Atomistry » Mercury » PDB 5lf8-6bvg » 5tjo
Atomistry »
  Mercury »
    PDB 5lf8-6bvg »
      5tjo »

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

Go back to Mercury Binding Sites List in 5tjo
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

Go back to Mercury Binding Sites List in 5tjo
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

Go back to Mercury Binding Sites List in 5tjo
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

Go back to Mercury Binding Sites List in 5tjo
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

Go back to Mercury Binding Sites List in 5tjo
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 Aug 11 06:55:57 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy