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Iodine in PDB 1hc0: Structure of Lysozyme with Periodate

Enzymatic activity of Structure of Lysozyme with Periodate

All present enzymatic activity of Structure of Lysozyme with Periodate:
3.2.1.17;

Protein crystallography data

The structure of Structure of Lysozyme with Periodate, PDB code: 1hc0 was solved by J.Ondracek, F.Jursik, J.Brynda, P.Rezacova, J.Sedlacek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.82
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.765, 77.765, 37.555, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1hc0:

The structure of Structure of Lysozyme with Periodate also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Lysozyme with Periodate (pdb code 1hc0). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Structure of Lysozyme with Periodate, PDB code: 1hc0:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 1hc0

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Iodine binding site 1 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

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

b:18.1
occ:0.25
 O A:HOH4136 1.0 33.2 0.8
I A:IOD132 1.5 21.9 0.8
O A:HOH4133 1.9 16.1 0.8
O A:HOH4134 2.1 13.0 0.8
O A:HOH1181 2.2 14.5 0.5
O A:HOH4131 2.6 19.4 0.8
O A:HOH4135 2.9 18.7 0.8
O A:HOH8132 3.2 24.3 0.5
O A:HOH4132 3.4 22.8 0.8
O A:HOH1064 3.7 28.2 1.0
O A:SER86 4.0 27.3 1.0
CA A:ASP87 4.4 21.2 1.0
I A:IOD136 4.4 30.5 0.5
CZ A:PHE3 4.5 16.7 1.0
O A:HOH1080 4.5 32.5 1.0
NZ A:LYS1 4.6 20.9 1.0
N A:ILE88 4.7 20.7 1.0
C A:SER86 4.8 23.4 1.0
CE2 A:PHE3 4.9 14.2 1.0
NH2 A:ARG14 5.0 29.6 1.0
N A:ASP87 5.0 18.8 1.0

Iodine binding site 2 out of 10 in 1hc0

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Iodine binding site 2 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I131

b:23.5
occ:0.55
 O A:HOH3132 1.4 23.6 0.6
O A:HOH3134 1.7 26.9 0.6
O A:HOH3133 1.8 16.5 0.6
O A:HOH3135 1.8 17.5 0.6
O A:HOH3136 1.9 0.9 0.6
O A:HOH3131 2.0 29.2 0.6
ND1 A:HIS15 3.8 21.1 1.0
ND2 A:ASN93 4.1 26.6 1.0
O A:HOH1168 4.4 23.3 0.5
O A:HIS15 4.5 20.9 1.0
OD1 A:ASN93 4.5 31.9 1.0
NZ A:LYS96 4.6 29.4 1.0
CA A:HIS15 4.6 12.2 1.0
CE1 A:HIS15 4.7 23.6 1.0
CG A:HIS15 4.8 17.9 1.0
CG A:ASN93 4.8 25.5 1.0
I A:IOD139 4.8 35.5 0.4
CB A:HIS15 4.8 14.4 1.0
C A:HIS15 4.9 16.6 1.0
O A:HOH1196 5.0 16.9 0.5

Iodine binding site 3 out of 10 in 1hc0

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Iodine binding site 3 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I132

b:21.9
occ:0.75
 I A:IOD130 1.5 18.1 0.2
O A:HOH4131 1.6 19.4 0.8
O A:HOH4134 1.8 13.0 0.8
O A:HOH4136 1.9 33.2 0.8
O A:HOH4135 1.9 18.7 0.8
O A:HOH4132 2.0 22.8 0.8
O A:HOH4133 2.0 16.1 0.8
O A:HOH1080 3.6 32.5 1.0
O A:HOH1181 3.6 14.5 0.5
NH2 A:ARG14 3.6 29.6 1.0
O A:HOH8132 4.2 24.3 0.5
OD1 A:ASP87 4.2 20.3 1.0
N A:ILE88 4.3 20.7 1.0
NE2 A:HIS15 4.3 21.6 1.0
CA A:ASP87 4.4 21.2 1.0
O A:HOH1064 4.5 28.2 1.0
CZ A:ARG14 4.7 14.6 1.0
CG1 A:ILE88 4.7 14.2 1.0
CG A:ASP87 4.8 37.3 1.0
CB A:ALA11 4.8 20.7 1.0
O A:SER86 4.8 27.3 1.0
NE A:ARG14 4.8 28.9 1.0
C A:ASP87 4.9 24.3 1.0
CB A:ASP87 5.0 30.6 1.0

Iodine binding site 4 out of 10 in 1hc0

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Iodine binding site 4 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I133

b:12.2
occ:0.47
 O A:HOH5134 1.6 21.3 1.0
O A:HOH5135 1.7 30.5 1.0
O A:HOH5132 1.7 17.8 1.0
O A:HOH5133 1.9 26.4 1.0
O A:HOH5131 2.0 20.4 1.0
O A:HOH5136 2.1 15.8 0.5
ND2 A:ASN44 3.8 16.2 1.0
O A:HOH1067 3.9 17.6 1.0
O A:HOH1024 4.0 20.9 1.0
O A:HOH1039 4.1 38.2 1.0
O A:GLU35 4.2 16.6 1.0
CA A:SER36 4.6 13.2 1.0
O A:HOH1102 4.7 35.0 1.0
C A:SER36 4.8 17.1 1.0
CG A:ASN44 4.8 16.5 1.0
OD1 A:ASN44 4.8 17.9 1.0
O A:SER36 4.9 14.9 1.0
CB A:ALA42 4.9 21.4 1.0
C A:GLU35 5.0 13.6 1.0

Iodine binding site 5 out of 10 in 1hc0

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Iodine binding site 5 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I134

b:16.5
occ:0.55
 O A:HOH6134 1.7 17.2 0.6
O A:HOH6133 1.8 9.5 0.6
O A:HOH6131 1.8 18.8 1.0
O A:HOH6135 1.9 31.9 1.0
O A:HOH6136 2.0 24.0 1.0
O A:HOH6132 2.0 9.6 0.6
OD2 A:ASP52 3.5 21.3 1.0
OE2 A:GLU35 3.6 18.9 1.0
OE1 A:GLU35 3.7 16.0 1.0
N A:VAL109 3.9 21.1 1.0
O A:HOH1059 4.0 29.9 1.0
CD A:GLU35 4.0 22.6 1.0
O A:HOH1146 4.1 21.9 0.5
CB A:VAL109 4.5 27.9 1.0
O A:HOH1095 4.6 38.0 1.0
O A:GLN57 4.6 16.3 1.0
CG A:ASP52 4.6 21.2 1.0
O A:HOH1007 4.7 19.7 1.0
N A:ALA110 4.7 12.9 1.0
CA A:TRP108 4.7 17.5 1.0
C A:TRP108 4.7 21.1 1.0
CA A:VAL109 4.7 22.6 1.0
CG2 A:VAL109 4.9 25.6 1.0
CB A:GLN57 4.9 14.6 1.0

Iodine binding site 6 out of 10 in 1hc0

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Iodine binding site 6 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:25.6
occ:0.23
 O A:HOH7135 1.7 23.2 0.2
O A:HOH7133 1.7 14.3 0.2
O A:HOH7131 1.7 34.3 0.2
O A:HOH7132 1.7 14.8 0.2
O A:HOH7136 1.7 11.9 0.2
O A:HOH7134 1.7 30.8 0.2
OD1 A:ASP18 3.8 26.7 1.0
OD2 A:ASP18 3.9 28.4 1.0
O A:HOH1143 4.0 34.0 0.5
CG A:ASP18 4.3 26.7 1.0
O A:HOH1026 4.4 28.3 1.0
OD1 A:ASN19 4.5 33.5 1.0
CB A:SER24 4.8 15.9 1.0
CD1 A:ILE124 4.8 23.1 1.0
ND2 A:ASN19 4.9 39.3 1.0
O A:HOH1139 5.0 24.0 0.5

Iodine binding site 7 out of 10 in 1hc0

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Iodine binding site 7 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I136

b:30.5
occ:0.46
 O A:HOH8133 1.7 42.3 0.5
O A:HOH8132 1.7 24.3 0.5
O A:HOH8131 1.7 0.9 0.5
OG A:SER86 3.5 32.1 1.0
O A:HOH1181 3.8 14.5 0.5
O A:HOH4133 4.0 16.1 0.8
O A:HOH1117 4.3 18.6 0.5
CB A:SER86 4.3 18.9 1.0
I A:IOD130 4.4 18.1 0.2
O A:SER86 4.7 27.3 1.0
C A:SER86 4.7 23.4 1.0
N A:ASP87 4.8 18.8 1.0
O A:HOH4136 4.9 33.2 0.8

Iodine binding site 8 out of 10 in 1hc0

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Iodine binding site 8 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I137

b:32.7
occ:0.38
 O A:HOH1136 1.4 7.5 0.5
O A:HOH1196 2.5 16.9 0.5
O A:HOH1103 3.5 39.9 1.0
OG1 A:THR89 3.6 20.4 1.0
O A:HOH1029 4.2 24.3 1.0
NH2 A:ARG14 4.2 29.6 1.0
NH1 A:ARG14 4.2 29.7 1.0
OD2 A:ASP87 4.2 39.7 1.0
OD1 A:ASP87 4.6 20.3 1.0
CB A:THR89 4.7 15.2 1.0
CZ A:ARG14 4.7 14.6 1.0
CG2 A:THR89 4.8 20.5 1.0
CG A:ASP87 4.8 37.3 1.0
CE1 A:HIS15 4.9 23.6 1.0

Iodine binding site 9 out of 10 in 1hc0

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Iodine binding site 9 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I138

b:32.4
occ:0.42
 O A:HOH2131 1.7 26.4 1.0
O A:HOH2132 1.7 14.5 0.4
O A:HOH1129 3.1 45.5 1.0
O A:THR69 3.3 20.9 1.0
O A:HOH1096 3.3 48.1 1.0
O A:HOH1077 3.5 27.7 0.5
CB A:SER72 3.8 34.2 1.0
C A:THR69 3.9 19.1 1.0
O A:HOH1135 4.0 9.6 0.2
N A:THR69 4.0 19.8 1.0
OD1 A:ASN65 4.0 27.1 1.0
C A:GLY67 4.1 33.9 1.0
CA A:GLY67 4.1 28.4 1.0
O A:HOH1061 4.1 19.8 1.0
N A:ARG68 4.3 18.8 1.0
CA A:THR69 4.5 21.0 1.0
O A:GLY67 4.5 24.5 1.0
N A:GLY67 4.5 12.0 1.0
OG A:SER72 4.6 43.7 1.0
O A:HOH1114 4.6 27.2 0.5
N A:PRO70 4.7 26.0 1.0
CA A:PRO70 4.8 28.5 1.0
N A:SER72 4.9 37.6 1.0
C A:ARG68 4.9 23.0 1.0
CA A:ARG68 5.0 20.2 1.0

Iodine binding site 10 out of 10 in 1hc0

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Iodine binding site 10 out of 10 in the Structure of Lysozyme with Periodate


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Lysozyme with Periodate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I139

b:35.5
occ:0.36
 O A:HOH1029 2.2 24.3 1.0
O A:HOH3134 3.4 26.9 0.6
NH1 A:ARG14 3.7 29.7 1.0
O A:HOH1123 3.8 26.9 0.5
O A:HOH3131 4.0 29.2 0.6
O A:HOH1022 4.2 20.7 1.0
O A:HOH1196 4.5 16.9 0.5
O A:HOH3136 4.6 0.9 0.6
CD A:ARG14 4.8 36.9 1.0
I A:IOD131 4.8 23.5 0.6
CZ A:ARG14 5.0 14.6 1.0

Reference:

J.Ondracek, M.S.Weiss, J.Brynda, J.Fiala, F.Jursik, P.Rezacova, L.B.Jenner, J.Sedlacek. Regular Arrangement of Periodates Bound to Lysozyme. Acta Crystallogr.,Sect.D V. 61 1181 2005.
ISSN: ISSN 0907-4449
PubMed: 16131750
DOI: 10.1107/S090744490501543X
Page generated: Sun Aug 11 12:12:23 2024

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