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Iodine in PDB 3otd: Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative

Protein crystallography data

The structure of Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative, PDB code: 3otd was solved by S.J.Hyde, B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.28
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 140.574, 140.574, 80.962, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 25.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative (pdb code 3otd). 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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative, PDB code: 3otd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3otd

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Iodine binding site 1 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I270

b:52.3
occ:0.65
 O A:HOH290 3.2 33.9 1.0
CE A:MET205 3.5 49.7 1.0
CB A:PRO247 3.8 43.0 1.0
NE2 A:HIS249 3.8 41.2 1.0
CE1 A:HIS249 4.0 41.1 1.0
CG A:PRO247 4.1 42.9 1.0
NE2 A:GLN52 4.1 49.6 1.0
CG2 A:THR55 4.2 31.6 1.0
CG A:GLN52 4.2 45.3 1.0
CB A:THR55 4.6 34.5 1.0
OG1 A:THR55 4.7 34.8 1.0
CD A:GLN52 4.7 48.0 1.0
OG1 A:THR210 4.8 33.0 1.0
CG2 A:THR210 4.8 31.8 1.0
SD A:MET205 5.0 47.2 1.0
CB A:GLN52 5.0 41.3 1.0

Iodine binding site 2 out of 10 in 3otd

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Iodine binding site 2 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I271

b:48.3
occ:0.42
 CZ A:PHE192 4.1 52.0 1.0
CE2 A:PHE192 4.3 53.2 1.0

Iodine binding site 3 out of 10 in 3otd

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Iodine binding site 3 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I272

b:65.5
occ:0.39
 CD A:PRO204 3.5 43.2 1.0
N A:MET205 3.5 41.2 1.0
CB A:MET205 3.7 41.2 1.0
CB A:LEU203 3.8 45.7 1.0
N A:PRO204 3.8 42.0 1.0
CB A:PRO204 4.2 41.9 1.0
CA A:MET205 4.3 40.7 1.0
CG A:PRO204 4.3 42.1 1.0
C A:LEU203 4.3 42.7 1.0
CA A:LEU203 4.4 43.9 1.0
CA A:PRO204 4.4 42.0 1.0
C A:PRO204 4.5 41.9 1.0
ND1 A:HIS249 4.5 42.1 1.0
CD2 A:LEU203 4.5 52.3 1.0
CG A:LEU203 4.6 49.8 1.0
CE1 A:HIS249 4.8 41.1 1.0
CG A:HIS249 4.9 41.9 1.0
CE A:MET205 4.9 49.7 1.0

Iodine binding site 4 out of 10 in 3otd

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Iodine binding site 4 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I273

b:68.4
occ:0.34
 NE2 A:GLN167 3.0 68.7 1.0
O A:HOH296 3.1 38.2 1.0
OE1 A:GLN166 3.3 58.5 1.0
CA A:ALA163 3.9 47.9 1.0
O A:TRP162 3.9 48.5 1.0
CD A:GLN167 4.1 68.8 1.0
N A:ALA163 4.2 48.3 1.0
C A:TRP162 4.2 48.6 1.0
CB A:GLN166 4.3 58.8 1.0
CD A:GLN166 4.3 58.4 1.0
CG A:GLN167 4.4 65.7 1.0
CB A:ALA163 4.4 43.9 1.0
CD A:PRO45 4.8 46.5 1.0
CG A:GLN166 4.8 58.7 1.0
CB A:TRP162 4.9 49.5 1.0

Iodine binding site 5 out of 10 in 3otd

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Iodine binding site 5 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I274

b:81.6
occ:0.30
 CD A:ARG92 3.7 55.8 1.0
O A:PHE89 3.9 57.1 1.0
CD1 A:PHE89 3.9 66.0 1.0
NH1 A:ARG92 4.2 65.3 1.0
NZ A:LYS95 4.2 53.1 1.0
CG A:LYS90 4.3 61.4 1.0
C A:PHE89 4.4 57.6 1.0
CG A:ARG92 4.5 51.9 1.0
CB A:PHE89 4.6 61.9 1.0
CA A:PHE89 4.7 59.1 1.0
CB A:LYS90 4.7 56.7 1.0
CE1 A:PHE89 4.8 66.8 1.0
NE A:ARG92 4.8 61.8 1.0
CG A:PHE89 4.8 64.4 1.0
CE A:LYS95 4.8 52.1 1.0
CG A:LYS95 4.8 45.1 1.0
CZ A:ARG92 5.0 64.2 1.0

Iodine binding site 6 out of 10 in 3otd

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Iodine binding site 6 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I275

b:57.8
occ:0.46
 O A:HOH282 3.3 35.1 1.0
NH1 A:ARG207 3.4 39.7 1.0
CD2 A:HIS152 3.5 51.8 1.0
NE2 A:HIS152 3.7 53.6 1.0
CD A:LYS208 4.0 48.8 1.0
CD A:ARG207 4.1 37.3 1.0
CB A:ARG207 4.2 35.2 1.0
CE2 A:TYR199 4.5 39.9 1.0
CG A:HIS152 4.5 49.2 1.0
CG A:ARG207 4.5 36.0 1.0
CZ A:ARG207 4.5 38.8 1.0
O A:ARG207 4.7 34.4 1.0
OD1 A:ASN200 4.7 61.3 1.0
NE A:ARG207 4.8 39.0 1.0
NZ A:LYS208 4.8 51.7 1.0
CE1 A:HIS152 4.8 51.3 1.0
CG A:LYS208 4.9 43.2 1.0
CE A:LYS208 5.0 52.2 1.0

