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Zinc in PDB 4dt3: Crystal Structure of Zinc-Charged Lysozyme

Enzymatic activity of Crystal Structure of Zinc-Charged Lysozyme

All present enzymatic activity of Crystal Structure of Zinc-Charged Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Zinc-Charged Lysozyme, PDB code: 4dt3 was solved by Y.J.An, C.S.Jeong, S.S.Cha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.38 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.102, 79.102, 36.816, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.8

Other elements in 4dt3:

The structure of Crystal Structure of Zinc-Charged Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Zinc-Charged Lysozyme (pdb code 4dt3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Zinc-Charged Lysozyme, PDB code: 4dt3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4dt3

Go back to Zinc Binding Sites List in 4dt3
Zinc binding site 1 out of 3 in the Crystal Structure of Zinc-Charged Lysozyme


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 Zinc-Charged Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:32.1
occ:1.00
OD2 A:ASP52 2.0 13.2 1.0
O A:HOH357 2.1 13.3 1.0
O A:HOH353 2.2 18.1 1.0
O A:HOH354 2.3 12.7 1.0
O A:HOH356 2.3 14.8 1.0
O A:HOH355 2.3 19.8 1.0
CG A:ASP52 3.1 11.6 1.0
OD1 A:ASP52 3.6 11.7 1.0
O A:HOH343 3.7 18.9 1.0
O A:HOH382 3.8 18.1 1.0
O A:GLN57 4.2 8.5 1.0
OE2 A:GLU35 4.2 15.7 1.0
OE1 A:GLU35 4.2 11.4 1.0
ND2 A:ASN46 4.3 10.5 1.0
O A:HOH346 4.3 19.7 1.0
O A:HOH404 4.3 25.3 1.0
CB A:ASP52 4.4 8.3 1.0
O A:HOH345 4.4 24.4 1.0
O2 A:EDO204 4.4 27.5 1.0
O A:HOH331 4.5 40.5 1.0
CB A:GLN57 4.6 6.6 1.0
O A:HOH381 4.6 34.3 1.0
CD A:GLU35 4.6 12.2 1.0

Zinc binding site 2 out of 3 in 4dt3

Go back to Zinc Binding Sites List in 4dt3
Zinc binding site 2 out of 3 in the Crystal Structure of Zinc-Charged Lysozyme


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 Zinc-Charged Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:38.9
occ:1.00
NE2 A:HIS15 2.1 19.3 1.0
O A:HOH350 2.3 11.1 1.0
O A:HOH351 2.4 8.9 1.0
O A:HOH352 2.4 22.2 1.0
CD2 A:HIS15 3.0 19.8 1.0
CE1 A:HIS15 3.2 21.3 1.0
CG A:HIS15 4.2 18.7 1.0
ND1 A:HIS15 4.3 20.1 1.0
CG1 A:ILE88 4.5 13.1 1.0
OD1 A:ASP87 4.5 27.2 1.0
OD2 A:ASP87 4.6 28.1 1.0
O A:HOH335 4.7 39.4 1.0
CG A:ASP87 4.7 26.6 1.0
N A:ILE88 4.8 16.8 1.0
CB A:ALA11 4.9 13.2 1.0
OG1 A:THR89 4.9 18.5 1.0
O A:ALA11 5.0 11.7 1.0

Zinc binding site 3 out of 3 in 4dt3

Go back to Zinc Binding Sites List in 4dt3
Zinc binding site 3 out of 3 in the Crystal Structure of Zinc-Charged Lysozyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Zinc-Charged Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:57.2
occ:1.00
O A:HOH317 2.2 11.7 1.0
O A:HOH308 2.3 12.1 1.0
O A:HOH373 2.5 22.4 1.0
O A:HOH375 2.5 21.1 1.0
O A:HOH374 4.3 26.8 1.0
N A:ARG5 4.3 12.9 1.0
CA A:GLY4 4.4 12.9 1.0
N A:CYS6 4.4 12.6 1.0
C A:GLY4 4.6 12.1 1.0
CB A:CYS6 4.6 15.1 1.0

Reference:

S.S.Cha, Y.J.An, C.S.Jeong, M.K.Kim, S.G.Lee, K.H.Lee, B.H.Oh. Experimental Phasing Using Zinc Anomalous Scattering Acta Crystallogr.,Sect.D V. 68 1253 2012.
ISSN: ISSN 0907-4449
PubMed: 22948927
DOI: 10.1107/S0907444912024420
Page generated: Wed Dec 16 05:12:38 2020

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