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Sodium in PDB 3umj: Crystal Structure of D311E Lipase

Enzymatic activity of Crystal Structure of D311E Lipase

All present enzymatic activity of Crystal Structure of D311E Lipase:
3.1.1.3;

Protein crystallography data

The structure of Crystal Structure of D311E Lipase, PDB code: 3umj was solved by R.Ruslan, R.N.Z.R.A.Rahman, T.C.Leow, M.S.M.Ali, M.Basri, A.B.Salleh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.17 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.323, 81.162, 100.140, 90.00, 96.49, 90.00
R / Rfree (%) 15.5 / 21.2

Other elements in 3umj:

The structure of Crystal Structure of D311E 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 D311E Lipase (pdb code 3umj). 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 D311E Lipase, PDB code: 3umj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3umj

Go back to Sodium Binding Sites List in 3umj
Sodium binding site 1 out of 2 in the Crystal Structure of D311E 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 D311E Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:26.2
occ:1.00
OH A:TYR29 2.9 4.3 1.0
N A:THR17 3.1 6.1 1.0
OG1 A:THR17 3.3 6.1 1.0
N A:PHE16 3.4 6.7 1.0
O A:THR17 3.5 3.9 1.0
CA A:GLY15 3.6 6.0 1.0
C A:GLY15 3.7 7.0 1.0
OG A:SER113 3.8 11.4 1.0
CZ A:TYR29 3.9 4.5 1.0
N A:GLY15 3.9 5.3 1.0
CB A:SER113 3.9 4.7 1.0
CE2 A:TYR29 3.9 2.0 1.0
CA A:THR17 4.0 5.4 1.0
C A:PHE16 4.1 7.3 1.0
C A:THR17 4.1 5.1 1.0
CB A:THR17 4.2 5.8 1.0
ND1 A:HIS112 4.2 6.1 1.0
CD1 A:PHE16 4.2 11.2 1.0
CA A:PHE16 4.3 6.2 1.0
CE1 A:HIS112 4.4 7.0 1.0
CE1 A:PHE16 4.4 16.9 1.0
CG A:PHE16 4.5 8.0 1.0
CG2 A:THR17 4.5 9.0 1.0
O A:GLY15 4.6 6.3 1.0
NE2 A:HIS358 4.6 4.8 1.0
CZ A:PHE16 4.8 16.6 1.0
CD2 A:PHE16 4.8 13.4 1.0
CE2 A:PHE16 5.0 15.1 1.0
CB A:PHE16 5.0 6.1 1.0

Sodium binding site 2 out of 2 in 3umj

Go back to Sodium Binding Sites List in 3umj
Sodium binding site 2 out of 2 in the Crystal Structure of D311E 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 D311E Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na904

b:44.2
occ:1.00
O B:HOH550 2.2 10.7 1.0
OG B:SER113 2.4 10.2 1.0
NE2 B:HIS358 3.2 9.5 1.0
CB B:SER113 3.2 7.1 1.0
CZ B:PHE16 3.3 20.6 1.0
CE2 B:PHE16 3.3 16.5 1.0
CE1 B:PHE16 3.4 19.6 1.0
CD2 B:PHE16 3.5 15.9 1.0
CD1 B:PHE16 3.6 14.6 1.0
N B:PHE16 3.6 5.4 1.0
CG B:PHE16 3.6 13.8 1.0
CD2 B:HIS358 3.8 2.4 1.0
N B:THR17 4.2 5.5 1.0
CA B:GLY15 4.3 5.2 1.0
C B:GLY15 4.4 5.0 1.0
CE1 B:HIS358 4.4 8.3 1.0
OH B:TYR29 4.5 4.6 1.0
CA B:PHE16 4.5 7.1 1.0
CB B:PHE16 4.6 7.6 1.0
CA B:SER113 4.7 6.5 1.0
C B:PHE16 4.7 5.9 1.0
CG2 B:THR17 4.7 4.6 1.0
CE1 B:HIS112 4.8 9.1 1.0
N B:GLN114 4.8 6.5 1.0
ND1 B:HIS112 4.9 7.0 1.0

Reference:

R.Ruslan, R.N.Z.R.A.Rahman, T.C.Leow, M.S.M.Ali, M.Basri, A.B.Salleh. Improvement of Thermal Stability Via Outer-Loop Ion Pair Interaction of Mutated T1 Lipase From Geobacillus Zalihae Strain T1 Int J Mol Sci V. 13 943 2012.
ISSN: ESSN 1422-0067
PubMed: 22312296
DOI: 10.3390/IJMS13010943
Page generated: Tue Dec 15 06:27:22 2020

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