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Iodine in PDB 3e3d: Structure of Hen Egg White Lysozyme with the Magic Triangle I3C

Enzymatic activity of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C

All present enzymatic activity of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C:
3.2.1.17;

Protein crystallography data

The structure of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C, PDB code: 3e3d was solved by T.Beck, T.Gruene, G.M.Sheldrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.40 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.830, 76.830, 38.870, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C (pdb code 3e3d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C, PDB code: 3e3d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 3e3d

Go back to Iodine Binding Sites List in 3e3d
Iodine binding site 1 out of 12 in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I130

b:19.8
occ:0.33
 I3 A:I3C130 0.0 19.8 0.3
C6 A:I3C130 2.1 17.5 0.3
C1 A:I3C130 3.0 17.2 0.3
C5 A:I3C130 3.0 16.4 0.3
O A:HOH1036 3.2 16.5 1.0
C7 A:I3C130 3.2 15.6 0.3
N13 A:I3C130 3.3 9.7 0.3
O8 A:I3C130 3.4 20.4 0.3
O A:ASN93 3.9 7.9 1.0
O9 A:I3C130 3.9 14.5 0.3
O A:HOH1086 4.2 29.7 1.0
C2 A:I3C130 4.3 15.2 0.3
C4 A:I3C130 4.4 13.0 0.3
CB A:LYS97 4.4 23.5 1.0
C A:ASN93 4.5 8.9 1.0
CA A:CYS76 4.7 10.6 1.0
O A:CYS76 4.8 13.1 1.0
C3 A:I3C130 4.9 15.0 0.3
CA A:CYS94 4.9 8.5 1.0
CB A:CYS76 4.9 10.9 1.0
SG A:CYS76 5.0 8.6 1.0
CB A:ASN93 5.0 15.4 1.0

Iodine binding site 2 out of 12 in 3e3d

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


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I130

b:13.5
occ:0.33
 I2 A:I3C130 0.0 13.5 0.3
C4 A:I3C130 2.1 13.0 0.3
OH A:TYR20 3.0 13.0 1.0
C3 A:I3C130 3.0 15.0 0.3
C5 A:I3C130 3.1 16.4 0.3
C10 A:I3C130 3.2 15.2 0.3
N13 A:I3C130 3.2 9.7 0.3
O12 A:I3C130 3.5 14.7 0.3
O A:HOH1117 3.6 28.0 1.0
O11 A:I3C130 3.7 16.8 0.3
O A:LYS96 3.7 9.7 1.0
OG A:SER100 3.9 13.1 1.0
C A:LYS96 4.0 10.3 1.0
N A:LYS97 4.1 10.3 1.0
CA A:LYS97 4.1 7.1 1.0
CB A:LYS96 4.3 9.2 1.0
CZ A:TYR20 4.3 8.7 1.0
C2 A:I3C130 4.3 15.2 0.3
C6 A:I3C130 4.4 17.5 0.3
CB A:SER100 4.5 11.0 1.0
NH2 A:ARG21 4.5 27.0 1.0
CB A:LYS97 4.7 23.5 1.0
CA A:LYS96 4.8 7.4 1.0
C1 A:I3C130 4.9 17.2 0.3
CE2 A:TYR20 4.9 8.1 1.0

Iodine binding site 3 out of 12 in 3e3d

Go back to Iodine Binding Sites List in 3e3d
Iodine binding site 3 out of 12 in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I130

b:17.7
occ:0.33
 I1 A:I3C130 0.0 17.7 0.3
C2 A:I3C130 2.1 15.2 0.3
C1 A:I3C130 3.0 17.2 0.3
C3 A:I3C130 3.0 15.0 0.3
C7 A:I3C130 3.2 15.6 0.3
C10 A:I3C130 3.3 15.2 0.3
O9 A:I3C130 3.4 14.5 0.3
O11 A:I3C130 3.6 16.8 0.3
O8 A:I3C130 3.8 20.4 0.3
O12 A:I3C130 3.8 14.7 0.3
O A:HOH1107 4.1 30.1 1.0
C6 A:I3C130 4.3 17.5 0.3
C4 A:I3C130 4.3 13.0 0.3
C5 A:I3C130 4.9 16.4 0.3

