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Mercury in PDB 4kr6: Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex

Enzymatic activity of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex

All present enzymatic activity of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex:
2.8.1.4;

Protein crystallography data

The structure of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex, PDB code: 4kr6 was solved by P.Neumann, R.Ficner, K.Lakomek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.652, 110.325, 119.313, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.8

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex (pdb code 4kr6). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 4 binding sites of Mercury where determined in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex, PDB code: 4kr6:
Jump to Mercury binding site number: 1; 2; 3; 4;

Mercury binding site 1 out of 4 in 4kr6

Go back to Mercury Binding Sites List in 4kr6
Mercury binding site 1 out of 4 in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg401

b:0.7
occ:0.43
CE1 A:TYR166 3.3 79.2 1.0
O A:GLU329 3.6 56.1 1.0
CG A:GLU329 3.7 64.7 1.0
O A:HOH524 3.8 64.5 1.0
CD1 A:TYR166 3.8 73.6 1.0
CG2 A:ILE330 3.9 55.4 1.0
C A:GLU329 4.0 41.2 1.0
CZ2 A:TRP192 4.0 40.9 1.0
CA A:ILE330 4.1 46.4 1.0
CD A:GLU329 4.2 75.6 1.0
CZ A:PHE230 4.2 36.5 1.0
CE2 A:PHE230 4.3 46.3 1.0
OE2 A:GLU329 4.3 83.2 1.0
N A:ILE330 4.3 43.3 1.0
CB A:ILE330 4.4 55.6 1.0
CZ A:TYR166 4.4 86.0 1.0
CE2 A:TRP192 4.5 38.0 1.0
NE1 A:TRP192 4.5 36.0 1.0
CB A:GLU329 4.6 44.7 1.0
OH A:TYR166 4.7 94.1 1.0
CH2 A:TRP192 4.8 40.8 1.0
CA A:GLU329 4.9 39.7 1.0
CB A:CYS165 5.0 88.0 1.0

Mercury binding site 2 out of 4 in 4kr6

Go back to Mercury Binding Sites List in 4kr6
Mercury binding site 2 out of 4 in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:0.6
occ:0.44
N A:ALA348 3.8 69.1 1.0
CB A:PHE347 3.9 56.8 1.0
CA A:ALA348 4.0 54.4 1.0
C A:PHE347 4.1 69.5 1.0
CB A:ALA348 4.1 54.0 1.0
O A:HOH513 4.2 38.2 1.0
NE2 A:GLN247 4.3 59.7 1.0
CD2 A:TYR263 4.3 42.5 1.0
CE2 A:TYR263 4.3 51.5 1.0
O A:HOH534 4.3 64.5 1.0
CA A:PHE347 4.6 62.6 1.0
O A:PHE347 4.6 76.7 1.0
CD2 A:LEU260 4.9 65.7 1.0
CG A:PHE347 5.0 66.3 1.0

Mercury binding site 3 out of 4 in 4kr6

Go back to Mercury Binding Sites List in 4kr6
Mercury binding site 3 out of 4 in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg403

b:0.2
occ:0.36
SG A:CYS344 2.1 74.3 1.0
CB A:PHE346 3.8 66.0 1.0
CB A:CYS344 3.8 0.5 1.0
CD2 A:PHE211 3.9 59.4 1.0
O A:CYS344 4.3 0.2 1.0
CE2 A:PHE211 4.3 62.8 1.0
CD2 A:PHE346 4.3 71.6 1.0
CG A:PHE346 4.4 67.5 1.0
CA A:PHE346 4.7 70.8 1.0
CA A:CYS344 4.8 0.1 1.0
C A:CYS344 4.8 0.8 1.0
N A:PHE346 4.9 81.0 1.0

Mercury binding site 4 out of 4 in 4kr6

Go back to Mercury Binding Sites List in 4kr6
Mercury binding site 4 out of 4 in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg401

b:0.4
occ:0.37
SG B:CYS344 2.4 0.7 1.0
CB B:CYS344 2.9 0.1 1.0
C B:CYS344 3.2 0.6 1.0
O B:CYS344 3.2 0.6 1.0
CA B:CYS344 3.4 0.9 1.0
N B:VAL345 3.8 0.8 1.0
N B:PHE346 4.0 0.5 1.0
CD2 B:PHE211 4.3 62.0 1.0
CA B:VAL345 4.3 0.7 1.0
C B:VAL345 4.4 0.1 1.0
CB B:PHE346 4.4 98.1 1.0
CA B:PHE211 4.6 76.2 1.0
CB B:PHE211 4.7 67.7 1.0
O B:PHE211 4.7 0.4 1.0
CA B:PHE346 4.8 99.1 1.0
N B:CYS344 4.8 0.6 1.0
CD2 B:PHE346 4.9 75.1 1.0
CG B:PHE346 4.9 85.2 1.0
CG B:PHE211 5.0 67.5 1.0

Reference:

P.Neumann, K.Lakomek, P.T.Naumann, W.M.Erwin, C.T.Lauhon, R.Ficner. Crystal Structure of A 4-Thiouridine Synthetase-Rna Complex Reveals Specificity of Trna U8 Modification. Nucleic Acids Res. V. 42 6673 2014.
ISSN: ISSN 0305-1048
PubMed: 24705700
DOI: 10.1093/NAR/GKU249
Page generated: Sun Dec 13 19:11:23 2020

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