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Chlorine in PDB 4ngz: Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K

Enzymatic activity of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K

All present enzymatic activity of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K:
3.2.1.17;

Protein crystallography data

The structure of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K, PDB code: 4ngz was solved by P.Benas, L.Legrand, M.Ries-Kautt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.57 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.589, 78.589, 37.017, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.5

Other elements in 4ngz:

The structure of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K also contains other interesting chemical elements:

Ytterbium (Yb) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K (pdb code 4ngz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K, PDB code: 4ngz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4ngz

Go back to Chlorine Binding Sites List in 4ngz
Chlorine binding site 1 out of 3 in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:19.5
occ:0.99
 OH A:TYR23 3.0 15.9 1.0
O A:HOH313 3.1 28.6 0.9
CZ A:TYR23 3.7 15.6 1.0
CE2 A:TYR23 3.7 15.3 1.0
CA A:GLY104 4.2 14.4 1.0
O A:ARG21 4.5 19.4 1.0
N A:GLY104 4.8 16.8 1.0
CE1 A:TYR23 4.8 14.3 1.0
CD2 A:TYR23 5.0 16.0 1.0

Chlorine binding site 2 out of 3 in 4ngz

Go back to Chlorine Binding Sites List in 4ngz
Chlorine binding site 2 out of 3 in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:24.9
occ:0.93
 OG A:SER24 3.0 19.4 1.0
N A:GLY26 3.2 16.8 1.0
CB A:SER24 3.5 19.6 1.0
CA A:GLY26 3.5 17.6 1.0
CA A:GLN121 3.6 22.7 1.0
CD1 A:ILE124 3.9 26.5 1.0
N A:GLN121 3.9 18.8 1.0
CB A:GLN121 4.1 27.7 1.0
N A:LEU25 4.2 16.8 1.0
O A:VAL120 4.2 17.3 1.0
C A:VAL120 4.2 17.7 1.0
CG1 A:ILE124 4.3 22.9 1.0
C A:LEU25 4.3 16.6 1.0
CG2 A:VAL120 4.3 20.1 1.0
C A:SER24 4.3 17.4 1.0
CA A:SER24 4.5 18.8 1.0
CG A:GLN121 4.5 38.4 1.0
C A:GLY26 4.6 15.3 1.0
N A:ASN27 4.7 15.3 1.0
CA A:LEU25 4.7 16.1 1.0
O A:SER24 4.8 15.6 1.0
C A:GLN121 4.8 21.8 1.0
CB A:LEU25 5.0 17.5 1.0

Chlorine binding site 3 out of 3 in 4ngz

Go back to Chlorine Binding Sites List in 4ngz
Chlorine binding site 3 out of 3 in the Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Previously De-Ionized Hew Lysozyme Crystallized in 0.5 M YBCL3/30% (V/V) Glycerol and Collected at 125K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:34.4
occ:0.95
 CE2 A:PHE38 3.7 15.9 1.0
NZ A:LYS33 3.9 25.4 1.0
CZ3 A:TRP123 3.9 23.1 1.0
CE A:LYS33 4.0 24.3 1.0
CD A:ARG5 4.2 21.6 1.0
CD A:LYS33 4.3 22.5 1.0
CB A:ARG5 4.3 20.2 1.0
CZ A:PHE38 4.4 14.7 1.0
CD2 A:PHE38 4.6 14.7 1.0
CG A:ARG5 4.6 20.6 1.0
NE A:ARG5 4.8 23.8 1.0
CE3 A:TRP123 4.8 20.9 1.0
CH2 A:TRP123 4.8 22.6 1.0
O A:HOH413 4.8 30.6 1.0

Reference:

P.Benas, N.Auzeil, L.Legrand, F.Brachet, A.Regazzetti, M.Ries-Kautt. Weak Protein-Cationic Co-Ion Interactions Addressed By X-Ray Crystallography and Mass Spectrometry. Acta Crystallogr.,Sect.D V. 70 2217 2014.
ISSN: ISSN 0907-4449
PubMed: 25084340
DOI: 10.1107/S1399004714011304
Page generated: Sun Jul 21 22:14:11 2024

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