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Iodine in PDB 4jxj: Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing

Enzymatic activity of Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing

All present enzymatic activity of Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing:
2.1.1.182;

Protein crystallography data

The structure of Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing, PDB code: 4jxj was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.380, 81.330, 38.490, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.5

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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing (pdb code 4jxj). 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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing, PDB code: 4jxj:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 4jxj

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Iodine binding site 1 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:25.8
occ:0.19
 CG1 A:ILE84 3.5 36.8 1.0
CA A:ILE84 3.7 35.6 1.0
NH2 A:ARG58 3.9 38.3 1.0
CB A:ILE84 3.9 35.5 1.0
CG2 A:ILE84 4.0 34.1 1.0
CD A:ARG58 4.0 31.5 1.0
CD1 A:TYR87 4.1 46.4 1.0
CE1 A:TYR87 4.3 48.4 1.0
N A:ILE84 4.4 37.2 1.0
CG A:ARG58 4.6 27.7 1.0
CD1 A:ILE84 4.8 37.2 1.0
CZ A:ARG58 4.8 35.8 1.0
NE A:ARG58 4.9 34.2 1.0
C A:ILE84 4.9 33.8 1.0
O A:ILE84 4.9 32.3 1.0
CE1 A:HIS88 4.9 28.9 1.0
O A:GLU83 4.9 39.0 1.0
C A:GLU83 5.0 39.5 1.0
ND1 A:HIS88 5.0 30.0 1.0

Iodine binding site 2 out of 12 in 4jxj

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Iodine binding site 2 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:15.2
occ:0.17
 O A:LYS110 2.4 20.7 1.0
OG1 A:THR112 3.3 18.1 1.0
N A:ASN45 3.4 19.5 1.0
C A:LYS110 3.6 19.4 1.0
O A:HOH514 3.6 33.0 1.0
O A:ASN45 3.6 17.0 1.0
CB A:SER44 3.8 21.6 1.0
CB A:LYS110 3.8 23.4 1.0
CB A:ASN45 4.0 20.4 1.0
CA A:SER44 4.1 21.8 1.0
CA A:ASN45 4.1 18.8 1.0
OG A:SER44 4.2 23.6 1.0
O A:HOH494 4.3 37.9 1.0
C A:SER44 4.3 20.0 1.0
N A:THR112 4.3 14.9 1.0
C A:ASN45 4.3 17.7 1.0
CA A:LYS110 4.3 21.1 1.0
CB A:THR112 4.4 16.2 1.0
CB A:ALA137 4.5 15.6 1.0
N A:ILE111 4.6 17.6 1.0
C A:ILE111 4.7 15.6 1.0
O A:HOH513 4.7 37.9 1.0
CA A:ILE111 4.8 16.5 1.0
CA A:THR112 4.9 15.7 1.0
O A:ASN109 5.0 21.1 1.0

Iodine binding site 3 out of 12 in 4jxj

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Iodine binding site 3 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:24.4
occ:0.38
 O A:HOH402 3.3 21.8 1.0
O A:TYR119 3.9 39.2 1.0
N A:GLN144 3.9 24.2 1.0
CA A:GLY122 3.9 24.9 1.0
CG A:GLN144 4.0 29.3 1.0
CA A:TYR119 4.0 35.8 1.0
CG2 A:VAL147 4.1 21.9 1.0
CD2 A:LEU143 4.1 27.1 1.0
N A:GLY122 4.3 26.9 1.0
CB A:LEU143 4.3 24.9 1.0
CB A:GLN144 4.3 27.1 1.0
C A:TYR119 4.4 36.8 1.0
CA A:LEU143 4.5 23.8 1.0
O A:PRO118 4.5 28.7 1.0
CB A:VAL147 4.6 20.4 1.0
CD A:GLN144 4.6 32.3 1.0
CB A:TYR119 4.7 38.0 1.0
CA A:GLN144 4.8 25.5 1.0
C A:LEU143 4.8 24.1 1.0
OE1 A:GLN144 4.8 33.4 1.0
CG1 A:VAL147 4.8 20.2 1.0
C A:GLY122 4.8 23.4 1.0
N A:THR123 4.8 22.9 1.0
N A:TYR119 4.9 34.0 1.0
CG A:LEU143 4.9 25.7 1.0

Iodine binding site 4 out of 12 in 4jxj

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Iodine binding site 4 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:26.5
occ:0.23
 N A:ARG162 3.6 19.5 1.0
CB A:PHE220 3.7 15.2 1.0
CA A:GLY161 3.8 21.6 1.0
CG A:PHE220 4.1 14.8 1.0
CD1 A:PHE220 4.2 15.0 1.0
C A:GLY161 4.2 20.1 1.0
O A:HOH435 4.2 34.3 1.0
CB A:ARG162 4.3 19.9 1.0
O A:PHE220 4.4 16.9 1.0
CA A:ARG162 4.6 19.3 1.0
CD2 A:PHE220 4.9 14.2 1.0
CA A:PHE220 5.0 15.9 1.0

Iodine binding site 5 out of 12 in 4jxj

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Iodine binding site 5 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:26.3
occ:0.62
 NH1 A:ARG162 3.6 20.6 1.0
CG2 A:THR123 3.9 23.9 1.0
CB A:ARG162 4.1 19.9 1.0
NH1 A:ARG150 4.1 34.3 1.0
CG A:ARG162 4.2 19.4 1.0
N A:LEU163 4.2 17.4 1.0
CD A:ARG162 4.3 20.2 1.0
CB A:LEU163 4.3 17.8 1.0
O A:HOH529 4.3 34.8 1.0
O A:HOH549 4.6 49.3 1.0
CA A:LEU163 4.6 17.2 1.0
CZ A:ARG162 4.7 20.5 1.0
C A:ARG162 4.9 18.6 1.0
NE A:ARG162 4.9 19.9 1.0

Iodine binding site 6 out of 12 in 4jxj

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Iodine binding site 6 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:23.3
occ:0.27
 O A:HOH506 3.9 29.8 1.0
CA A:GLU149 4.1 25.1 1.0
CB A:CYS152 4.1 24.1 1.0
CG A:LYS175 4.2 35.9 1.0
CB A:LYS175 4.2 33.9 1.0
CB A:GLU149 4.3 29.3 1.0
CE A:LYS175 4.5 37.0 1.0
SG A:CYS152 4.7 24.6 1.0
CD A:LYS175 4.7 36.5 1.0
N A:GLU149 4.7 22.7 1.0
O A:VAL148 4.8 20.5 1.0

Iodine binding site 7 out of 12 in 4jxj

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Iodine binding site 7 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:19.3
occ:0.21
 N A:ALA180 3.7 29.6 1.0
CD2 A:LEU30 4.1 30.1 1.0
CA A:VAL179 4.3 27.4 1.0
CB A:ALA180 4.3 32.5 1.0
CD1 A:LEU30 4.4 28.7 1.0
CB A:ALA183 4.5 34.9 1.0
C A:VAL179 4.5 28.1 1.0
CG1 A:VAL179 4.6 27.1 1.0
CA A:ALA180 4.6 30.9 1.0
O A:ASP178 4.6 26.9 1.0
O A:ALA180 4.8 29.1 1.0
CG A:LEU30 4.8 27.9 1.0
CB A:VAL179 5.0 26.7 1.0

Iodine binding site 8 out of 12 in 4jxj

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Iodine binding site 8 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:20.5
occ:0.15
 O A:HOH442 2.8 38.3 1.0
CA A:PRO204 3.5 25.5 1.0
CB A:PRO204 3.6 25.8 1.0
CD1 A:LEU208 3.9 24.1 1.0
CD2 A:LEU262 4.0 21.4 1.0
O A:HOH486 4.1 40.6 1.0
N A:ASN205 4.1 26.0 1.0
C A:PRO204 4.4 25.3 1.0
CG A:PRO204 4.6 25.4 1.0
N A:PRO204 4.6 25.7 1.0
CG A:LEU262 4.7 20.6 1.0
CD1 A:LEU262 4.8 20.2 1.0

Iodine binding site 9 out of 12 in 4jxj

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Iodine binding site 9 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I310

b:26.1
occ:0.22
 CD2 A:LEU214 2.2 21.9 1.0
CG A:LEU214 3.5 21.4 1.0
CA A:LEU214 3.6 18.5 1.0
N A:LEU214 3.8 18.3 1.0
CB A:LEU214 3.9 20.3 1.0
O A:GLU213 3.9 18.1 1.0
C A:GLU213 4.0 18.2 1.0
NH2 A:ARG162 4.1 21.1 1.0
O A:HOH512 4.1 37.2 1.0
CG A:GLU213 4.2 21.2 1.0
OE2 A:GLU213 4.5 23.6 1.0
CD A:GLU213 4.5 21.8 1.0
CB A:GLU213 4.5 19.8 1.0
CD1 A:LEU214 4.6 22.5 1.0
CA A:GLU213 4.9 17.8 1.0
CB A:LYS217 5.0 17.3 1.0
C A:LEU214 5.0 17.7 1.0

Iodine binding site 10 out of 12 in 4jxj

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Iodine binding site 10 out of 12 in the Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing


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 Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I311

b:27.6
occ:0.49
 O A:HOH450 3.0 37.7 1.0
N A:ARG223 3.6 31.2 1.0
O A:HOH417 4.0 28.0 1.0
CB A:ARG223 4.0 32.9 1.0
CA A:GLY222 4.2 27.5 1.0
NH1 A:ARG224 4.4 34.8 1.0
C A:GLY222 4.4 28.7 1.0
CA A:ARG223 4.4 31.1 1.0

Reference:

D.M.Dranow, J.Abendroth, T.E.Edwards, D.Lorimer. Crystal Structure of Ribosomal Rna Small Subunit Methyltransferase A From Rickettsia Bellii Determined By Iodide Sad Phasing To Be Published.
Page generated: Sun Aug 11 18:26:46 2024

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