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Zinc in PDB 2dsn: Crystal Structure of T1 Lipase

Enzymatic activity of Crystal Structure of T1 Lipase

All present enzymatic activity of Crystal Structure of T1 Lipase:
3.1.1.3;

Protein crystallography data

The structure of Crystal Structure of T1 Lipase, PDB code: 2dsn was solved by H.Matsumura, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.33 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.731, 81.270, 99.912, 90.00, 97.09, 90.00
R / Rfree (%) 17.4 / 18.8

Other elements in 2dsn:

The structure of Crystal Structure of T1 Lipase also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of T1 Lipase (pdb code 2dsn). 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 T1 Lipase, PDB code: 2dsn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2dsn

Go back to Zinc Binding Sites List in 2dsn
Zinc binding site 1 out of 2 in the Crystal Structure of T1 Lipase


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 T1 Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:13.6
occ:1.00
OD2 A:ASP238 2.0 10.7 1.0
OD1 A:ASP61 2.1 10.0 1.0
NE2 A:HIS81 2.1 11.5 1.0
NE2 A:HIS87 2.1 11.9 1.0
OD2 A:ASP61 2.6 13.2 1.0
CG A:ASP61 2.7 12.1 1.0
CG A:ASP238 2.7 11.1 1.0
OD1 A:ASP238 2.8 12.4 1.0
CD2 A:HIS81 3.0 11.3 1.0
CD2 A:HIS87 3.1 11.3 1.0
CE1 A:HIS81 3.2 12.5 1.0
CE1 A:HIS87 3.2 9.7 1.0
OG A:SER58 3.9 9.7 1.0
CB A:ASP61 4.2 10.7 1.0
CB A:ASP238 4.2 10.8 1.0
CG A:HIS81 4.2 9.8 1.0
ND1 A:HIS81 4.2 11.2 1.0
CG A:HIS87 4.2 9.8 1.0
ND1 A:HIS87 4.2 10.5 1.0
O A:HOH2229 4.3 13.2 1.0
CD1 A:TRP60 4.5 10.5 1.0
CD2 A:HIS85 4.7 16.3 1.0
CA A:ASP61 4.8 8.8 1.0
N A:ASP61 4.8 8.5 1.0
O A:ASP238 4.9 11.6 1.0
CD1 A:TYR77 5.0 10.1 1.0
CB A:SER58 5.0 10.8 1.0
CB A:HIS85 5.0 13.6 1.0

Zinc binding site 2 out of 2 in 2dsn

Go back to Zinc Binding Sites List in 2dsn
Zinc binding site 2 out of 2 in the Crystal Structure of T1 Lipase


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 T1 Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:15.1
occ:1.00
OD2 B:ASP238 2.0 12.6 1.0
OD1 B:ASP61 2.1 11.7 1.0
NE2 B:HIS81 2.1 11.9 1.0
NE2 B:HIS87 2.2 10.6 1.0
OD2 B:ASP61 2.7 13.5 1.0
CG B:ASP238 2.7 12.3 1.0
CG B:ASP61 2.7 12.4 1.0
OD1 B:ASP238 2.8 13.3 1.0
CD2 B:HIS81 3.0 12.8 1.0
CD2 B:HIS87 3.1 12.4 1.0
CE1 B:HIS81 3.1 11.7 1.0
CE1 B:HIS87 3.2 12.8 1.0
OG B:SER58 3.9 10.3 1.0
CB B:ASP238 4.1 11.0 1.0
CG B:HIS81 4.2 12.2 1.0
ND1 B:HIS81 4.2 13.5 1.0
CB B:ASP61 4.2 11.3 1.0
CG B:HIS87 4.2 11.6 1.0
ND1 B:HIS87 4.3 12.2 1.0
O B:HOH2213 4.4 13.6 1.0
CD1 B:TRP60 4.6 11.2 1.0
CD2 B:HIS85 4.7 15.8 1.0
CA B:ASP61 4.8 11.8 1.0
N B:ASP61 4.8 11.3 1.0
O B:ASP238 4.9 11.2 1.0
CB B:HIS85 5.0 13.7 1.0
CB B:SER58 5.0 12.6 1.0

Reference:

H.Matsumura, T.Yamamoto, T.C.Leow, T.Mori, A.B.Salleh, M.Basri, T.Inoue, Y.Kai, R.N.Z.R.A.Rahman. Novel Cation-Pi Interaction Revealed By Crystal Structure of Thermoalkalophilic Lipase Proteins V. 70 592 2007.
ISSN: ISSN 0887-3585
PubMed: 17932933
DOI: 10.1002/PROT.21799
Page generated: Wed Oct 16 22:51:58 2024

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