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 Dec 12 12:57:27 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