Iodine binding site 4 out of 12 in 3e3d

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


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I131

b:10.0
occ:0.60
 I3 A:I3C131 0.0 10.0 0.6
C6 A:I3C131 2.1 3.3 0.6
C1 A:I3C131 3.0 8.2 0.6
C5 A:I3C131 3.1 3.2 0.6
C7 A:I3C131 3.2 12.6 0.6
N13 A:I3C131 3.3 2.3 0.6
O9 A:I3C131 3.6 9.1 0.6
O A:HOH1070 3.7 27.2 1.0
O8 A:I3C131 3.7 13.2 0.6
O A:HOH1141 3.9 28.1 1.0
O A:HOH1084 4.2 23.3 1.0
C2 A:I3C131 4.4 9.5 0.6
C4 A:I3C131 4.4 6.4 0.6
O A:HOH1145 4.4 32.4 1.0
O A:HOH1053 4.4 16.0 1.0
O A:HOH1126 4.6 40.0 1.0
C3 A:I3C131 4.9 7.0 0.6

Iodine binding site 5 out of 12 in 3e3d

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


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I131

b:6.2
occ:0.60
 I2 A:I3C131 0.0 6.2 0.6
C4 A:I3C131 2.1 6.4 0.6
C5 A:I3C131 3.0 3.2 0.6
C3 A:I3C131 3.0 7.0 0.6
N13 A:I3C131 3.1 2.3 0.6
C10 A:I3C131 3.3 9.7 0.6
O11 A:I3C131 3.6 7.4 0.6
O12 A:I3C131 3.8 6.2 0.6
O A:HOH1026 4.0 8.1 1.0
CE A:LYS33 4.3 13.6 1.0
CH2 A:TRP123 4.3 15.8 1.0
C6 A:I3C131 4.3 3.3 0.6
C2 A:I3C131 4.3 9.5 0.6
CZ A:PHE34 4.4 6.4 1.0
CE1 A:PHE34 4.4 9.3 1.0
C1 A:I3C131 4.8 8.2 0.6
CZ2 A:TRP123 4.9 11.8 1.0
NZ A:LYS33 4.9 12.6 1.0

Iodine binding site 6 out of 12 in 3e3d

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


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I131

b:6.8
occ:0.60
 I1 A:I3C131 0.0 6.8 0.6
C2 A:I3C131 2.1 9.5 0.6
C3 A:I3C131 3.0 7.0 0.6
C1 A:I3C131 3.1 8.2 0.6
C10 A:I3C131 3.2 9.7 0.6
C7 A:I3C131 3.2 12.6 0.6
O8 A:I3C131 3.4 13.2 0.6
O12 A:I3C131 3.6 6.2 0.6
O11 A:I3C131 3.7 7.4 0.6
O9 A:I3C131 3.8 9.1 0.6
O A:HOH1073 4.0 14.2 1.0
C4 A:I3C131 4.3 6.4 0.6
OD1 A:ASN37 4.4 11.2 1.0
C6 A:I3C131 4.4 3.3 0.6
ND2 A:ASN37 4.4 13.6 1.0
NZ A:LYS33 4.6 12.6 1.0
O A:HOH1053 4.7 16.0 1.0
CG A:ASN37 4.7 8.3 1.0
O A:HOH1032 4.9 12.9 1.0
C5 A:I3C131 4.9 3.2 0.6

