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Chlorine in PDB 6f1r: Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment

Enzymatic activity of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment

All present enzymatic activity of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment:
3.2.1.17;

Protein crystallography data

The structure of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment, PDB code: 6f1r was solved by A.Camara-Artigas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.44 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.694, 78.694, 37.660, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 16.4

Other elements in 6f1r:

The structure of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment (pdb code 6f1r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment, PDB code: 6f1r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6f1r

Go back to Chlorine Binding Sites List in 6f1r
Chlorine binding site 1 out of 5 in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:19.9
occ:1.00
 H A:GLY26 2.4 16.4 1.0
HG A:SER24 2.7 21.7 1.0
HA A:GLN121 2.8 22.4 1.0
HA3 A:GLY26 2.9 16.7 1.0
HB2 A:SER24 3.0 19.7 1.0
OG A:SER24 3.1 18.1 1.0
N A:GLY26 3.2 13.7 1.0
HD11 A:ILE124 3.4 27.3 1.0
HG23 A:VAL120 3.4 21.0 1.0
CA A:GLY26 3.5 13.9 1.0
HG12 A:ILE124 3.5 25.4 1.0
HG2 A:GLN121 3.5 26.0 1.0
HB2 A:GLN121 3.5 24.6 1.0
CB A:SER24 3.6 16.4 1.0
CA A:GLN121 3.6 18.6 1.0
HD13 A:ILE124 3.7 27.3 1.0
CD1 A:ILE124 3.9 22.8 1.0
CB A:GLN121 3.9 20.6 1.0
N A:GLN121 3.9 17.7 1.0
CG A:GLN121 4.1 21.6 1.0
H A:ASN27 4.1 15.3 1.0
HA2 A:GLY26 4.1 16.7 1.0
HB3 A:SER24 4.2 19.7 1.0
CG1 A:ILE124 4.2 21.2 1.0
H A:GLN121 4.2 21.2 1.0
H A:LEU25 4.2 17.9 1.0
N A:LEU25 4.3 14.9 1.0
C A:VAL120 4.3 17.0 1.0
HG3 A:GLN121 4.3 26.0 1.0
CG2 A:VAL120 4.3 17.5 1.0
O A:VAL120 4.3 16.8 1.0
C A:LEU25 4.4 13.8 1.0
C A:SER24 4.4 14.5 1.0
C A:GLY26 4.5 13.2 1.0
HB3 A:LEU25 4.5 18.8 1.0
HG21 A:VAL120 4.6 21.0 1.0
N A:ASN27 4.6 12.8 1.0
HG13 A:ILE124 4.6 25.4 1.0
CA A:SER24 4.6 14.7 1.0
HD12 A:ILE124 4.8 27.3 1.0
HB A:VAL120 4.8 20.2 1.0
CA A:LEU25 4.8 14.7 1.0
C A:GLN121 4.8 17.8 1.0
HB3 A:GLN121 4.9 24.6 1.0
O A:SER24 4.9 15.1 1.0
HG22 A:VAL120 4.9 21.0 1.0
HG23 A:ILE124 4.9 24.2 1.0
HD22 A:ASN27 5.0 16.9 1.0
HG21 A:ILE124 5.0 24.2 1.0

Chlorine binding site 2 out of 5 in 6f1r

Go back to Chlorine Binding Sites List in 6f1r
Chlorine binding site 2 out of 5 in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:15.7
occ:1.00
 HH A:TYR23 2.4 15.8 1.0
OH A:TYR23 3.0 13.2 1.0
O A:HOH359 3.1 27.3 1.0
O A:HOH347 3.2 16.2 1.0
HE2 A:TYR23 3.2 14.7 1.0
HA3 A:GLY104 3.4 16.6 1.0
CZ A:TYR23 3.7 12.2 1.0
CE2 A:TYR23 3.7 12.2 1.0
HA2 A:GLY104 4.1 16.6 1.0
CA A:GLY104 4.2 13.8 1.0
O A:ARG21 4.6 14.6 1.0
N A:GLY104 4.7 14.7 1.0
H A:MET105 4.8 14.3 1.0
CE1 A:TYR23 4.9 12.8 1.0
H A:GLY104 4.9 17.6 1.0
CD2 A:TYR23 4.9 12.4 1.0

