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Iodine in PDB 5ygu: Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf

Enzymatic activity of Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf

All present enzymatic activity of Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf:
5.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf, PDB code: 5ygu was solved by Q.Wang, Z.Y.Guan, D.L.Zhang, T.T.Zou, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.99 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.418, 86.418, 173.093, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.9

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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf (pdb code 5ygu). 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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf, PDB code: 5ygu:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 5ygu

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Iodine binding site 1 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:79.6
occ:0.54
 CB A:PRO129 4.1 48.5 1.0
CD A:ARG131 4.2 83.8 1.0
O A:PHE130 4.2 56.7 1.0
C A:PHE130 4.3 54.9 1.0
N A:PHE130 4.4 55.8 1.0
N A:ARG131 4.5 59.5 1.0
CG A:PRO186 4.5 56.6 1.0
CA A:ARG131 4.5 57.9 1.0
CG A:ARG131 4.7 79.2 1.0
C A:PRO129 4.8 57.3 1.0
CA A:PRO129 4.9 51.5 1.0
CA A:PHE130 4.9 50.1 1.0
CA A:SER126 5.0 63.2 1.0

Iodine binding site 2 out of 12 in 5ygu

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Iodine binding site 2 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:70.9
occ:0.56
 O A:HOH460 2.0 60.7 1.0
NH1 A:ARG209 3.9 44.1 1.0
CG A:GLN72 3.9 42.8 1.0
C4 A:TLA301 4.0 58.5 1.0
CD A:GLN72 4.0 51.7 1.0
CB A:GLN72 4.0 33.4 1.0
CB A:ASN157 4.0 46.6 1.0
O41 A:TLA301 4.1 61.7 1.0
C3 A:TLA301 4.2 71.0 1.0
NE2 A:GLN72 4.3 58.5 1.0
O4 A:TLA301 4.4 56.2 1.0
OE1 A:GLN72 4.4 58.7 1.0
O3 A:TLA301 4.5 70.0 1.0
ND2 A:ASN157 4.6 49.8 1.0
CG A:ASN157 4.7 50.8 1.0
O A:HOH438 4.8 57.4 1.0
CA A:GLN72 5.0 47.9 1.0

Iodine binding site 3 out of 12 in 5ygu

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Iodine binding site 3 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:0.2
occ:0.55
 NE2 A:HIS201 3.6 59.9 1.0
CE1 A:HIS201 3.7 60.7 1.0
CG A:GLU241 3.7 57.6 1.0
CG A:ARG203 3.9 45.7 1.0
CD A:ARG203 3.9 50.9 1.0
CB A:GLU241 4.0 54.2 1.0
NE A:ARG203 4.1 55.0 1.0
NH2 A:ARG239 4.3 62.6 1.0
CD A:GLU241 4.5 56.5 1.0
CD2 A:HIS201 4.9 54.1 1.0
ND1 A:HIS201 5.0 59.6 1.0

Iodine binding site 4 out of 12 in 5ygu

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Iodine binding site 4 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:55.6
occ:0.85
 C A:PHE25 4.1 50.6 1.0
N A:SER26 4.1 48.0 1.0
OG A:SER26 4.2 54.0 1.0
CB A:SER26 4.2 49.3 1.0
O A:PHE25 4.4 53.3 1.0
CB A:PHE24 4.4 48.5 1.0
CA A:PHE25 4.5 50.2 1.0
O A:PHE24 4.5 50.4 1.0
N A:PHE25 4.5 50.3 1.0
C A:PHE24 4.5 48.1 1.0
CD2 A:LEU29 4.7 40.4 1.0
CA A:SER26 4.7 44.5 1.0

Iodine binding site 5 out of 12 in 5ygu

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Iodine binding site 5 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:0.5
occ:0.54
 CD1 A:LEU149 3.7 64.2 1.0
CG A:LEU149 3.9 60.5 1.0
CD2 A:LEU149 4.1 53.9 1.0
CG2 A:THR147 4.5 50.8 1.0

Iodine binding site 6 out of 12 in 5ygu

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Iodine binding site 6 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:41.5
occ:0.86
 O A:HOH414 3.4 51.9 1.0
N A:ARG78 3.8 43.6 1.0
N A:CYS79 3.8 36.3 1.0
CA A:GLY76 3.8 37.9 1.0
CB A:ARG78 3.8 52.4 1.0
C A:GLY76 3.9 48.1 1.0
N A:GLY76 4.0 36.1 1.0
SG A:CYS79 4.1 52.7 1.0
CE1 A:PHE13 4.1 39.5 1.0
N A:ALA77 4.1 40.9 1.0
CG A:ARG78 4.1 47.1 1.0
CZ A:ARG78 4.1 44.0 1.0
CA A:ARG78 4.2 49.2 1.0
NH1 A:ARG78 4.2 45.0 1.0
CA A:GLY8 4.3 36.2 1.0
O A:GLY76 4.3 45.1 1.0
CZ A:PHE13 4.4 38.6 1.0
NH2 A:ARG78 4.4 43.1 1.0
NE A:ARG78 4.4 41.8 1.0
C A:ARG78 4.5 47.4 1.0
CB A:CYS79 4.5 36.9 1.0
N A:GLY8 4.5 40.9 1.0
CA A:CYS79 4.8 42.9 1.0
C A:ALA77 4.8 47.9 1.0
CD A:ARG78 4.9 47.6 1.0
O A:GLY74 5.0 48.4 1.0

Iodine binding site 7 out of 12 in 5ygu

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Iodine binding site 7 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:53.3
occ:1.00
 OD1 A:ASN11 3.5 46.7 1.0
NH2 A:ARG78 3.5 43.1 1.0
NH1 A:ARG78 3.6 45.0 1.0
O A:HOH442 3.7 49.8 1.0
CA A:GLY218 3.8 38.6 1.0
N A:GLY218 3.8 44.2 1.0
O A:GLY8 4.0 43.1 1.0
CZ A:ARG78 4.1 44.0 1.0
CD1 A:LEU247 4.3 41.5 1.0
CB A:LEU9 4.3 34.5 1.0
CD2 A:LEU247 4.4 41.5 1.0
CD1 A:LEU9 4.4 32.4 1.0
CB A:ALA216 4.5 42.9 1.0
CG A:LEU9 4.6 39.9 1.0
C A:GLY8 4.6 34.4 1.0
CG A:ASN11 4.7 43.3 1.0
C A:CYS217 4.7 44.9 1.0
CG A:LEU247 4.9 50.1 1.0
O A:ALA216 4.9 47.7 1.0
C A:ALA216 4.9 44.6 1.0

Iodine binding site 8 out of 12 in 5ygu

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Iodine binding site 8 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:48.1
occ:0.67
 NE A:ARG85 3.4 60.5 1.0
NE A:ARG82 3.6 43.9 1.0
NH2 A:ARG82 3.7 54.9 1.0
CB A:ARG85 4.0 48.0 1.0
CD A:ARG85 4.0 55.7 1.0
OD1 A:ASP112 4.0 85.1 1.0
CZ A:ARG82 4.1 49.1 1.0
CG1 A:VAL108 4.3 48.1 1.0
CA A:ARG82 4.3 48.3 1.0
CB A:ARG82 4.3 41.8 1.0
CG A:ARG82 4.3 42.1 1.0
O A:ARG82 4.4 55.1 1.0
CZ A:ARG85 4.4 62.8 1.0
NH2 A:ARG85 4.5 70.7 1.0
CD A:ARG82 4.5 41.2 1.0
CG A:LEU86 4.6 49.9 1.0
CG A:ARG85 4.6 52.5 1.0
CD2 A:LEU86 4.7 45.9 1.0
C A:ARG82 4.8 47.2 1.0
CG A:ASP112 5.0 77.7 1.0

Iodine binding site 9 out of 12 in 5ygu

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Iodine binding site 9 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I310

b:51.3
occ:0.64
 OG1 A:THR99 3.4 47.0 1.0
N A:ASN101 3.7 66.5 1.0
N A:GLN72 3.8 43.5 1.0
C A:ALA71 3.9 52.2 1.0
CB A:THR99 4.0 44.2 1.0
C A:GLN72 4.0 51.8 1.0
CB A:ASN101 4.1 79.8 1.0
N A:CYS73 4.1 48.9 1.0
O A:GLN72 4.2 40.1 1.0
CA A:ALA71 4.2 54.0 1.0
CA A:ASN101 4.3 74.1 1.0
N A:ALA100 4.3 55.1 1.0
O A:ALA71 4.4 52.8 1.0
CA A:GLN72 4.4 47.9 1.0
CB A:ALA71 4.5 51.5 1.0
CA A:CYS73 4.5 54.7 1.0
CB A:ALA100 4.5 52.4 1.0
C A:ASN101 4.5 73.8 1.0
C A:ALA100 4.7 65.2 1.0
N A:GLY102 4.7 67.5 1.0
CA A:ALA100 4.7 57.2 1.0
C A:THR99 4.8 49.8 1.0
ND2 A:ASN101 4.9 88.5 1.0
CG2 A:THR99 4.9 40.5 1.0
CG A:ASN101 4.9 88.4 1.0

Iodine binding site 10 out of 12 in 5ygu

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Iodine binding site 10 out of 12 in the Crystal Structure of Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf


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 Escherichia Coli (Strain K12) Mrna Decapping Complex Rpph-Dapf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I311

b:59.7
occ:0.72
 N A:ALA171 3.8 58.1 1.0
CG1 A:VAL164 4.1 58.1 1.0
CD2 A:LEU175 4.2 57.1 1.0
CA A:ALA170 4.3 59.2 1.0
CE2 A:PHE193 4.3 56.3 1.0
CD2 A:PHE193 4.4 43.4 1.0
CB A:ALA171 4.4 52.8 1.0
CB A:ALA170 4.5 57.9 1.0
C A:ALA170 4.6 53.0 1.0
CA A:ALA171 4.6 56.1 1.0
O A:HOH448 4.8 56.6 1.0

Reference:

Q.Wang, D.Zhang, Z.Guan, D.Li, K.Pei, J.Liu, T.Zou, P.Yin. Dapf Stabilizes the Substrate-Favoring Conformation of Rpph to Stimulate Its Rna-Pyrophosphohydrolase Activity in Escherichia Coli. Nucleic Acids Res. V. 46 6880 2018.
ISSN: ESSN 1362-4962
PubMed: 29931175
DOI: 10.1093/NAR/GKY528
Page generated: Sun Aug 11 22:21:12 2024

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