Atomistry » Sodium » PDB 2czs-2e4r » 2dsn
Atomistry »
  Sodium »
    PDB 2czs-2e4r »
      2dsn »

Sodium 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:

Zinc (Zn) 2 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of T1 Lipase (pdb code 2dsn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of T1 Lipase, PDB code: 2dsn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2dsn

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of T1 Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2101

b:19.8
occ:0.58
O A:HOH2202 2.6 32.0 1.0
OG A:SER113 2.7 17.8 1.0
NE2 A:HIS358 2.8 14.0 1.0
CZ A:PHE16 3.1 18.4 1.0
CE2 A:PHE16 3.2 19.5 1.0
CB A:SER113 3.3 12.9 1.0
CE1 A:PHE16 3.4 18.6 1.0
CD2 A:HIS358 3.4 12.6 1.0
CD2 A:PHE16 3.5 19.0 1.0
CD1 A:PHE16 3.7 17.1 1.0
CG A:PHE16 3.7 15.7 1.0
CE1 A:HIS358 4.0 13.9 1.0
N A:PHE16 4.1 9.4 1.0
CE1 A:HIS112 4.6 11.5 1.0
CA A:SER113 4.7 11.4 1.0
CG A:HIS358 4.7 12.1 1.0
N A:THR17 4.7 13.3 1.0
CG2 A:ILE319 4.8 13.4 1.0
CB A:PHE16 4.8 12.8 1.0
OG1 A:THR17 4.9 25.1 1.0
CA A:PHE16 4.9 11.1 1.0
CA A:GLY15 4.9 9.3 1.0
OH A:TYR29 4.9 12.0 1.0
ND1 A:HIS358 5.0 13.0 1.0
C A:GLY15 5.0 8.8 1.0
ND1 A:HIS112 5.0 10.8 1.0

Sodium binding site 2 out of 2 in 2dsn

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of T1 Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2102

b:19.8
occ:0.48
OG B:SER113 2.6 18.6 1.0
O B:HOH2203 2.7 29.6 1.0
NE2 B:HIS358 2.8 12.0 1.0
CZ B:PHE16 2.9 23.7 1.0
CE2 B:PHE16 3.0 23.5 1.0
CE1 B:PHE16 3.2 22.9 1.0
CB B:SER113 3.3 14.3 1.0
CD2 B:PHE16 3.3 21.5 1.0
CD2 B:HIS358 3.4 11.8 1.0
CD1 B:PHE16 3.6 19.3 1.0
CG B:PHE16 3.6 17.6 1.0
CE1 B:HIS358 4.0 13.9 1.0
N B:PHE16 4.2 12.4 1.0
CE1 B:HIS112 4.7 13.0 1.0
CG B:HIS358 4.7 12.4 1.0
CG2 B:ILE319 4.7 12.9 1.0
CA B:SER113 4.7 12.4 1.0
CB B:PHE16 4.8 15.0 1.0
CA B:PHE16 4.9 12.6 1.0
CA B:GLY15 4.9 12.2 1.0
ND1 B:HIS358 4.9 11.1 1.0
OH B:TYR29 5.0 13.4 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: Tue Dec 15 05:47:38 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