Chlorine binding site 3 out of 5 in 6f1r

Go back to Chlorine Binding Sites List in 6f1r
Chlorine binding site 3 out of 5 in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:31.3
occ:1.00
 H A:ILE88 2.5 19.1 1.0
HG12 A:ILE88 2.7 19.4 1.0
HA A:ASP87 2.9 22.9 1.0
HE1 A:HIS15 3.1 25.6 1.0
O A:HOH425 3.2 30.8 1.0
N A:ILE88 3.3 15.9 1.0
HB1 A:ALA11 3.3 21.0 1.0
O A:HOH305 3.4 27.9 1.0
HZ A:PHE3 3.4 21.1 1.0
HG23 A:ILE88 3.5 19.7 1.0
CG1 A:ILE88 3.7 16.2 1.0
CA A:ASP87 3.8 19.1 1.0
CE1 A:HIS15 3.8 21.3 1.0
C A:ASP87 4.1 17.0 1.0
HG13 A:ILE88 4.1 19.4 1.0
O A:SER86 4.1 19.6 0.7
HB2 A:ALA11 4.1 21.0 1.0
CB A:ALA11 4.1 17.5 1.0
O A:SER86 4.2 18.0 0.3
CG A:ASP87 4.2 24.3 1.0
OD1 A:ASP87 4.3 23.9 1.0
CB A:ILE88 4.3 15.7 1.0
CG2 A:ILE88 4.3 16.4 1.0
CZ A:PHE3 4.3 17.6 1.0
CA A:ILE88 4.3 15.1 1.0
HH21 A:ARG14 4.4 42.2 1.0
OD2 A:ASP87 4.5 27.3 1.0
HE2 A:PHE3 4.5 20.5 1.0
CB A:ASP87 4.5 21.8 1.0
HD13 A:ILE88 4.5 20.3 1.0
NE2 A:HIS15 4.5 22.1 1.0
CD1 A:ILE88 4.5 16.9 1.0
HD11 A:ILE88 4.6 20.3 1.0
HG21 A:ILE88 4.6 19.7 1.0
ND1 A:HIS15 4.6 20.5 1.0
HB3 A:ALA11 4.6 21.0 1.0
H A:THR89 4.7 18.7 1.0
HD1 A:HIS15 4.7 24.6 1.0
O A:HOH320 4.7 30.5 1.0
HB2 A:ASP87 4.8 26.1 1.0
N A:ASP87 4.8 18.3 1.0
CE2 A:PHE3 4.8 17.1 1.0
C A:SER86 4.9 18.6 0.7
C A:SER86 4.9 18.1 0.3
HG1 A:THR89 4.9 23.7 1.0

