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Chlorine in PDB 6f2i: Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4

Enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4

All present enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4, PDB code: 6f2i was solved by S.Engilberge, F.Riobe, S.Di Pietro, E.Girard, E.Dumont, O.Maury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.07 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.149, 78.149, 37.960, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.3

Other elements in 6f2i:

The structure of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 also contains other interesting chemical elements:

Terbium (Tb) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 (pdb code 6f2i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4, PDB code: 6f2i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6f2i

Go back to Chlorine Binding Sites List in 6f2i
Chlorine binding site 1 out of 4 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:18.6
occ:1.00
 H A:THR69 2.3 15.3 1.0
HG A:SER72 3.0 16.9 1.0
HA2 A:GLY67 3.1 11.9 1.0
O A:HOH366 3.1 12.9 1.0
H A:GLY67 3.2 11.6 1.0
O A:HOH438 3.2 35.7 1.0
O A:HOH337 3.3 37.0 1.0
N A:THR69 3.3 15.0 1.0
O A:THR69 3.3 17.3 1.0
H A:ARG68 3.5 16.4 1.0
C A:THR69 3.5 17.7 1.0
CA A:GLY67 3.6 14.6 1.0
OD1 A:ASN65 3.6 15.9 1.0
C A:GLY67 3.6 17.3 1.0
N A:ARG68 3.6 15.4 1.0
HB A:THR69 3.7 14.7 1.0
N A:GLY67 3.7 13.3 1.0
OG A:SER72 3.8 15.8 1.0
CA A:THR69 3.9 15.2 1.0
O A:HOH404 4.0 16.0 1.0
HA A:PRO70 4.0 21.6 1.0
H A:ASP66 4.1 12.1 1.0
N A:PRO70 4.2 19.4 1.0
O A:GLY67 4.3 19.6 1.0
CB A:THR69 4.3 16.3 1.0
OD1 A:ASP66 4.3 11.1 1.0
C A:ARG68 4.3 18.6 1.0
HG1 A:THR69 4.4 13.2 1.0
H A:SER72 4.4 19.3 1.0
CA A:ARG68 4.5 15.5 1.0
HA A:ARG68 4.6 16.2 1.0
HA3 A:GLY67 4.6 14.8 1.0
CA A:PRO70 4.6 21.0 1.0
HA A:ASN65 4.7 11.9 1.0
NA A:NA208 4.7 13.4 1.0
HD3 A:PRO70 4.8 19.7 1.0
C A:ASP66 4.8 14.1 1.0
CG A:ASN65 4.8 15.5 1.0
N A:ASP66 4.9 10.6 1.0
OG1 A:THR69 4.9 12.8 1.0
HA A:THR69 4.9 16.2 1.0
O A:HOH306 5.0 28.6 1.0
CB A:SER72 5.0 16.6 1.0

Chlorine binding site 2 out of 4 in 6f2i

Go back to Chlorine Binding Sites List in 6f2i
Chlorine binding site 2 out of 4 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:18.5
occ:1.00
 H A:GLY26 2.2 14.6 1.0
HG A:SER24 2.5 17.8 1.0
HA A:GLN121 2.7 18.1 1.0
HB2 A:SER24 2.8 16.2 1.0
HA3 A:GLY26 2.8 14.4 1.0
HG2 A:GLN121 3.0 31.8 1.0
N A:GLY26 3.1 11.8 1.0
OG A:SER24 3.1 18.9 1.0
O A:HOH403 3.1 37.2 1.0
HD11 A:ILE124 3.2 36.1 1.0
CB A:SER24 3.4 15.7 1.0
HD13 A:ILE124 3.5 36.0 1.0
CA A:GLY26 3.5 12.0 1.0
HG23 A:VAL120 3.5 22.4 1.0
HB2 A:GLN121 3.5 21.1 1.0
HG12 A:ILE124 3.6 22.8 1.0
CA A:GLN121 3.6 18.3 1.0
CD1 A:ILE124 3.8 36.1 1.0
CG A:GLN121 3.8 32.0 1.0
CB A:GLN121 3.8 20.5 1.0
H A:LEU25 4.0 11.3 1.0
N A:GLN121 4.1 18.1 1.0
N A:LEU25 4.1 12.0 1.0
H A:ASN27 4.1 12.3 1.0
HB3 A:SER24 4.1 16.4 1.0
HB3 A:LEU25 4.2 12.2 1.0
HG3 A:GLN121 4.2 32.8 1.0
HA2 A:GLY26 4.2 11.3 1.0
CG1 A:ILE124 4.2 23.3 1.0
C A:LEU25 4.3 12.1 1.0
C A:SER24 4.3 13.8 1.0
C A:VAL120 4.4 19.4 1.0
O A:VAL120 4.5 18.0 1.0
H A:GLN121 4.5 19.2 1.0
CA A:SER24 4.5 13.2 1.0
CG2 A:VAL120 4.5 22.2 1.0
C A:GLY26 4.6 12.8 1.0
CA A:LEU25 4.6 11.2 1.0
N A:ASN27 4.7 10.7 1.0
HG13 A:ILE124 4.7 22.3 1.0
HD12 A:ILE124 4.7 36.3 1.0
HG21 A:VAL120 4.7 22.5 1.0
O A:SER24 4.8 13.2 1.0
HE21 A:GLN121 4.8 52.0 1.0
C A:GLN121 4.8 20.6 1.0
HB A:VAL120 4.9 21.1 1.0
HD22 A:ASN27 4.9 12.5 1.0
O A:HOH382 4.9 16.6 1.0
HB3 A:GLN121 4.9 19.6 1.0
CB A:LEU25 4.9 11.8 1.0

