Atomistry » Mercury » PDB 6bzi-6rjj » 6fxx
Atomistry »
  Mercury »
    PDB 6bzi-6rjj »
      6fxx »

Mercury in PDB 6fxx: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak

Enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak:
1.14.11.4;

Protein crystallography data

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak, PDB code: 6fxx was solved by L.Scietti, A.Chiapparino, F.De Giorgi, M.Fumagalli, L.Khoriauli, S.Nergadze, S.Basu, V.Olieric, B.Banushi, E.Giulotto, P.Gissen, F.Forneris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.679, 100.330, 225.954, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.8

Other elements in 6fxx:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Iron (Fe) 2 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak (pdb code 6fxx). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 3 binding sites of Mercury where determined in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak, PDB code: 6fxx:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in 6fxx

Go back to Mercury Binding Sites List in 6fxx
Mercury binding site 1 out of 3 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak


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 Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg802

b:84.7
occ:1.00
 SG A:CYS144 2.8 89.2 1.0
O A:GLU147 3.0 0.5 1.0
O A:TRP145 3.4 0.1 1.0
C A:TRP145 3.6 0.9 1.0
N A:GLU147 3.8 0.2 1.0
C A:CYS144 3.8 85.4 1.0
N A:TRP145 3.8 0.5 1.0
C A:GLU147 3.9 0.1 1.0
CG2 A:THR196 3.9 86.2 1.0
N A:PRO146 4.0 0.5 1.0
O A:CYS144 4.1 88.4 1.0
CB A:CYS144 4.1 87.9 1.0
CD1 A:LEU150 4.2 0.4 1.0
CA A:GLU147 4.2 0.8 1.0
CA A:CYS144 4.3 84.6 1.0
CA A:TRP145 4.3 0.9 1.0
CD A:PRO146 4.3 0.7 1.0
OG1 A:THR196 4.3 81.0 1.0
CB A:GLU147 4.3 0.3 1.0
CB A:LEU150 4.4 99.5 1.0
CB A:THR196 4.5 83.8 1.0
OH A:TYR154 4.5 81.7 1.0
C A:PRO146 4.6 0.4 1.0
CG A:LEU150 4.6 0.3 1.0
CE1 A:TYR154 4.9 86.4 1.0
CA A:PRO146 4.9 0.4 1.0
N A:TRP148 5.0 98.7 1.0

Mercury binding site 2 out of 3 in 6fxx

Go back to Mercury Binding Sites List in 6fxx
Mercury binding site 2 out of 3 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak


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 Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg803

b:78.7
occ:1.00
 CD1 A:LEU709 3.3 67.7 1.0
N A:CYS691 3.4 74.6 1.0
CB A:CYS691 3.5 72.1 1.0
O3 A:AKG805 3.7 45.2 1.0
CG2 A:ILE700 3.9 73.5 1.0
C A:GLY690 3.9 94.2 1.0
CA A:GLY690 3.9 93.2 1.0
CB A:ILE700 4.1 74.5 1.0
CA A:CYS691 4.1 74.3 1.0
NH1 A:ARG729 4.1 72.0 1.0
CG A:PRO703 4.2 73.7 1.0
O A:ILE700 4.5 77.3 1.0
CB A:PRO703 4.5 72.1 1.0
ND2 A:ASN676 4.6 92.4 1.0
CG A:LEU709 4.6 66.6 1.0
CG1 A:ILE700 4.8 73.8 1.0
CG A:ASN676 4.8 97.7 1.0
SG A:CYS691 4.8 71.1 1.0
OD1 A:ASN676 4.8 0.7 1.0
O A:GLY690 4.8 0.0 1.0
C5 A:AKG805 4.9 53.4 1.0

Mercury binding site 3 out of 3 in 6fxx

Go back to Mercury Binding Sites List in 6fxx
Mercury binding site 3 out of 3 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak


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 Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg804

b:0.1
occ:1.00
 O A:ILE461 2.5 52.8 1.0
O A:ASP490 2.5 63.6 1.0
SG A:CYS494 3.0 72.1 1.0
C A:ASP490 3.3 73.7 1.0
CE2 A:TYR460 3.3 57.9 1.0
CB A:ASP490 3.4 81.4 1.0
CZ A:TYR460 3.4 57.2 1.0
CD2 A:PHE493 3.5 53.1 1.0
CA A:ASP490 3.5 78.0 1.0
OH A:TYR460 3.6 57.3 1.0
C A:ILE461 3.7 52.2 1.0
CD2 A:TYR460 4.0 58.0 1.0
CB A:SER462 4.0 52.8 1.0
CE2 A:PHE493 4.1 52.0 1.0
CE1 A:TYR460 4.2 56.5 1.0
CA A:SER462 4.2 51.5 1.0
CG A:ASP490 4.3 89.8 1.0
N A:MET491 4.4 70.1 1.0
OD1 A:ASP490 4.4 77.3 1.0
N A:SER462 4.4 51.5 1.0
CB A:CYS494 4.5 77.2 1.0
CG A:PHE493 4.5 53.8 1.0
N A:CYS494 4.6 74.0 1.0
N A:ILE461 4.6 53.6 1.0
CB A:PHE493 4.6 55.4 1.0
CG A:TYR460 4.7 57.3 1.0
CD1 A:TYR460 4.7 56.6 1.0
CA A:ILE461 4.8 52.4 1.0
CA A:MET491 4.9 73.8 1.0
N A:ASP490 5.0 84.2 1.0

Reference:

L.Scietti, A.Chiapparino, F.De Giorgi, M.Fumagalli, L.Khoriauli, S.Nergadze, S.Basu, V.Olieric, L.Cucca, B.Banushi, A.Profumo, E.Giulotto, P.Gissen, F.Forneris. Molecular Architecture of the Multifunctional Collagen Lysyl Hydroxylase and Glycosyltransferase LH3. Nat Commun V. 9 3163 2018.
ISSN: ESSN 2041-1723
PubMed: 30089812
DOI: 10.1038/S41467-018-05631-5
Page generated: Sun Aug 11 07:16:24 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy