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Iodine in PDB 3uvi: Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant

Enzymatic activity of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant

All present enzymatic activity of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant:
2.4.2.29;

Protein crystallography data

The structure of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant, PDB code: 3uvi was solved by S.Jakobi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.08 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.019, 64.984, 70.488, 90.00, 95.60, 90.00
R / Rfree (%) 16.5 / 19.1

Other elements in 3uvi:

The structure of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant (pdb code 3uvi). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant, PDB code: 3uvi:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3uvi

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Iodine binding site 1 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I388

b:23.2
occ:0.50
 I A:IOD388 0.0 23.2 0.5
I A:IOD388 2.6 37.9 0.5
OH A:TYR381 3.2 13.8 1.0
O A:HOH837 3.3 33.6 1.0
O A:HOH701 3.6 15.7 1.0
CD A:LYS264 3.6 23.6 0.5
CE2 A:TYR381 4.0 14.2 1.0
CZ A:TYR381 4.1 11.6 1.0
CG A:PRO299 4.1 20.9 1.0
CG A:LYS264 4.1 18.0 0.5
CB A:LYS264 4.2 17.3 0.5
CE1 A:PHE294 4.2 13.7 1.0
CD A:PRO265 4.3 13.0 1.0
CB A:LYS264 4.3 17.3 0.5
O A:HOH419 4.3 36.1 1.0
CD A:PRO299 4.3 12.9 1.0
CD A:LYS264 4.4 21.6 0.5
CG A:LYS264 4.5 18.6 0.5
CE A:LYS264 4.6 24.4 0.5
NZ A:LYS264 4.8 22.7 0.5
O A:HOH819 4.9 30.6 1.0
CD1 A:PHE294 4.9 14.2 1.0
CB A:PRO299 4.9 13.4 1.0

Iodine binding site 2 out of 10 in 3uvi

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Iodine binding site 2 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I388

b:37.9
occ:0.50
 I A:IOD388 0.0 37.9 0.5
I A:IOD388 2.6 23.2 0.5
O A:HOH654 3.3 42.6 1.0
CD A:LYS264 3.4 23.6 0.5
O A:HOH484 3.7 40.3 1.0
CG A:LYS264 3.8 18.0 0.5
OE1 A:GLN292 3.9 30.3 1.0
CE1 A:PHE294 4.0 13.7 1.0
NE2 A:GLN292 4.1 26.7 1.0
CD2 A:LEU283 4.2 19.3 1.0
CG A:LYS264 4.3 18.6 0.5
CD A:LYS264 4.3 21.6 0.5
CD A:GLN292 4.3 28.1 1.0
CZ A:PHE294 4.3 16.9 1.0
CB A:LYS264 4.6 17.3 0.5
CE A:LYS264 4.7 23.5 0.5
CB A:LYS264 4.8 17.3 0.5
CD1 A:LEU283 4.8 21.2 1.0
CE A:LYS264 4.8 24.4 0.5
CG A:PRO299 4.8 20.9 1.0
CG A:LEU283 4.9 16.5 1.0

Iodine binding site 3 out of 10 in 3uvi

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Iodine binding site 3 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I389

b:14.1
occ:0.57
 O A:HOH653 3.2 24.2 1.0
O A:HOH727 3.6 21.9 1.0
O A:HOH716 3.6 17.8 1.0
N A:ALA53 3.6 13.5 1.0
N A:LEU54 3.9 13.2 1.0
CG A:LEU54 4.0 17.8 1.0
CB A:LEU54 4.0 12.4 1.0
CA A:LYS52 4.1 16.7 1.0
OG1 A:THR285 4.3 46.2 1.0
CD1 A:LEU54 4.3 20.4 1.0
CG2 A:THR347 4.3 11.4 1.0
CG A:LYS52 4.4 18.4 1.0
C A:LYS52 4.4 16.6 1.0
CD1 A:ILE351 4.4 20.4 1.0
O A:VAL45 4.4 16.8 1.0
CA A:LEU54 4.5 13.2 1.0
C A:ALA53 4.6 19.0 1.0
CA A:ALA53 4.6 16.6 1.0
O A:VAL51 4.7 29.1 1.0
NZ A:LYS52 4.7 25.3 1.0
CB A:LYS52 4.8 15.7 1.0
O A:LEU54 4.8 13.8 1.0
CG2 A:THR285 4.8 38.6 1.0
CG2 A:VAL59 4.9 12.4 1.0

