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Iodine in PDB 6pbb: Crystal Structure of Hen Egg White Lysozyme in Complex with I3C

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C, PDB code: 6pbb was solved by J.Q.Truong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.51 / 1.89
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.160, 77.160, 38.201, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24

Other elements in 6pbb:

The structure of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C (pdb code 6pbb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C, PDB code: 6pbb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 6pbb

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Iodine binding site 1 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


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 in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:0.2
occ:0.54
 I3 A:I3C201 0.0 0.2 0.5
C6 A:I3C201 2.1 0.7 0.5
C5 A:I3C201 3.0 0.6 0.5
C1 A:I3C201 3.1 0.6 0.5
N13 A:I3C201 3.2 0.7 0.5
C7 A:I3C201 3.3 0.9 0.5
HN13 A:I3C201 3.4 0.1 0.5
HN1A A:I3C201 3.5 0.1 0.5
O9 A:I3C201 3.7 0.1 0.5
O8 A:I3C201 3.7 0.9 0.5
C4 A:I3C201 4.4 0.2 0.5
C2 A:I3C201 4.4 0.6 0.5
C3 A:I3C201 4.9 0.2 0.5

Iodine binding site 2 out of 12 in 6pbb

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Iodine binding site 2 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


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 in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:0.5
occ:0.54
 I2 A:I3C201 0.0 0.5 0.5
C4 A:I3C201 2.1 0.2 0.5
C3 A:I3C201 3.0 0.2 0.5
C5 A:I3C201 3.0 0.6 0.5
N13 A:I3C201 3.2 0.7 0.5
C10 A:I3C201 3.2 0.3 0.5
HN1A A:I3C201 3.5 0.1 0.5
HN13 A:I3C201 3.5 0.1 0.5
O11 A:I3C201 3.6 0.2 0.5
O12 A:I3C201 3.7 0.1 0.5
NE A:ARG45 4.3 59.2 1.0
C2 A:I3C201 4.3 0.6 0.5
C6 A:I3C201 4.4 0.7 0.5
CZ A:ARG45 4.5 63.3 1.0
NH2 A:ARG45 4.6 66.9 1.0
C1 A:I3C201 4.9 0.6 0.5
CD A:ARG45 4.9 52.6 1.0

Iodine binding site 3 out of 12 in 6pbb

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Iodine binding site 3 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


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 in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:0.7
occ:0.54
 I1 A:I3C201 0.0 0.7 0.5
C2 A:I3C201 2.1 0.6 0.5
O A:HOH349 3.0 47.6 1.0
C1 A:I3C201 3.0 0.6 0.5
C3 A:I3C201 3.0 0.2 0.5
C7 A:I3C201 3.2 0.9 0.5
C10 A:I3C201 3.2 0.3 0.5
O12 A:I3C201 3.7 0.1 0.5
O8 A:I3C201 3.7 0.9 0.5
O9 A:I3C201 3.7 0.1 0.5
O11 A:I3C201 3.7 0.2 0.5
O A:ASN46 4.3 44.1 1.0
C4 A:I3C201 4.4 0.2 0.5
C6 A:I3C201 4.4 0.7 0.5
CD A:ARG45 4.6 52.6 1.0
CB A:ARG45 4.6 36.5 1.0
C A:ASN46 4.7 42.0 1.0
O A:ARG45 4.8 36.5 1.0
CA A:THR47 4.9 53.1 1.0
C5 A:I3C201 4.9 0.6 0.5
CG A:ARG45 4.9 42.2 1.0
C A:ARG45 5.0 33.6 1.0

Iodine binding site 4 out of 12 in 6pbb

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Iodine binding site 4 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


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 in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:45.4
occ:0.57
 I3 A:I3C202 0.0 45.4 0.6
C6 A:I3C202 2.1 47.3 0.6
C5 A:I3C202 3.1 46.6 0.6
C1 A:I3C202 3.1 48.9 0.6
N13 A:I3C202 3.2 45.5 0.6
C7 A:I3C202 3.3 47.7 0.6
HN13 A:I3C202 3.4 54.6 0.6
HN1A A:I3C202 3.5 54.6 0.6
O9 A:I3C202 3.7 48.2 0.6
O8 A:I3C202 3.8 47.3 0.6
CD A:LYS97 4.1 40.1 1.0
O A:ASN93 4.1 32.5 1.0
CB A:LYS97 4.3 31.6 1.0
C4 A:I3C202 4.4 47.7 0.6
C2 A:I3C202 4.4 51.6 0.6
C A:ASN93 4.7 32.6 1.0
O A:CYS76 4.7 39.7 1.0
CG A:LYS97 4.8 35.2 1.0
CA A:CYS76 4.8 36.9 1.0
C3 A:I3C202 4.9 50.5 0.6
SG A:CYS76 4.9 30.7 1.0

Iodine binding site 5 out of 12 in 6pbb

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Iodine binding site 5 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


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 in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:48.0
occ:0.57
 I2 A:I3C202 0.0 48.0 0.6
C4 A:I3C202 2.1 47.7 0.6
C3 A:I3C202 3.0 50.5 0.6
C5 A:I3C202 3.1 46.6 0.6
C10 A:I3C202 3.2 52.1 0.6
N13 A:I3C202 3.3 45.5 0.6
OH A:TYR20 3.3 37.5 1.0
HN1A A:I3C202 3.5 54.6 0.6
O11 A:I3C202 3.5 52.6 0.6
HN13 A:I3C202 3.5 54.6 0.6
O12 A:I3C202 3.7 52.7 0.6
O A:LYS96 3.9 30.7 1.0
OG A:SER100 3.9 38.2 1.0
C A:LYS96 4.1 30.4 1.0
CA A:LYS97 4.2 31.7 1.0
N A:LYS97 4.2 28.8 1.0
C2 A:I3C202 4.3 51.6 0.6
C6 A:I3C202 4.4 47.3 0.6
CB A:LYS96 4.4 32.1 1.0
NH2 A:ARG21 4.4 49.7 0.6
CB A:SER100 4.5 41.4 1.0
CZ A:TYR20 4.6 36.0 1.0
CB A:LYS97 4.8 31.6 1.0
C1 A:I3C202 4.9 48.9 0.6
CA A:LYS96 4.9 29.8 1.0

Iodine binding site 6 out of 12 in 6pbb

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Iodine binding site 6 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I202

b:55.6
occ:0.57
 I1 A:I3C202 0.0 55.6 0.6
C2 A:I3C202 2.1 51.6 0.6
C1 A:I3C202 3.0 48.9 0.6
C3 A:I3C202 3.1 50.5 0.6
C7 A:I3C202 3.2 47.7 0.6
C10 A:I3C202 3.3 52.1 0.6
O8 A:I3C202 3.5 47.3 0.6
O12 A:I3C202 3.6 52.7 0.6
O9 A:I3C202 3.7 48.2 0.6
O11 A:I3C202 3.8 52.6 0.6
C4 A:I3C202 4.4 47.7 0.6
C6 A:I3C202 4.4 47.3 0.6
NZ A:LYS97 4.4 49.6 1.0
C5 A:I3C202 4.9 46.6 0.6

Iodine binding site 7 out of 12 in 6pbb

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Iodine binding site 7 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:56.2
occ:0.26
 I3 A:I3C203 0.0 56.2 0.3
C6 A:I3C203 2.1 53.0 0.3
C5 A:I3C203 3.0 51.2 0.3
C1 A:I3C203 3.1 52.2 0.3
N13 A:I3C203 3.2 51.1 0.3
C7 A:I3C203 3.3 52.8 0.3
HN13 A:I3C203 3.4 61.3 0.3
HN1A A:I3C203 3.4 61.3 0.3
O8 A:I3C203 3.5 53.3 0.3
O A:HOH318 3.6 52.9 1.0
O9 A:I3C203 3.9 53.2 0.3
C4 A:I3C203 4.3 49.5 0.3
C2 A:I3C203 4.4 50.7 0.3
C3 A:I3C203 4.9 50.4 0.3

Iodine binding site 8 out of 12 in 6pbb

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Iodine binding site 8 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:46.8
occ:0.26
 I2 A:I3C203 0.0 46.8 0.3
C4 A:I3C203 2.1 49.5 0.3
C5 A:I3C203 3.0 51.2 0.3
C3 A:I3C203 3.1 50.4 0.3
N13 A:I3C203 3.2 51.1 0.3
C10 A:I3C203 3.3 50.5 0.3
HN1A A:I3C203 3.4 61.3 0.3
HN13 A:I3C203 3.4 61.3 0.3
O11 A:I3C203 3.7 50.9 0.3
O12 A:I3C203 3.8 50.8 0.3
ND2 A:ASN106 3.8 27.1 1.0
OD1 A:ASN103 4.2 56.7 1.0
C6 A:I3C203 4.3 53.0 0.3
C2 A:I3C203 4.4 50.7 0.3
CG A:ASN106 4.4 28.6 1.0
O A:ASN103 4.7 26.7 1.0
CG A:ASN103 4.8 52.7 1.0
CA A:ASN103 4.9 36.8 1.0
C1 A:I3C203 4.9 52.2 0.3
CB A:ASN103 4.9 43.2 1.0
CB A:ASN106 4.9 25.3 1.0

Iodine binding site 9 out of 12 in 6pbb

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Iodine binding site 9 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:49.4
occ:0.26
 I1 A:I3C203 0.0 49.4 0.3
C2 A:I3C203 2.1 50.7 0.3
C1 A:I3C203 3.1 52.2 0.3
C3 A:I3C203 3.1 50.4 0.3
C10 A:I3C203 3.2 50.5 0.3
C7 A:I3C203 3.2 52.8 0.3
O9 A:I3C203 3.5 53.2 0.3
O12 A:I3C203 3.6 50.8 0.3
O11 A:I3C203 3.7 50.9 0.3
O8 A:I3C203 3.8 53.3 0.3
C6 A:I3C203 4.4 53.0 0.3
C4 A:I3C203 4.4 49.5 0.3
C5 A:I3C203 4.9 51.2 0.3

Iodine binding site 10 out of 12 in 6pbb

Go back to Iodine Binding Sites List in 6pbb
Iodine binding site 10 out of 12 in the Crystal Structure of Hen Egg White Lysozyme in Complex with I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Hen Egg White Lysozyme in Complex with I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:65.0
occ:0.32
 I3 A:I3C204 0.0 65.0 0.3
C6 A:I3C204 2.1 65.2 0.3
C5 A:I3C204 3.1 66.6 0.3
C1 A:I3C204 3.1 64.3 0.3
N13 A:I3C204 3.2 66.0 0.3
C7 A:I3C204 3.2 62.1 0.3
HN13 A:I3C204 3.5 79.2 0.3
HN1A A:I3C204 3.5 79.2 0.3
O9 A:I3C204 3.5 61.3 0.3
O8 A:I3C204 3.8 61.3 0.3
CE A:LYS33 4.0 33.2 1.0
CH2 A:TRP123 4.3 29.9 1.0
C4 A:I3C204 4.4 69.1 0.3
C2 A:I3C204 4.4 65.5 0.3
NZ A:LYS33 4.4 36.0 1.0
CE1 A:PHE34 4.7 27.3 1.0
CZ2 A:TRP123 4.9 30.5 1.0
C3 A:I3C204 4.9 66.6 0.3
CZ A:PHE34 4.9 28.5 1.0

Reference:

J.Q.Truong, S.Panjikar, L.Shearwin-Whyatt, J.B.Bruning, K.E.Shearwin. Combining Random Microseed Matrix Screening and the Magic Triangle For the Efficient Structure Solution of A Potential Lysin From Bacteriophage P68. Acta Crystallogr D Struct V. 75 670 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31282476
DOI: 10.1107/S2059798319009008
Page generated: Sun Aug 11 23:50:04 2024

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