Iodine binding site 7 out of 12 in 3e3d

Go back to Iodine Binding Sites List in 3e3d
Iodine binding site 7 out of 12 in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I132

b:6.0
occ:0.31
 I3 A:I3C132 0.0 6.0 0.3
C6 A:I3C132 2.1 4.4 0.3
C1 A:I3C132 3.0 5.0 0.3
C5 A:I3C132 3.1 2.9 0.3
C7 A:I3C132 3.2 3.9 0.3
N13 A:I3C132 3.2 2.4 0.3
O9 A:I3C132 3.5 11.0 0.3
O8 A:I3C132 3.7 5.9 0.3
C2 A:I3C132 4.4 4.0 0.3
C4 A:I3C132 4.4 7.0 0.3
C3 A:I3C132 4.9 7.0 0.3

Iodine binding site 8 out of 12 in 3e3d

Go back to Iodine Binding Sites List in 3e3d
Iodine binding site 8 out of 12 in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I132

b:9.9
occ:0.31
 I2 A:I3C132 0.0 9.9 0.3
C4 A:I3C132 2.1 7.0 0.3
C3 A:I3C132 3.0 7.0 0.3
C5 A:I3C132 3.1 2.9 0.3
C10 A:I3C132 3.2 5.9 0.3
N13 A:I3C132 3.3 2.4 0.3
O11 A:I3C132 3.5 3.8 0.3
O12 A:I3C132 3.6 9.1 0.3
C2 A:I3C132 4.4 4.0 0.3
C6 A:I3C132 4.4 4.4 0.3
C1 A:I3C132 4.9 5.0 0.3

Iodine binding site 9 out of 12 in 3e3d

Go back to Iodine Binding Sites List in 3e3d
Iodine binding site 9 out of 12 in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I132

b:8.1
occ:0.31
 I1 A:I3C132 0.0 8.1 0.3
C2 A:I3C132 2.1 4.0 0.3
C1 A:I3C132 3.1 5.0 0.3
C3 A:I3C132 3.1 7.0 0.3
C10 A:I3C132 3.3 5.9 0.3
C7 A:I3C132 3.3 3.9 0.3
O8 A:I3C132 3.5 5.9 0.3
O11 A:I3C132 3.7 3.8 0.3
O12 A:I3C132 3.7 9.1 0.3
O9 A:I3C132 3.9 11.0 0.3
C6 A:I3C132 4.4 4.4 0.3
C4 A:I3C132 4.4 7.0 0.3
C5 A:I3C132 4.9 2.9 0.3

Iodine binding site 10 out of 12 in 3e3d

Go back to Iodine Binding Sites List in 3e3d
Iodine binding site 10 out of 12 in the Structure of Hen Egg White Lysozyme with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Hen Egg White Lysozyme with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I133

b:16.5
occ:0.25
 I3 A:I3C133 0.0 16.5 0.2
C6 A:I3C133 2.1 11.0 0.2
C1 A:I3C133 3.0 10.3 0.2
C5 A:I3C133 3.1 8.0 0.2
C7 A:I3C133 3.2 13.0 0.2
N13 A:I3C133 3.3 9.4 0.2
O8 A:I3C133 3.6 13.7 0.2
O9 A:I3C133 3.6 10.4 0.2
O A:HOH1147 3.8 24.2 1.0
NZ A:LYS1 4.2 12.7 0.6
CB A:SER86 4.2 14.9 1.0
O A:HOH1015 4.3 10.0 0.5
C2 A:I3C133 4.3 9.9 0.2
C4 A:I3C133 4.4 7.4 0.2
OG A:SER86 4.4 27.9 1.0
CD A:LYS1 4.6 10.8 0.6
CD A:LYS1 4.7 9.9 0.4
C3 A:I3C133 4.9 5.1 0.2

Reference:

T.Beck, A.Krasauskas, T.Gruene, G.M.Sheldrick. A Magic Triangle For Experimental Phasing of Macromolecules Acta Crystallogr.,Sect.D V. 64 1179 2008.
ISSN: ISSN 0907-4449
PubMed: 19020357
DOI: 10.1107/S0907444908030266
Page generated: Sun Aug 11 15:01:49 2024

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