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Mercury in PDB 5tjo: Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)

Enzymatic activity of Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)

All present enzymatic activity of Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative):
2.4.1.37; 2.4.1.40;

Protein crystallography data

The structure of Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative), PDB code: 5tjo was solved by M.S.G.Legg, S.M.L.Gagnon, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.57
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 52.710, 150.650, 79.180, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.6

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative) (pdb code 5tjo). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative), PDB code: 5tjo:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 5tjo

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Mercury binding site 1 out of 6 in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)


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 Gtb + B Trisaccharide (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg401

b:27.5
occ:0.41
 O A:HOH688 2.4 32.8 1.0
SG A:CYS284 2.4 20.1 0.5
SG A:CYS284 2.9 30.3 0.5
CB A:CYS284 3.0 23.5 0.5
CB A:CYS284 3.1 28.1 0.5
CD2 A:LEU280 3.5 24.9 1.0
N A:LEU306 3.7 18.2 1.0
CA A:LEU306 3.8 18.7 1.0
O A:ASP302 3.8 22.7 1.0
CB A:LEU306 3.9 18.9 1.0
C A:HIS305 4.3 19.8 1.0
CD1 A:LEU306 4.4 21.2 1.0
CA A:CYS284 4.4 26.2 0.5
CB A:HIS305 4.5 21.7 1.0
CA A:CYS284 4.5 24.1 0.5
CG A:LEU280 4.6 23.0 1.0
C A:ASP302 4.6 23.8 1.0
O A:LEU280 4.7 21.2 1.0
O A:HIS305 4.7 19.3 1.0
CG A:LEU306 4.8 20.1 1.0
HG A:HG403 4.8 25.1 0.2
CB A:ASP302 4.8 32.2 1.0
CA A:HIS305 5.0 20.3 1.0
HG A:HG402 5.0 38.3 0.2
CA A:ASP302 5.0 27.6 1.0

Mercury binding site 2 out of 6 in 5tjo

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Mercury binding site 2 out of 6 in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)


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 Gtb + B Trisaccharide (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:38.3
occ:0.25
 SD A:MET288 2.4 42.6 1.0
SG A:CYS284 2.6 30.3 0.5
OD2 A:ASP302 3.2 43.3 1.0
CB A:CYS284 3.6 28.1 0.5
C A:CYS284 3.7 26.1 1.0
N A:HIS285 3.8 26.3 1.0
CB A:CYS284 3.8 23.5 0.5
CG A:MET288 3.8 32.0 1.0
CE A:MET288 3.9 42.0 1.0
O A:CYS284 3.9 27.8 1.0
CA A:HIS285 3.9 29.2 1.0
CG A:ASP302 4.1 37.4 1.0
CA A:CYS284 4.3 26.2 0.5
CA A:CYS284 4.4 24.1 0.5
CB A:MET288 4.5 29.1 1.0
CB A:HIS285 4.6 32.1 1.0
CB A:ASP302 4.7 32.2 1.0
OD1 A:ASP302 4.9 47.2 1.0
O A:THR281 4.9 22.7 1.0
HG A:HG401 5.0 27.5 0.4

Mercury binding site 3 out of 6 in 5tjo

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Mercury binding site 3 out of 6 in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)


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 Gtb + B Trisaccharide (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg403

b:25.1
occ:0.25
 O A:HOH686 2.4 38.0 1.0
SG A:CYS284 2.5 20.1 0.5
O A:HIS305 3.2 19.3 1.0
CA A:CYS284 3.3 24.1 0.5
CA A:CYS284 3.3 26.2 0.5
N A:CYS284 3.4 24.8 1.0
CB A:CYS284 3.5 23.5 0.5
CB A:TYR309 3.6 17.8 1.0
O A:HOH626 3.6 29.1 1.0
C A:ALA283 3.8 25.0 1.0
C A:HIS305 3.8 19.8 1.0
CB A:CYS284 3.8 28.1 0.5
CB A:HIS305 4.0 21.7 1.0
O A:ALA283 4.0 26.3 1.0
CD1 A:TYR309 4.0 18.1 1.0
CB A:ALA283 4.2 24.1 1.0
CG A:TYR309 4.2 17.2 1.0
CA A:HIS305 4.3 20.3 1.0
N A:TYR309 4.3 18.2 1.0
CA A:TYR309 4.3 18.1 1.0
O A:HOH670 4.4 44.4 1.0
O A:LEU280 4.6 21.2 1.0
CA A:ALA283 4.6 23.6 1.0
C A:CYS284 4.7 26.1 1.0
N A:LEU306 4.7 18.2 1.0
CB A:ALA287 4.8 24.9 1.0
SG A:CYS284 4.8 30.3 0.5
HG A:HG401 4.8 27.5 0.4
ND1 A:HIS305 4.9 26.4 1.0
CG A:HIS305 4.9 23.6 1.0

Mercury binding site 4 out of 6 in 5tjo

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Mercury binding site 4 out of 6 in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)


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 Gtb + B Trisaccharide (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg404

b:25.9
occ:0.60
 O A:HOH684 1.8 33.0 1.0
SG A:CYS209 2.2 27.0 1.0
O A:HOH683 2.3 27.2 1.0
OG1 A:THR119 2.8 24.0 1.0
CB A:CYS209 3.3 20.8 1.0
HG A:HG405 3.8 28.7 0.2
CB A:THR119 3.8 21.1 1.0
CG2 A:THR119 3.9 21.7 1.0
CA A:CYS209 4.1 18.6 1.0
CG1 A:VAL277 4.3 18.6 1.0
N A:CYS209 4.7 17.4 1.0
CD1 A:LEU207 4.8 24.9 1.0
CB A:LEU207 5.0 21.3 1.0
CZ A:PHE270 5.0 20.5 1.0
O A:VAL208 5.0 19.1 1.0

Mercury binding site 5 out of 6 in 5tjo

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Mercury binding site 5 out of 6 in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg405

b:28.7
occ:0.25
 O A:HOH680 2.8 25.7 1.0
OG1 A:THR119 2.9 24.0 1.0
CE1 A:PHE121 3.3 39.5 1.0
O A:HOH684 3.3 33.0 1.0
CD1 A:PHE121 3.3 38.0 1.0
O A:THR119 3.5 21.0 1.0
CB A:THR119 3.7 21.1 1.0
HG A:HG404 3.8 25.9 0.6
C A:THR119 3.8 20.7 1.0
CB A:CYS209 3.9 20.8 1.0
O A:HOH512 4.0 27.4 1.0
CA A:CYS209 4.0 18.6 1.0
O A:VAL210 4.2 20.1 1.0
N A:VAL120 4.3 20.0 1.0
N A:VAL210 4.3 17.9 1.0
O A:HOH683 4.4 27.2 1.0
CA A:VAL120 4.4 21.1 1.0
CA A:THR119 4.4 20.0 1.0
C A:CYS209 4.4 17.6 1.0
CZ A:PHE121 4.6 40.9 1.0
SG A:CYS209 4.7 27.0 1.0
CG A:PHE121 4.7 33.7 1.0
N A:PHE121 4.7 22.6 1.0
C A:VAL120 4.8 22.8 1.0

Mercury binding site 6 out of 6 in 5tjo

Go back to Mercury Binding Sites List in 5tjo
Mercury binding site 6 out of 6 in the Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative)


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Gtb + B Trisaccharide (Mercury Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg406

b:32.8
occ:0.40
 SG A:CYS80 2.0 48.3 1.0
O A:GLY98 2.6 26.2 1.0
CB A:CYS80 3.0 46.1 1.0
CA A:CYS80 3.2 41.4 1.0
O A:HOH625 3.6 34.3 1.0
O A:CYS80 3.7 40.0 1.0
C A:GLY98 3.7 23.2 1.0
C A:CYS80 3.8 39.1 1.0
O A:HOH618 4.0 46.6 1.0
CA A:THR99 4.3 20.1 1.0
O A:HOH668 4.4 35.4 1.0
N A:THR99 4.4 20.1 1.0
N A:CYS80 4.5 42.6 1.0
CA A:GLY98 4.7 22.9 1.0
N A:ARG81 4.9 37.4 1.0
C A:THR99 4.9 20.6 1.0
O A:THR99 5.0 22.4 1.0

Reference:

S.M.L.Gagnon, M.S.G.Legg, N.Sindhuwinata, J.A.Letts, A.R.Johal, B.Schuman, S.N.Borisova, M.M.Palcic, T.Peters, S.V.Evans. High-Resolution Crystal Structures and Std uc(Nmr) Mapping of Human Abo(H) Blood Group Glycosyltransferases in Complex with Trisaccharide Reaction Products Suggest A Molecular Basis For Product Release. Glycobiology V. 27 966 2017.
ISSN: ESSN 1460-2423
PubMed: 28575295
DOI: 10.1093/GLYCOB/CWX053
Page generated: Sun Dec 13 19:13:17 2020

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