Iodine binding site 4 out of 10 in 3uvi

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Iodine binding site 4 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I390

b:23.9
occ:0.37
 O A:HOH737 3.3 29.5 1.0
N A:GLY236 3.8 21.5 1.0
CA A:ALA232 4.0 19.3 1.0
N A:GLY234 4.0 27.0 1.0
N A:GLU235 4.1 25.3 1.0
CA A:GLY236 4.2 24.9 1.0
CA A:GLY234 4.2 32.0 1.0
C A:ALA232 4.3 22.9 1.0
OE1 A:GLU235 4.3 22.9 1.0
CD A:GLU235 4.4 26.3 1.0
C A:GLY234 4.4 32.6 1.0
CE A:MET240 4.4 18.9 0.5
OE2 A:GLU235 4.4 24.7 1.0
N A:VAL233 4.6 19.4 1.0
C A:GLY236 4.7 18.6 1.0
CB A:ALA232 4.8 23.5 1.0
N A:ALA232 4.8 18.2 1.0
C A:GLU235 4.8 25.6 1.0
O A:ALA232 4.9 26.1 1.0

Iodine binding site 5 out of 10 in 3uvi

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Iodine binding site 5 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I391

b:17.6
occ:0.34
 O A:HOH568 3.3 21.1 1.0
O A:HOH852 3.4 32.0 1.0
O A:HOH848 3.7 33.6 1.0
CG1 A:VAL248 3.8 13.6 1.0
O A:HOH552 3.8 18.1 1.0
N A:PRO249 3.9 10.1 1.0
CA A:PRO249 3.9 10.7 1.0
O A:ARG274 4.0 12.6 1.0
CG A:PRO249 4.0 14.7 1.0
C A:VAL248 4.1 9.8 1.0
CG A:LYS24 4.2 12.8 1.0
CD A:PRO249 4.2 11.5 1.0
CB A:VAL248 4.3 9.4 1.0
CD A:LYS24 4.3 14.9 1.0
O A:VAL248 4.3 10.7 1.0
CA A:GLY275 4.3 9.3 1.0
CB A:PRO249 4.3 13.5 1.0
CB A:LYS24 4.4 9.3 1.0
O A:HOH503 4.5 34.9 1.0
O A:HOH427 4.6 14.3 1.0
CE A:LYS24 4.6 14.0 1.0
O A:LYS24 4.7 10.3 1.0
C A:ARG274 4.8 9.1 1.0
CE1 A:HIS257 4.8 11.8 1.0
CA A:VAL248 4.8 10.4 1.0
N A:GLY275 5.0 8.3 1.0

Iodine binding site 6 out of 10 in 3uvi

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Iodine binding site 6 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I392

b:18.3
occ:0.65
 N A:ASN301 3.6 10.8 1.0
NE A:ARG306 4.0 35.9 1.0
CA A:ILE300 4.0 10.8 1.0
CE2 A:PHE307 4.1 10.9 1.0
CB A:ILE300 4.2 12.1 1.0
CZ A:PHE307 4.2 12.7 1.0
C A:ILE300 4.3 11.6 1.0
O A:ASN301 4.4 10.9 1.0
CG2 A:ILE300 4.5 16.1 1.0
CA A:ASN301 4.6 12.1 1.0
NH2 A:ARG306 4.7 41.7 1.0
CB A:ASN304 4.7 10.1 1.0
ND2 A:ASN304 4.8 16.3 1.0
CD A:ARG306 4.8 25.6 1.0
CZ A:ARG306 4.8 44.7 1.0
CB A:ASN301 4.9 12.9 1.0
C A:ASN301 4.9 10.0 1.0
CG A:ASN304 5.0 13.7 1.0

Iodine binding site 7 out of 10 in 3uvi

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Iodine binding site 7 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I393

b:26.2
occ:0.51
 I A:IOD393 0.0 26.2 0.5
I A:IOD393 1.7 35.9 0.5
O A:HOH863 3.3 35.7 1.0
CA A:THR47 4.1 14.9 1.0
CD A:LYS52 4.2 24.1 1.0
O A:HOH470 4.2 28.1 1.0
CB A:THR47 4.3 19.2 1.0
CG2 A:THR47 4.5 19.1 1.0
C A:THR47 4.6 21.2 1.0
O A:GLY46 4.7 22.4 1.0
O A:THR47 4.8 25.2 1.0
CE A:LYS52 4.9 23.4 1.0
CD2 A:LEU74 5.0 14.3 1.0