Iodine binding site 7 out of 10 in 3otd

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Iodine binding site 7 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I270

b:47.0
occ:0.54
 O B:HOH290 3.1 32.8 1.0
CE B:MET205 3.5 50.9 1.0
CB B:PRO247 3.9 45.0 1.0
NE2 B:HIS249 3.9 40.7 1.0
NE2 B:GLN52 4.0 51.5 1.0
CE1 B:HIS249 4.1 39.5 1.0
CG2 B:THR55 4.1 31.8 1.0
CG B:GLN52 4.1 44.8 1.0
CG B:PRO247 4.1 44.6 1.0
CB B:THR55 4.5 34.2 1.0
OG1 B:THR55 4.6 34.2 1.0
CD B:GLN52 4.6 47.6 1.0
CG2 B:THR210 4.8 32.5 1.0
CB B:GLN52 4.9 40.5 1.0
OG1 B:THR210 4.9 36.9 1.0
SD B:MET205 4.9 52.7 1.0
CA B:GLN52 5.0 37.6 1.0

Iodine binding site 8 out of 10 in 3otd

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Iodine binding site 8 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I271

b:59.3
occ:0.38
 CD B:PRO204 3.6 43.3 1.0
N B:MET205 3.6 41.7 1.0
CB B:MET205 3.7 42.8 1.0
CB B:LEU203 3.9 43.3 1.0
N B:PRO204 4.0 42.5 1.0
CA B:MET205 4.3 41.8 1.0
CB B:PRO204 4.4 42.0 1.0
CG B:PRO204 4.4 42.8 1.0
ND1 B:HIS249 4.5 39.6 1.0
C B:LEU203 4.5 42.0 1.0
CA B:LEU203 4.5 43.0 1.0
CD2 B:LEU203 4.6 51.8 1.0
CA B:PRO204 4.6 42.3 1.0
C B:PRO204 4.6 42.7 1.0
CE1 B:HIS249 4.7 39.5 1.0
CG B:LEU203 4.7 47.4 1.0
CE B:MET205 4.7 50.9 1.0
CG B:HIS249 4.9 39.9 1.0
CG B:MET205 5.0 46.3 1.0

Iodine binding site 9 out of 10 in 3otd

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Iodine binding site 9 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I272

b:77.3
occ:0.33
 CD B:ARG92 3.5 53.3 1.0
NH1 B:ARG92 3.8 63.9 1.0
NZ B:LYS95 4.1 50.8 1.0
CD1 B:PHE89 4.2 63.0 1.0
O B:PHE89 4.2 55.9 1.0
CG B:ARG92 4.4 49.8 1.0
NE B:ARG92 4.5 59.7 1.0
CE B:LYS95 4.6 51.2 1.0
CG B:LYS90 4.6 60.8 1.0
CZ B:ARG92 4.7 61.9 1.0
C B:PHE89 4.8 56.8 1.0
CG B:LYS95 4.8 44.4 1.0
CE1 B:PHE89 4.9 63.4 1.0
CB B:PHE89 5.0 60.8 1.0
CB B:LYS90 5.0 55.5 1.0

Iodine binding site 10 out of 10 in 3otd

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Iodine binding site 10 out of 10 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1)- Nai Derivative


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 Human Trnahis Guanylyltransferase (THG1)- Nai Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I273

b:63.6
occ:0.38
 NE2 B:GLN167 3.0 66.7 1.0
O B:HOH277 3.1 33.8 1.0
OE1 B:GLN166 3.2 59.8 1.0
CA B:ALA163 3.9 48.5 1.0
O B:TRP162 4.0 49.6 1.0
CD B:GLN167 4.1 65.9 1.0
CB B:GLN166 4.1 59.3 1.0
N B:ALA163 4.2 48.4 1.0
CG B:GLN167 4.2 64.2 1.0
CD B:GLN166 4.3 59.9 1.0
C B:TRP162 4.3 49.1 1.0
CB B:ALA163 4.4 46.3 1.0
CG B:GLN166 4.7 59.0 1.0
CD B:PRO45 5.0 48.4 1.0
CB B:TRP162 5.0 50.4 1.0

Reference:

S.J.Hyde, B.E.Eckenroth, B.A.Smith, W.A.Eberley, N.H.Heintz, J.E.Jackman, S.Doublie. Trnahis Guanylyltransferase (THG1), A Unique 3'-5' Nucleotidyl Transferase, Shares Unexpected Structural Homology with Canonical 5'-3' Dna Polymerases. Proc.Natl.Acad.Sci.Usa V. 107 20305 2010.
ISSN: ISSN 0027-8424
PubMed: 21059936
DOI: 10.1073/PNAS.1010436107
Page generated: Sun Aug 11 15:59:35 2024

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