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Iodine in PDB 6fro: Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.

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

All present enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.:
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 and 100 Mm Potassium Iodide., PDB code: 6fro 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) 39.41 / 1.42
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.832, 78.832, 35.360, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 27.6

Other elements in 6fro:

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

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

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide. (pdb code 6fro). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide., PDB code: 6fro:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 6fro

Go back to Iodine Binding Sites List in 6fro
Iodine binding site 1 out of 5 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:28.0
occ:0.50
H051 A:7MT208 3.0 16.7 0.8
HA3 A:GLY102 3.0 22.0 1.0
C A:GLY102 3.4 22.8 1.0
H072 A:7MT208 3.4 20.2 0.8
N06 A:7MT208 3.5 14.6 0.8
HB3 A:ASN103 3.5 16.7 1.0
O A:GLY102 3.6 21.2 1.0
N A:ASN103 3.7 16.9 1.0
C05 A:7MT208 3.7 17.2 0.8
CA A:GLY102 3.7 21.1 1.0
C07 A:7MT208 3.8 19.9 0.8
HA A:ASN103 3.8 13.8 1.0
H071 A:7MT208 3.8 19.0 0.8
H A:ASN103 4.0 16.4 1.0
H052 A:7MT208 4.1 17.3 0.8
CA A:ASN103 4.2 13.5 1.0
CB A:ASN103 4.4 17.0 1.0
HA2 A:GLY102 4.4 22.3 1.0
N A:GLY102 4.8 21.3 1.0
H041 A:7MT208 4.8 18.4 0.8
O26 A:7MT208 4.9 16.6 0.8
H A:GLY102 4.9 22.8 1.0
C04 A:7MT208 4.9 18.5 0.8
HB2 A:ASN103 5.0 14.6 1.0

Iodine binding site 2 out of 5 in 6fro

Go back to Iodine Binding Sites List in 6fro
Iodine binding site 2 out of 5 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:35.2
occ:0.60
HG A:SER24 2.4 26.1 1.0
H A:GLY26 2.4 20.7 1.0
HA A:GLN121 2.5 22.8 1.0
HB2 A:GLN121 2.7 24.4 1.0
HB2 A:SER24 2.9 22.7 1.0
HA3 A:GLY26 3.0 17.7 1.0
O A:HOH332 3.1 33.8 1.0
OG A:SER24 3.2 26.0 1.0
N A:GLY26 3.3 19.0 1.0
HG23 A:VAL120 3.4 22.4 1.0
CA A:GLN121 3.4 23.2 1.0
HG12 A:ILE124 3.5 28.7 1.0
CB A:GLN121 3.6 25.4 1.0
CB A:SER24 3.6 22.2 1.0
CA A:GLY26 3.7 17.4 1.0
HD11 A:ILE124 3.8 42.1 1.0
N A:GLN121 3.9 21.1 1.0
HD13 A:ILE124 4.0 41.7 1.0
HB3 A:GLN121 4.2 24.3 1.0
HB3 A:LEU25 4.2 23.0 1.0
CD1 A:ILE124 4.2 42.5 1.0
H A:GLN121 4.3 20.4 1.0
HB3 A:SER24 4.3 21.1 1.0
N A:LEU25 4.3 21.8 1.0
C A:VAL120 4.3 23.0 1.0
HA2 A:GLY26 4.3 18.0 1.0
O A:VAL120 4.3 22.5 1.0
H A:LEU25 4.3 22.4 1.0
CG1 A:ILE124 4.3 30.1 1.0
H A:ASN27 4.4 15.7 1.0
C A:SER24 4.4 21.8 1.0
CG2 A:VAL120 4.4 21.8 1.0
C A:LEU25 4.5 22.4 1.0
HG3 A:GLN121 4.5 44.0 1.0
CA A:SER24 4.6 18.6 1.0
C A:GLN121 4.6 29.1 1.0
CG A:GLN121 4.7 42.9 1.0
HG23 A:ILE124 4.7 25.9 1.0
HG21 A:ILE124 4.7 27.2 1.0
C A:GLY26 4.7 18.3 1.0
CA A:LEU25 4.8 21.1 1.0
HG21 A:VAL120 4.8 21.3 1.0
O A:SER24 4.8 21.2 1.0
O A:GLN121 4.8 32.5 1.0
N A:ASN27 4.9 16.1 1.0
HG13 A:ILE124 4.9 30.8 1.0
HG22 A:VAL120 5.0 21.9 1.0
HB A:VAL120 5.0 21.9 1.0

Iodine binding site 3 out of 5 in 6fro

Go back to Iodine Binding Sites List in 6fro
Iodine binding site 3 out of 5 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:41.0
occ:0.50
H A:ILE88 2.8 31.5 1.0
HG12 A:ILE88 2.8 31.5 1.0
HE1 A:HIS15 2.9 45.8 1.0
HA A:ASP87 3.2 35.0 1.0
HZ A:PHE3 3.3 36.6 1.0
HB1 A:ALA11 3.3 35.3 1.0
HG23 A:ILE88 3.7 30.7 1.0
O A:HOH414 3.8 21.6 1.0
N A:ILE88 3.8 30.7 1.0
CE1 A:HIS15 3.8 45.5 1.0
CG1 A:ILE88 3.9 29.8 1.0
HB2 A:ALA11 4.1 37.2 1.0
CB A:ALA11 4.2 35.5 1.0
HE1 A:PHE3 4.2 40.4 1.0
CA A:ASP87 4.3 33.9 1.0
CZ A:PHE3 4.3 35.9 1.0
O A:SER86 4.3 36.8 1.0
HG13 A:ILE88 4.4 30.5 1.0
OD2 A:ASP87 4.5 42.2 1.0
C A:ASP87 4.5 34.7 1.0
CG2 A:ILE88 4.6 29.0 1.0
HD13 A:ILE88 4.6 31.6 1.0
CB A:ILE88 4.6 28.6 1.0
HD11 A:ILE88 4.6 33.6 1.0
NE2 A:HIS15 4.6 46.6 1.0
CD1 A:ILE88 4.7 32.0 1.0
ND1 A:HIS15 4.7 44.5 1.0
CE1 A:PHE3 4.7 38.3 1.0
HD1 A:HIS15 4.7 43.6 1.0
CA A:ILE88 4.8 27.6 1.0
HA A:ALA11 4.8 38.0 1.0
HB3 A:ALA11 4.8 33.5 1.0
HG21 A:ILE88 5.0 28.4 1.0
H A:THR89 5.0 34.5 1.0

Iodine binding site 4 out of 5 in 6fro

Go back to Iodine Binding Sites List in 6fro
Iodine binding site 4 out of 5 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:22.2
occ:0.70
H292 A:7MT208 3.1 22.9 0.8
HH2 A:TRP62 3.4 43.8 1.0
O27 A:7MT208 3.8 24.7 0.8
CH2 A:TRP62 3.9 41.8 1.0
C18 A:7MT208 3.9 24.0 0.8
C29 A:7MT208 4.0 22.7 0.8
H291 A:7MT208 4.0 22.8 0.8
H032 A:7MT208 4.1 25.2 0.8
HZ3 A:TRP62 4.2 43.1 1.0
CZ3 A:TRP62 4.3 41.2 1.0
C16 A:7MT208 4.4 25.8 0.8
O28 A:7MT208 4.4 21.8 0.8
H151 A:7MT208 4.4 25.5 0.8
C15 A:7MT208 4.6 26.1 0.8
CZ2 A:TRP62 4.7 39.5 1.0
C11 A:7MT208 4.7 21.1 0.8
H031 A:7MT208 4.8 25.5 0.8
C03 A:7MT208 4.8 25.4 0.8
HZ2 A:TRP62 4.9 40.1 1.0
H191 A:7MT208 4.9 18.8 0.8
N09 A:7MT208 5.0 24.4 0.8

Iodine binding site 5 out of 5 in 6fro

Go back to Iodine Binding Sites List in 6fro
Iodine binding site 5 out of 5 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Potassium Iodide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:43.6
occ:0.60
H291 A:7MT208 3.4 22.8 0.8
H081 A:7MT208 4.1 23.2 0.8
C29 A:7MT208 4.4 22.7 0.8
H031 A:7MT208 4.4 25.5 0.8
H191 A:7MT208 4.5 18.8 0.8
H292 A:7MT208 4.7 22.9 0.8
C08 A:7MT208 4.8 23.0 0.8
H082 A:7MT208 4.9 23.1 0.8
N09 A:7MT208 5.0 24.4 0.8

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: Sun Dec 13 19:43:56 2020

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