SER145 4.7 10.2 1.0
OD1 A:ASP186 4.7 13.2 1.0
CG A:GLN189 4.7 10.8 1.0
OD2 A:ASP142 4.8 12.0 1.0
CB A:SER145 4.9 8.7 1.0
O A:HOH444 4.9 37.1 1.0
CB A:GLN189 4.9 10.5 1.0
N A:ASP142 4.9 9.3 1.0
CD A:ARG106 5.0 10.7 1.0

Reference:

A.Mac Sweeney, S.G.Parrado, D.Vinzenz, A.Bernardi, A.Hein, U.Bodendorf, P.Erbel, C.Logel, B.Gerhartz. Structural Basis For the Substrate Specificity of Bone Morphogenetic Protein 1/Tolloid-Like Metalloproteases To Be Published.
Page generated: Wed Dec 16 04:15:42 2020

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