Iodine binding site 8 out of 10 in 3uvi

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Iodine binding site 8 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I393

b:35.9
occ:0.49
 I A:IOD393 0.0 35.9 0.5
I A:IOD393 1.7 26.2 0.5
CE A:MET93 3.6 13.6 0.5
CD A:LYS52 4.0 24.1 1.0
CG2 A:THR47 4.1 19.1 1.0
O A:GLY46 4.1 22.4 1.0
CE A:LYS52 4.2 23.4 1.0
CA A:THR47 4.4 14.9 1.0
CB A:THR47 4.5 19.2 1.0
CD2 A:LEU74 4.7 14.3 1.0
O A:HOH863 4.7 35.7 1.0

Iodine binding site 9 out of 10 in 3uvi

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Iodine binding site 9 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I394

b:17.5
occ:0.37
 OG1 A:THR285 3.0 46.2 1.0
O A:HOH716 3.3 17.8 1.0
O A:SER281 3.4 12.9 1.0
CB A:THR285 3.4 25.1 1.0
N A:VAL45 3.5 8.8 1.0
CG2 A:VAL45 3.5 13.8 0.3
CG A:PRO284 3.7 12.7 1.0
N A:THR285 3.7 16.8 1.0
O A:HOH505 3.9 15.2 1.0
CA A:PRO44 3.9 7.6 1.0
CA A:THR285 4.1 20.5 1.0
CD A:PRO284 4.2 12.8 1.0
CB A:PRO44 4.2 11.3 1.0
CG2 A:VAL45 4.2 18.0 0.7
C A:PRO44 4.2 9.5 1.0
O A:VAL282 4.3 13.4 1.0
CA A:VAL282 4.3 11.2 1.0
CE2 A:PHE42 4.4 11.2 1.0
C A:VAL282 4.4 13.7 1.0
C A:SER281 4.4 12.6 1.0
CB A:VAL45 4.5 16.9 0.7
CB A:PRO284 4.5 13.4 1.0
CB A:VAL45 4.5 16.8 0.3
CZ A:PHE42 4.5 9.1 1.0
CA A:VAL45 4.6 11.7 0.7
CA A:VAL45 4.6 11.8 0.3
CG1 A:ILE351 4.6 13.2 1.0
C A:PRO284 4.6 20.1 1.0
N A:PRO284 4.6 13.2 1.0
CD1 A:ILE351 4.7 20.4 1.0
CG2 A:THR285 4.7 38.6 1.0
O A:VAL45 4.8 16.8 1.0
CA A:PRO284 4.9 14.0 1.0
N A:VAL282 4.9 13.0 1.0
CG1 A:VAL45 4.9 18.2 0.3

Iodine binding site 10 out of 10 in 3uvi

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Iodine binding site 10 out of 10 in the Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Trna-Guanine Transglycosylase C158S C281S W326E E339Q Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I395

b:25.3
occ:0.38
 O A:HOH868 3.3 37.8 1.0
CG A:GLN359 4.0 9.3 1.0
CG A:GLN356 4.0 11.2 1.0
CB A:GLN359 4.0 8.1 1.0
CB A:GLN356 4.2 9.9 1.0
O A:GLN356 4.2 9.3 1.0
O A:HOH785 4.3 32.4 1.0
CA A:GLN356 4.3 7.9 1.0
CD2 A:HIS319 4.4 32.4 1.0
CG A:LYS360 4.4 17.2 0.5
CE A:LYS360 4.5 26.7 0.5
NZ A:LYS360 4.5 29.0 0.5
CG A:LYS360 4.5 17.2 0.5
C A:GLN356 4.7 8.6 1.0
NE2 A:HIS319 4.8 37.0 1.0
CE A:LYS360 4.8 27.1 0.5
OE1 A:GLN356 4.8 15.4 1.0
CD A:GLN356 4.9 14.9 1.0

Reference:

S.Jakobi, T.X.Nguyen, F.Debaene, A.Metz, S.Sanglier-Cianferani, K.Reuter, G.Klebe. Hot-Spot Analysis to Dissect the Functional Protein-Protein Interface of A Trna-Modifying Enzyme. Proteins V. 82 2713 2014.
ISSN: ISSN 0887-3585
PubMed: 24975703
DOI: 10.1002/PROT.24637
Page generated: Sun Dec 13 19:30:50 2020

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