Atomistry » Zinc » PDB 3czn-3d7g » 3d2z
Atomistry »
  Zinc »
    PDB 3czn-3d7g »
      3d2z »

Zinc in PDB 3d2z: Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys

Enzymatic activity of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys

All present enzymatic activity of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys:
3.5.1.28;

Protein crystallography data

The structure of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys, PDB code: 3d2z was solved by F.Kerff, S.Petrella, R.Herman, E.Sauvage, F.Mercier, A.Luxen, J.M.Frere, B.Joris, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 2.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.160, 89.160, 183.640, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 26.5

Other elements in 3d2z:

The structure of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys (pdb code 3d2z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys, PDB code: 3d2z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3d2z

Go back to Zinc Binding Sites List in 3d2z
Zinc binding site 1 out of 2 in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn262

b:19.6
occ:1.00
OD1 A:ASP161 1.9 9.6 1.0
ND1 A:HIS151 1.9 10.9 1.0
O A:HOH322 2.0 2.2 1.0
ND1 A:HIS35 2.3 13.2 1.0
CG A:ASP161 2.8 9.2 1.0
CG A:HIS151 2.9 10.1 1.0
CE1 A:HIS151 3.0 11.2 1.0
OD2 A:ASP161 3.0 9.8 1.0
CE1 A:HIS35 3.1 12.8 1.0
CB A:HIS151 3.2 9.1 1.0
CG A:HIS35 3.3 12.9 1.0
CB A:HIS35 3.7 12.2 1.0
N B:ALA1 3.9 32.9 1.0
CD2 A:HIS151 4.0 10.8 1.0
NE2 A:HIS151 4.0 10.9 1.0
CB B:ALA1 4.1 32.4 1.0
CB A:ASP161 4.2 8.4 1.0
CA A:HIS35 4.3 11.8 1.0
NE2 A:HIS35 4.3 13.3 1.0
CD2 A:HIS35 4.4 13.0 1.0
CA B:ALA1 4.6 32.2 1.0
CD A:LYS159 4.7 8.8 1.0
CA A:HIS151 4.8 8.4 1.0
CG A:LYS159 4.8 9.0 1.0
O A:TYR36 4.9 11.1 1.0
OE2 A:GLU104 4.9 15.5 1.0
N A:TYR36 4.9 11.9 1.0
NZ A:LYS159 5.0 9.2 1.0
O A:HIS84 5.0 14.3 1.0

Zinc binding site 2 out of 2 in 3d2z

Go back to Zinc Binding Sites List in 3d2z
Zinc binding site 2 out of 2 in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn263

b:52.6
occ:1.00
O A:HOH337 3.0 2.0 1.0
NE1 A:TRP73 4.0 16.1 1.0
CZ2 A:TRP73 4.5 15.6 1.0
CE2 A:TRP73 4.6 16.1 1.0

Reference:

F.Kerff, S.Petrella, F.Mercier, E.Sauvage, R.Herman, A.Pennartz, A.Zervosen, A.Luxen, J.M.Frere, B.Joris, P.Charlier. Specific Structural Features of the N-Acetylmuramoyl-L-Alanine Amidase Amid From Escherichia Coli and Mechanistic Implications For Enzymes of This Family. J.Mol.Biol. V. 397 249 2010.
ISSN: ISSN 0022-2836
PubMed: 20036252
DOI: 10.1016/J.JMB.2009.12.038
Page generated: Wed Dec 16 04:11:59 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