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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 Dec 13 19:14:02 2020

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