Chlorine binding site 4 out of 5 in 6f1r

Go back to Chlorine Binding Sites List in 6f1r
Chlorine binding site 4 out of 5 in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:21.5
occ:1.00
 H A:THR69 2.4 19.3 1.0
N A:THR69 3.2 16.1 1.0
HA2 A:GLY67 3.2 19.4 1.0
O A:HOH426 3.2 39.7 1.0
O A:THR69 3.2 18.6 1.0
O A:HOH383 3.2 15.8 1.0
H A:GLY67 3.2 18.7 1.0
O A:HOH438 3.3 32.4 1.0
C A:GLY67 3.5 16.6 1.0
H A:ARG68 3.5 18.5 1.0
N A:ARG68 3.5 15.4 1.0
C A:THR69 3.5 17.8 1.0
CA A:GLY67 3.6 16.2 1.0
HB A:THR69 3.7 18.6 1.0
N A:GLY67 3.7 15.6 1.0
OD1 A:ASN65 3.7 18.1 1.0
O A:HOH354 3.8 33.1 1.0
OG A:SER72 3.8 22.2 1.0
CA A:THR69 3.8 16.3 1.0
O A:HOH393 4.0 20.6 1.0
O A:GLY67 4.1 19.1 1.0
C A:ARG68 4.2 17.5 1.0
CB A:THR69 4.2 15.5 1.0
H A:ASP66 4.3 15.8 1.0
CA A:ARG68 4.3 16.8 1.0
HA A:PRO70 4.3 26.5 1.0
OD1 A:ASP66 4.3 13.8 1.0
N A:PRO70 4.3 19.6 1.0
HA A:ARG68 4.4 20.1 1.0
HG1 A:THR69 4.4 17.8 1.0
HA3 A:GLY67 4.5 19.4 1.0
HA A:THR69 4.7 19.6 1.0
H A:SER72 4.7 29.0 1.0
NA A:NA206 4.7 18.1 1.0
C A:ASP66 4.8 14.6 1.0
CA A:PRO70 4.8 22.1 1.0
OG1 A:THR69 4.9 14.8 1.0
CG A:ASN65 4.9 17.5 1.0
HA A:ASN65 4.9 17.0 1.0
N A:ASP66 4.9 13.2 1.0
HB3 A:SER72 5.0 27.3 1.0

Chlorine binding site 5 out of 5 in 6f1r

Go back to Chlorine Binding Sites List in 6f1r
Chlorine binding site 5 out of 5 in the Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Tetragonal Lysozyme Crystallized at 298 K and pH 4.5 with Phosphate Bound: Control Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:35.2
occ:1.00
 HE2 A:PHE38 2.8 17.7 1.0
HZ1 A:LYS33 2.9 26.2 1.0
HZ3 A:TRP123 3.0 23.9 1.0
O A:HOH424 3.2 34.6 1.0
HD3 A:ARG5 3.3 24.9 1.0
HB2 A:ARG5 3.3 23.3 1.0
HD3 A:LYS33 3.5 20.8 1.0
CE2 A:PHE38 3.7 14.8 1.0
NZ A:LYS33 3.8 21.8 1.0
CZ3 A:TRP123 3.9 19.9 1.0
HZ2 A:LYS33 4.1 26.2 1.0
HZ A:PHE38 4.2 16.7 1.0
HE2 A:LYS33 4.2 23.5 1.0
HZ3 A:LYS33 4.2 26.2 1.0
CD A:ARG5 4.3 20.7 1.0
CB A:ARG5 4.3 19.4 1.0
CD A:LYS33 4.3 17.3 1.0
CE A:LYS33 4.3 19.6 1.0
CZ A:PHE38 4.4 13.9 1.0
HE A:ARG5 4.4 25.9 1.0
HD2 A:PHE38 4.5 17.1 1.0
HE3 A:TRP123 4.6 22.2 1.0
CD2 A:PHE38 4.6 14.2 1.0
HB3 A:ARG5 4.6 23.3 1.0
HH2 A:TRP123 4.6 24.6 1.0
CG A:ARG5 4.7 19.7 1.0
HG3 A:ARG5 4.7 23.7 1.0
CE3 A:TRP123 4.7 18.5 1.0
CH2 A:TRP123 4.8 20.5 1.0
NE A:ARG5 4.8 21.5 1.0
HD2 A:LYS33 4.8 20.8 1.0
HD2 A:ARG5 4.9 24.9 1.0
H A:ARG5 4.9 21.0 1.0

Reference:

M.Plaza-Garrido, M.C.Salinas-Garcia, A.Camara-Artigas. Orthorhombic Lysozyme Crystallization at Acidic pH Values Driven By Phosphate Binding. Acta Crystallogr D Struct V. 74 480 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29717719
DOI: 10.1107/S205979831800517X
Page generated: Sat Jul 27 22:52:55 2024

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