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Iodine in PDB 6d13: Crystal Structure of E.Coli Rpph-Dapf Complex

Enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf Complex

All present enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf Complex:
5.1.1.7;

Protein crystallography data

The structure of Crystal Structure of E.Coli Rpph-Dapf Complex, PDB code: 6d13 was solved by A.Gao, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.06
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.810, 85.810, 177.374, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 26.4

Other elements in 6d13:

The structure of Crystal Structure of E.Coli Rpph-Dapf Complex also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of E.Coli Rpph-Dapf Complex (pdb code 6d13). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of E.Coli Rpph-Dapf Complex, PDB code: 6d13:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 6d13

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Iodine binding site 1 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:0.1
occ:1.00
 CA A:GLY76 3.6 81.3 1.0
N A:ARG78 3.8 62.4 1.0
C A:GLY76 3.8 84.3 1.0
N A:GLY76 3.9 90.8 1.0
N A:CYS79 3.9 60.8 1.0
N A:ALA77 3.9 78.2 1.0
CE2 A:PHE13 4.0 61.7 1.0
CB A:ARG78 4.1 71.0 1.0
O A:HOH404 4.1 59.4 1.0
CZ A:ARG78 4.2 67.6 1.0
NH2 A:ARG78 4.3 62.3 1.0
SG A:CYS79 4.3 97.6 1.0
CA A:ARG78 4.4 67.8 1.0
NH1 A:ARG78 4.4 54.5 1.0
CB A:CYS79 4.5 72.2 1.0
CG A:ARG78 4.5 74.2 1.0
O A:GLY76 4.5 85.4 1.0
CZ A:PHE13 4.6 65.2 1.0
CA A:GLY8 4.6 70.5 1.0
C A:ARG78 4.6 77.2 1.0
NE A:ARG78 4.6 68.2 1.0
C A:ALA77 4.7 74.4 1.0
CA A:CYS79 4.8 65.8 1.0
CD2 A:PHE13 4.9 67.2 1.0
CA A:ALA77 4.9 72.7 1.0
N A:GLY8 4.9 65.2 1.0
O A:GLY74 5.0 84.7 1.0

Iodine binding site 2 out of 10 in 6d13

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Iodine binding site 2 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:0.6
occ:0.88
 NH2 A:ARG78 3.8 62.3 1.0
ND2 A:ASN11 3.9 93.2 1.0
N A:GLY218 3.9 82.6 1.0
CB A:ALA216 4.0 92.3 1.0
NH1 A:ARG78 4.1 54.5 1.0
O A:HOH404 4.1 59.4 1.0
CA A:GLY218 4.2 66.4 1.0
O A:GLY8 4.2 81.4 1.0
CB A:LEU9 4.2 78.5 1.0
CD1 A:LEU9 4.4 66.3 1.0
CZ A:ARG78 4.4 67.6 1.0
O A:ALA216 4.4 96.9 1.0
CD1 A:LEU247 4.5 77.8 1.0
C A:ALA216 4.5 98.2 1.0
CG A:LEU9 4.6 77.0 1.0
C A:CYS217 4.7 84.0 1.0
C A:GLY8 4.8 75.7 1.0
CD2 A:LEU247 4.9 89.4 1.0
CA A:ALA216 4.9 93.2 1.0
CG A:ASN11 4.9 95.7 1.0
N A:CYS217 4.9 98.1 1.0

Iodine binding site 3 out of 10 in 6d13

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Iodine binding site 3 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:77.8
occ:0.92
 OG A:SER26 3.3 74.4 1.0
C A:PHE25 3.8 78.1 1.0
O A:PHE25 3.9 79.0 1.0
CB A:SER26 4.0 61.8 1.0
N A:SER26 4.0 91.9 1.0
CD2 A:LEU29 4.1 63.2 1.0
CA A:PHE25 4.3 78.7 1.0
N A:PHE25 4.4 91.1 1.0
O A:PHE24 4.5 71.5 1.0
CA A:SER26 4.5 73.4 1.0
C A:PHE24 4.6 86.9 1.0
CB A:LEU29 4.7 65.0 1.0
CB A:PHE24 4.7 81.9 1.0

Iodine binding site 4 out of 10 in 6d13

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Iodine binding site 4 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:0.1
occ:0.61
 NE A:ARG85 3.7 77.7 1.0
NE A:ARG82 3.7 81.9 1.0
OD1 A:ASP112 3.8 0.1 1.0
CD A:ARG85 4.2 76.9 1.0
CB A:ARG85 4.2 74.5 1.0
CG A:ARG82 4.4 79.9 1.0
NH2 A:ARG82 4.5 94.2 1.0
CD2 A:LEU86 4.5 78.3 1.0
CD A:ARG82 4.5 78.1 1.0
CZ A:ARG82 4.6 86.0 1.0
CG A:ASP112 4.6 0.4 1.0
CG1 A:VAL108 4.7 70.7 1.0
CZ A:ARG85 4.7 85.0 1.0
O A:ARG82 4.7 84.0 1.0
CB A:ARG82 4.7 84.6 1.0
CA A:ARG82 4.8 81.1 1.0
CG A:LEU86 4.8 75.6 1.0
CG A:ARG85 4.9 73.6 1.0
NH2 A:ARG85 4.9 96.8 1.0

Iodine binding site 5 out of 10 in 6d13

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Iodine binding site 5 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:0.0
occ:0.84
 NE A:ARG142 3.6 79.9 1.0
N A:ARG142 3.8 89.1 1.0
NH2 A:ARG142 3.8 86.4 1.0
CD A:ARG184 3.8 0.2 1.0
CB A:ARG142 3.9 85.3 1.0
NH1 A:ARG184 3.9 0.9 1.0
CZ A:ARG142 4.0 87.5 1.0
O A:ILE140 4.0 0.1 1.0
CG A:ARG142 4.1 84.7 1.0
CE1 A:HIS182 4.1 0.1 1.0
NE2 A:HIS182 4.3 0.5 1.0
CA A:ARG142 4.4 85.9 1.0
CD A:ARG142 4.5 78.2 1.0
NE A:ARG184 4.6 0.6 1.0
O A:ARG142 4.6 92.8 1.0
CG A:ARG184 4.7 0.7 1.0
CZ A:ARG184 4.7 0.6 1.0
CA A:MET141 4.8 89.4 1.0
C A:MET141 4.8 95.0 1.0
C A:ARG142 5.0 99.2 1.0

Iodine binding site 6 out of 10 in 6d13

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Iodine binding site 6 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:0.8
occ:0.72
 N A:ALA171 3.8 0.4 1.0
CB A:ALA170 4.0 96.1 1.0
CA A:ALA170 4.1 0.2 1.0
CD2 A:LEU175 4.1 71.6 1.0
CG1 A:VAL164 4.3 62.5 1.0
C A:ALA170 4.5 0.3 1.0
CD2 A:PHE193 4.8 85.5 1.0
CE2 A:PHE193 4.8 82.6 1.0
CA A:ALA171 4.8 0.1 1.0
O A:ALA171 4.8 95.8 1.0
CB A:ALA171 5.0 0.5 1.0
C A:ALA171 5.0 96.2 1.0

Iodine binding site 7 out of 10 in 6d13

Go back to Iodine Binding Sites List in 6d13
Iodine binding site 7 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:0.5
occ:0.47
 CD A:ARG131 4.2 0.8 1.0
CB A:ARG131 4.6 87.0 1.0
CA A:ARG131 4.6 78.3 1.0
CB A:PRO129 4.7 77.6 1.0
O A:PHE130 4.8 73.0 1.0
CG A:PRO186 4.8 89.3 1.0
CG A:ARG131 4.9 0.1 1.0
C A:PHE130 4.9 73.7 1.0
N A:ARG131 4.9 76.3 1.0

Iodine binding site 8 out of 10 in 6d13

Go back to Iodine Binding Sites List in 6d13
Iodine binding site 8 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:0.4
occ:0.44
 NE2 A:HIS37 3.8 94.9 1.0
CE1 A:HIS37 4.4 98.5 1.0
CD A:ARG36 4.7 59.6 1.0
CB A:ARG36 4.7 62.3 1.0
CD2 A:HIS37 4.7 94.7 1.0
CG A:ARG36 5.0 52.1 1.0

Iodine binding site 9 out of 10 in 6d13

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Iodine binding site 9 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I201

b:94.7
occ:0.83
 CG A:PRO50 4.0 74.9 1.0
CD A:PRO50 4.0 68.3 1.0
CA B:ARG134 4.1 74.9 1.0
NH2 B:ARG145 4.1 0.4 1.0
CB B:ARG134 4.3 85.3 1.0
O B:VAL133 4.3 82.3 1.0
CZ B:ARG134 4.4 95.4 1.0
CD B:ARG141 4.4 92.2 1.0
NH2 B:ARG134 4.4 89.3 1.0
CG B:ARG134 4.6 94.3 1.0
NE B:ARG134 4.7 96.6 1.0
N B:ARG134 4.7 76.1 1.0
NH1 B:ARG134 4.7 0.8 1.0
NE B:ARG141 4.8 92.9 1.0
C B:VAL133 4.8 79.2 1.0
NH1 B:ARG141 4.8 99.8 1.0
CZ B:ARG141 4.9 0.7 1.0
CB A:PRO50 4.9 82.5 1.0

Iodine binding site 10 out of 10 in 6d13

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Iodine binding site 10 out of 10 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 E.Coli Rpph-Dapf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I202

b:0.2
occ:0.68
 NH1 B:ARG82 3.5 0.2 1.0
N B:ARG82 3.5 98.4 1.0
CG B:ARG82 3.6 0.6 1.0
CB B:ARG82 3.7 0.0 1.0
N B:LYS81 4.0 0.6 1.0
CD B:ARG82 4.1 0.2 1.0
CB B:PRO80 4.2 0.7 1.0
CA B:ARG82 4.2 0.7 1.0
CB B:LYS81 4.4 0.8 1.0
C B:LYS81 4.5 0.9 1.0
CA B:LYS81 4.5 1.0 1.0
CZ B:ARG82 4.6 0.6 1.0
C B:PRO80 4.7 0.8 1.0
NE B:ARG82 4.8 96.1 1.0
CA B:PRO80 4.9 0.4 1.0

Reference:

A.Gao, N.Vasilyev, D.J.Luciano, R.Levenson-Palmer, J.Richards, W.M.Marsiglia, N.J.Traaseth, J.G.Belasco, A.Serganov. Structural and Kinetic Insights Into Stimulation of Rpph-Dependent Rna Degradation By the Metabolic Enzyme Dapf. Nucleic Acids Res. V. 46 6841 2018.
ISSN: ESSN 1362-4962
PubMed: 29733359
DOI: 10.1093/NAR/GKY327
Page generated: Sun Aug 11 22:50:08 2024

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