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Iodine in PDB 1sd5: Crystal Structure of RV1626

Protein crystallography data

The structure of Crystal Structure of RV1626, PDB code: 1sd5 was solved by J.P.Morth, V.Feng, L.J.Perry, D.I.Svergun, P.A.Tucker, Tb Structuralgenomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.68
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 44.558, 44.558, 180.965, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.6

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of RV1626 (pdb code 1sd5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of RV1626, PDB code: 1sd5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in 1sd5

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Iodine binding site 1 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:22.4
occ:0.75
 NH1 A:ARG184 3.7 19.4 1.0
CD A:ARG184 4.0 9.9 1.0
CG2 A:VAL191 4.1 10.3 1.0
CG2 A:THR186 4.2 8.2 1.0
CA A:VAL191 4.3 9.8 1.0
O A:HOH475 4.3 23.3 1.0
CG2 A:VAL194 4.3 12.5 1.0
N A:VAL191 4.5 9.5 1.0
O A:ARG190 4.5 10.1 1.0
CB A:VAL194 4.6 13.9 1.0
C A:ARG190 4.6 10.3 1.0
CZ A:ARG184 4.7 14.0 1.0
CB A:VAL191 4.8 9.4 1.0
NE A:ARG184 4.8 11.4 1.0
CB A:ARG184 5.0 7.5 1.0
CG1 A:VAL194 5.0 13.6 1.0

Iodine binding site 2 out of 19 in 1sd5

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Iodine binding site 2 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:18.6
occ:1.00
 O A:HOH451 3.5 25.1 1.0
O A:HOH560 3.6 33.6 1.0
CB A:HIS57 3.9 6.7 1.0
O A:HOH620 4.1 33.9 1.0
O A:LEU53 4.1 8.2 1.0
CB A:LEU17 4.1 7.7 1.0
CG2 A:VAL41 4.2 12.4 1.0
CG A:PRO59 4.2 7.2 1.0
CB A:PRO59 4.2 7.3 1.0
CB A:LEU53 4.2 5.2 1.0
CD A:PRO59 4.2 8.3 1.0
CA A:GLY42 4.2 11.9 1.0
CD1 A:LEU17 4.3 11.7 1.0
N A:GLY42 4.3 11.2 1.0
O A:VAL41 4.4 9.7 1.0
ND1 A:HIS57 4.4 14.5 1.0
C A:LEU53 4.4 9.7 1.0
C A:VAL41 4.5 10.1 1.0
CD2 A:LEU17 4.5 9.2 1.0
CG A:LEU17 4.5 8.2 1.0
CG A:HIS57 4.5 9.2 1.0
CA A:LEU53 4.8 6.9 1.0
CA A:LEU17 4.9 9.3 1.0
N A:ALA54 4.9 8.6 1.0
CB A:VAL41 4.9 9.8 1.0
N A:PRO59 4.9 8.5 1.0

Iodine binding site 3 out of 19 in 1sd5

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Iodine binding site 3 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:21.2
occ:0.90
 NZ A:LYS58 3.9 8.4 1.0
CG A:GLU55 4.0 11.5 1.0
O A:HOH553 4.0 29.6 1.0
CB A:GLU55 4.0 7.9 1.0
CE A:LYS58 4.1 7.3 1.0
CG A:LYS83 4.2 14.2 1.0
O A:HOH582 4.2 42.4 1.0
CB A:LYS83 4.3 11.7 1.0
O A:GLU55 4.3 10.3 1.0
CA A:GLU55 4.3 7.7 1.0
CD A:GLU55 4.4 11.7 1.0
CD A:LYS83 4.5 16.2 1.0
CD1 A:ILE85 4.6 17.6 1.0
CG2 A:ILE85 4.6 19.1 1.0
CE A:LYS83 4.6 18.4 1.0
OE2 A:GLU55 4.8 24.6 1.0
C A:GLU55 4.8 9.2 1.0
OE1 A:GLU55 4.8 13.8 1.0

Iodine binding site 4 out of 19 in 1sd5

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Iodine binding site 4 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:19.1
occ:0.50
 O A:HOH565 3.5 36.5 1.0
O A:HOH460 3.5 18.9 1.0
CA A:PRO123 4.0 8.7 1.0
CG2 A:ILE122 4.2 12.6 1.0
CB A:GLU126 4.2 9.6 1.0
N A:PRO123 4.3 9.1 1.0
CG A:GLU126 4.4 16.3 1.0
CG A:PRO123 4.4 13.0 1.0
CB A:PRO123 4.4 11.2 1.0
CD A:GLU126 4.6 23.1 1.0
O A:ILE122 4.6 8.9 1.0
C A:ILE122 4.6 6.6 1.0
OE1 A:GLU126 4.7 29.3 1.0
CD A:PRO123 4.7 10.3 1.0
O A:HOH423 4.9 17.7 1.0

Iodine binding site 5 out of 19 in 1sd5

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Iodine binding site 5 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:29.6
occ:0.70
 O A:HOH504 3.6 25.6 1.0
NH1 A:ARG84 3.9 15.0 1.0
CG A:ARG148 4.0 18.7 1.0
O A:HOH558 4.1 38.4 1.0
CD A:ARG148 4.1 16.6 1.0
CD A:ARG152 4.2 15.6 1.0
O A:HOH452 4.3 28.5 1.0
CD2 A:LEU149 4.5 26.0 1.0
O A:ARG148 4.6 17.6 1.0
CB A:ARG152 4.7 10.1 1.0
CD1 A:ILE135 4.7 22.7 1.0
C A:ARG148 4.7 16.2 1.0
CB A:ARG148 4.7 15.6 1.0
CA A:LEU149 4.8 16.5 1.0
OE2 A:GLU139 4.8 18.4 1.0
N A:LEU149 4.9 14.8 1.0
CG A:ARG152 4.9 14.4 1.0
NE A:ARG152 5.0 20.2 1.0

Iodine binding site 6 out of 19 in 1sd5

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Iodine binding site 6 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:24.5
occ:0.50
 O A:HOH426 3.4 16.0 1.0
CD2 A:PHE132 3.8 5.4 1.0
CG1 A:VAL129 4.0 10.7 1.0
NE A:ARG133 4.0 31.9 1.0
CE2 A:PHE132 4.2 8.1 1.0
O A:HOH591 4.2 36.4 1.0
CD A:PRO13 4.2 27.9 1.0
CG A:PRO87 4.3 10.2 1.0
NH1 A:ARG133 4.4 38.5 1.0
CD A:PRO87 4.4 10.5 1.0
CG A:PRO13 4.5 11.9 1.0
CG A:ARG133 4.6 13.7 1.0
CZ A:ARG133 4.6 34.8 1.0
CG2 A:VAL129 4.7 8.7 1.0
CB A:VAL129 4.8 8.3 1.0
CG A:PHE132 4.9 6.8 1.0
CD A:ARG133 4.9 20.3 1.0
O A:VAL129 4.9 8.7 1.0

Iodine binding site 7 out of 19 in 1sd5

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Iodine binding site 7 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:21.1
occ:0.30
 I A:IOD407 0.0 21.1 0.3
I A:IOD407 1.7 17.8 0.3
CG1 A:ILE135 3.0 15.8 1.0
CD1 A:ILE135 3.3 22.7 1.0
NH2 A:ARG152 3.3 25.0 1.0
O A:ARG131 3.5 7.3 1.0
O A:HOH429 3.6 22.9 1.0
NE A:ARG152 3.6 20.2 1.0
CZ A:ARG152 3.9 24.1 1.0
CD A:GLU134 4.1 7.8 1.0
CB A:ARG131 4.1 5.8 1.0
C A:ARG131 4.2 8.9 1.0
OE2 A:GLU134 4.2 8.2 1.0
CA A:ARG131 4.3 7.7 1.0
CG A:GLU134 4.3 6.1 1.0
CA A:ALA108 4.3 13.5 1.0
CB A:ALA108 4.4 15.3 1.0
CB A:ILE135 4.4 9.9 1.0
OE1 A:GLU134 4.4 9.1 1.0
N A:ILE135 4.4 7.1 1.0
CB A:GLU134 4.5 5.2 1.0
CG A:ARG131 4.6 5.4 1.0
N A:ALA108 4.7 12.1 1.0
CA A:ILE135 4.8 7.2 1.0
C A:GLY107 4.8 14.7 1.0
O A:GLY107 4.9 16.5 1.0
O A:HOH554 4.9 36.8 1.0
CD A:ARG152 4.9 15.6 1.0
OE2 A:GLU156 5.0 10.9 1.0

Iodine binding site 8 out of 19 in 1sd5

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Iodine binding site 8 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:17.8
occ:0.30
 I A:IOD407 0.0 17.8 0.3
I A:IOD407 1.7 21.1 0.3
O A:HOH429 3.3 22.9 1.0
NH2 A:ARG152 3.5 25.0 1.0
O A:HOH554 3.8 36.8 1.0
OE2 A:GLU156 3.8 10.9 1.0
NH2 A:ARG104 3.9 21.0 1.0
NE A:ARG152 3.9 20.2 1.0
OE2 A:GLU134 4.0 8.2 1.0
CD A:GLU134 4.0 7.8 1.0
CG A:ARG131 4.1 5.4 1.0
OE1 A:GLU134 4.1 9.1 1.0
CB A:ARG131 4.1 5.8 1.0
CZ A:ARG152 4.2 24.1 1.0
CD A:GLU156 4.3 13.0 1.0
CD A:ARG131 4.4 6.3 1.0
CA A:ARG131 4.6 7.7 1.0
O A:ARG131 4.6 7.3 1.0
OE1 A:GLU156 4.7 17.6 1.0
CG1 A:ILE135 4.7 15.8 1.0
CD1 A:ILE135 4.8 22.7 1.0
CG A:GLU134 4.8 6.1 1.0
NZ A:LYS159 4.8 9.6 1.0
CZ A:ARG104 4.9 20.4 1.0
NE A:ARG104 4.9 22.1 1.0
NE A:ARG131 4.9 8.3 1.0

Iodine binding site 9 out of 19 in 1sd5

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Iodine binding site 9 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:23.2
occ:0.33
 I A:IOD408 0.0 23.2 0.3
O A:HOH601 2.5 39.7 1.0
I A:IOD408 2.8 28.2 0.3
O A:HOH421 3.2 17.5 1.0
O A:HOH485 3.4 27.0 1.0
O A:GLU141 3.9 16.4 1.0
O A:HOH461 4.2 30.8 1.0
CG2 A:THR187 4.2 12.1 1.0
CB A:THR187 4.3 8.2 1.0
CE A:LYS189 4.4 29.1 1.0
O A:HOH611 4.4 35.3 1.0
CA A:VAL142 4.4 13.9 1.0
CB A:LYS189 4.4 13.8 1.0
CG2 A:VAL142 4.5 13.8 1.0
O A:HOH430 4.5 20.0 1.0
CD A:LYS189 4.6 21.4 1.0
OG1 A:THR187 4.7 9.7 1.0
C A:GLU141 4.7 14.5 1.0
CG A:GLU141 4.8 21.6 0.7
CB A:VAL142 4.9 13.7 1.0
N A:VAL142 4.9 13.4 1.0
OE2 A:GLU141 5.0 17.1 0.7
CG1 A:VAL142 5.0 15.7 1.0

Iodine binding site 10 out of 19 in 1sd5

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Iodine binding site 10 out of 19 in the Crystal Structure of RV1626


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 RV1626 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:28.2
occ:0.33
 I A:IOD408 0.0 28.2 0.3
I A:IOD408 2.8 23.2 0.3
OE2 A:GLU141 2.8 17.1 0.7
N A:LYS189 3.5 11.9 1.0
CD A:GLU141 3.7 24.3 0.7
CG A:GLU141 3.7 21.6 0.7
CG2 A:VAL142 3.7 13.8 1.0
CB A:LYS189 3.7 13.8 1.0
CB A:THR187 3.8 8.2 1.0
N A:MET188 4.0 10.9 1.0
O A:HOH485 4.1 27.0 1.0
CA A:LYS189 4.2 12.7 1.0
CB A:MET188 4.3 13.6 1.0
CG2 A:THR151 4.4 8.9 1.0
CB A:GLU141 4.5 17.8 0.7
CB A:GLU141 4.5 16.8 0.3
OG1 A:THR187 4.5 9.7 1.0
CG2 A:THR187 4.5 12.1 1.0
C A:MET188 4.5 12.2 1.0
CA A:MET188 4.5 12.0 1.0
O A:GLU141 4.5 16.4 1.0
OE2 A:GLU141 4.6 23.9 0.3
C A:THR187 4.6 9.9 1.0
C A:GLU141 4.6 14.5 1.0
CA A:THR187 4.6 9.5 1.0
N A:VAL142 4.8 13.4 1.0
CA A:VAL142 4.9 13.9 1.0
CB A:VAL142 4.9 13.7 1.0
OE1 A:GLU141 4.9 25.7 0.7

Reference:

J.P.Morth, V.Feng, L.J.Perry, D.I.Svergun, P.A.Tucker. The Crystal and Solution Structure of A Putative Transcriptional Antiterminator From Mycobacterium Tuberculosis. Structure V. 12 1595 2004.
ISSN: ISSN 0969-2126
PubMed: 15341725
DOI: 10.1016/J.STR.2004.06.018
Page generated: Sun Aug 11 12:47:27 2024

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