Chlorine binding site 3 out of 4 in 6f2i

Go back to Chlorine Binding Sites List in 6f2i
Chlorine binding site 3 out of 4 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:22.1
occ:1.00
 H A:ILE88 2.4 11.6 1.0
O A:HOH460 2.6 50.1 1.0
HG12 A:ILE88 2.7 16.2 1.0
HA A:ASP87 2.8 13.9 1.0
HZ A:PHE3 2.9 16.5 1.0
O A:HOH373 3.0 25.4 1.0
HB1 A:ALA11 3.2 15.1 1.0
HG23 A:ILE88 3.3 15.7 1.0
N A:ILE88 3.3 11.8 1.0
O A:HOH322 3.4 19.9 1.0
HE1 A:HIS15 3.5 18.1 1.0
HH22 A:ARG14 3.7 20.5 1.0
CG1 A:ILE88 3.7 14.1 1.0
CA A:ASP87 3.8 14.0 1.0
CZ A:PHE3 3.9 14.6 1.0
HE2 A:PHE3 3.9 17.2 1.0
O A:SER86 3.9 18.6 1.0
C A:ASP87 4.0 13.7 1.0
HB2 A:ALA11 4.1 14.1 1.0
HH21 A:ARG14 4.1 19.1 1.0
CB A:ALA11 4.1 13.4 1.0
OD1 A:ASP87 4.1 19.3 1.0
HG13 A:ILE88 4.2 12.9 1.0
CG2 A:ILE88 4.2 15.1 1.0
NH2 A:ARG14 4.3 19.5 1.0
CB A:ILE88 4.3 13.1 1.0
CA A:ILE88 4.4 11.3 1.0
CE2 A:PHE3 4.4 15.4 1.0
HB3 A:ALA11 4.5 11.6 1.0
CE1 A:HIS15 4.5 19.1 1.0
H A:THR89 4.6 12.6 1.0
HD13 A:ILE88 4.6 16.3 1.0
CG A:ASP87 4.6 19.7 1.0
CB A:ASP87 4.6 16.0 1.0
CD1 A:ILE88 4.7 15.0 1.0
HZ3 A:LYS1 4.7 22.2 1.0
N A:ASP87 4.7 14.9 1.0
C A:SER86 4.8 16.7 1.0
HG21 A:ILE88 4.8 14.5 1.0
HD11 A:ILE88 4.8 16.0 1.0
HB2 A:ASP87 4.9 18.9 1.0
HG22 A:ILE88 5.0 14.1 1.0
CE1 A:PHE3 5.0 13.3 1.0

Chlorine binding site 4 out of 4 in 6f2i

Go back to Chlorine Binding Sites List in 6f2i
Chlorine binding site 4 out of 4 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:16.6
occ:1.00
 OH A:TYR23 3.0 12.8 1.0
O A:HOH399 3.1 33.0 1.0
HE2 A:TYR23 3.1 12.5 1.0
O A:HOH349 3.3 17.1 1.0
HA3 A:GLY104 3.4 10.2 1.0
HH A:TYR23 3.5 13.7 1.0
O A:HOH363 3.5 33.5 1.0
CZ A:TYR23 3.6 11.8 1.0
CE2 A:TYR23 3.7 11.2 1.0
CA A:GLY104 4.3 11.5 1.0
HA2 A:GLY104 4.4 13.5 1.0
O A:ARG21 4.5 14.7 1.0
H A:MET105 4.6 10.2 1.0
HH21 A:ARG21 4.6 32.0 0.5
HB3 A:ARG21 4.7 15.4 1.0
HE A:ARG21 4.7 39.6 0.5
CE1 A:TYR23 4.8 11.5 1.0
CD2 A:TYR23 4.9 11.5 1.0
N A:GLY104 4.9 12.2 1.0

Reference:

S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, C.Breyton, B.Franzetti, S.Shima, E.Girard, E.Dumont, O.Maury. Unveiling the Binding Modes of the Crystallophore, A Terbium-Based Nucleating and Phasing Molecular Agent For Protein Crystallography. Chemistry V. 24 9739 2018.
ISSN: ISSN 1521-3765
PubMed: 29806881
DOI: 10.1002/CHEM.201802172
Page generated: Sat Jul 27 22:55:19 2024

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