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Zinc 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:

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 D311E Lipase (pdb code 3umj). 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 D311E Lipase, PDB code: 3umj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3umj

Go back to Zinc Binding Sites List in 3umj
Zinc binding site 1 out of 2 in the Crystal Structure of D311E 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 D311E Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:12.8
occ:1.00
OD2 A:ASP238 2.1 9.1 1.0
NE2 A:HIS81 2.1 3.8 1.0
OD1 A:ASP61 2.1 5.7 1.0
NE2 A:HIS87 2.3 6.0 1.0
OD2 A:ASP61 2.8 7.2 1.0
CG A:ASP238 2.8 5.7 1.0
CG A:ASP61 2.8 6.4 1.0
OD1 A:ASP238 2.9 2.3 1.0
CD2 A:HIS81 3.0 6.7 1.0
CD2 A:HIS87 3.2 4.2 1.0
CE1 A:HIS81 3.2 5.0 1.0
CE1 A:HIS87 3.3 2.0 1.0
OG A:SER58 3.9 4.1 1.0
CG A:HIS81 4.2 5.9 1.0
CB A:ASP238 4.2 5.8 1.0
O A:HOH510 4.3 11.4 1.0
ND1 A:HIS81 4.3 8.7 1.0
CB A:ASP61 4.3 3.6 1.0
CG A:HIS87 4.4 3.5 1.0
ND1 A:HIS87 4.4 2.7 1.0
CD1 A:TRP60 4.5 7.0 1.0
CD2 A:HIS85 4.7 4.2 1.0
CA A:ASP61 4.9 4.0 1.0
N A:ASP61 4.9 3.6 1.0
CB A:SER58 5.0 2.2 1.0
O A:ASP238 5.0 6.2 1.0
CD1 A:TYR77 5.0 4.7 1.0
CB A:HIS85 5.0 2.1 1.0

Zinc binding site 2 out of 2 in 3umj

Go back to Zinc Binding Sites List in 3umj
Zinc binding site 2 out of 2 in the Crystal Structure of D311E 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 D311E Lipase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:13.4
occ:1.00
OD2 B:ASP238 2.0 11.8 1.0
OD1 B:ASP61 2.0 3.0 1.0
NE2 B:HIS81 2.1 4.6 1.0
NE2 B:HIS87 2.2 6.1 1.0
CG B:ASP61 2.7 4.6 1.0
OD2 B:ASP61 2.8 7.3 1.0
CG B:ASP238 2.8 9.9 1.0
OD1 B:ASP238 2.9 7.3 1.0
CE1 B:HIS81 3.0 8.1 1.0
CD2 B:HIS87 3.1 2.4 1.0
CD2 B:HIS81 3.1 4.2 1.0
CE1 B:HIS87 3.3 5.8 1.0
OG B:SER58 3.9 6.6 1.0
ND1 B:HIS81 4.2 8.5 1.0
CB B:ASP238 4.2 5.6 1.0
CG B:HIS81 4.2 8.8 1.0
CB B:ASP61 4.2 2.5 1.0
CG B:HIS87 4.3 8.2 1.0
ND1 B:HIS87 4.4 5.1 1.0
CD1 B:TRP60 4.5 2.0 1.0
O B:HOH444 4.5 10.3 1.0
CD2 B:HIS85 4.8 9.4 1.0
N B:ASP61 4.8 3.9 1.0
CA B:ASP61 4.8 3.0 1.0
O B:ASP238 4.9 7.7 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: Wed Dec 16 04:54:58 2020

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