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Manganese in PDB 8one: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose

Enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose:
1.14.11.4; 2.4.1.50; 2.4.1.66;

Protein crystallography data

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose, PDB code: 8one was solved by D.Mattoteia, M.De Marco, A.Pinnola, S.Faravelli, L.Scietti, F.Forneris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.44 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.09, 100.181, 223.794, 90, 90, 90
R / Rfree (%) 20.4 / 22.8

Other elements in 8one:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose (pdb code 8one). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose, PDB code: 8one:

Manganese binding site 1 out of 1 in 8one

Go back to Manganese Binding Sites List in 8one
Manganese binding site 1 out of 1 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1004

b:23.6
occ:1.00
 O2A A:UPG1009 2.1 33.5 1.0
O2B A:UPG1009 2.2 27.8 1.0
OD2 A:ASP115 2.2 26.5 1.0
NE2 A:HIS253 2.2 25.7 1.0
OD2 A:ASP112 2.3 26.0 1.0
OD1 A:ASP115 2.3 18.3 1.0
CG A:ASP115 2.6 26.1 1.0
CD2 A:HIS253 3.2 24.4 1.0
CG A:ASP112 3.2 28.8 1.0
CE1 A:HIS253 3.2 23.8 1.0
PB A:UPG1009 3.5 35.0 1.0
CB A:ASP112 3.5 24.4 1.0
PA A:UPG1009 3.5 33.0 1.0
O3A A:UPG1009 3.9 43.6 1.0
CB A:ASP115 4.1 20.6 1.0
O1B A:UPG1009 4.1 42.3 1.0
O3C A:UPG1009 4.2 27.7 1.0
ND1 A:HIS253 4.3 30.1 1.0
CG A:HIS253 4.3 23.4 1.0
C5C A:UPG1009 4.3 38.8 1.0
OD1 A:ASP112 4.4 32.4 1.0
O5C A:UPG1009 4.5 31.4 1.0
O1A A:UPG1009 4.5 47.4 1.0
CA A:ASN255 4.5 24.8 1.0
O A:HOH1183 4.6 45.9 1.0
O3B A:UPG1009 4.7 42.3 1.0
CB A:ASN255 4.8 29.2 1.0
O6' A:UPG1009 4.8 46.1 1.0
C1' A:UPG1009 4.9 65.4 1.0
O A:ASP115 4.9 21.9 1.0
N A:ASP115 4.9 18.4 1.0
NZ A:LYS259 4.9 24.9 1.0
CA A:ASP115 4.9 19.7 1.0
CG2 A:VAL116 5.0 20.7 1.0
N A:ASN255 5.0 21.9 1.0

Reference:

D.Mattoteia, A.Chiapparino, M.Fumagalli, M.De Marco, F.De Giorgi, L.Negro, A.Pinnola, S.Faravelli, T.Roscioli, L.Scietti, F.Forneris. Identification of Regulatory Molecular 'Hot Spots' For Lh/Plod Collagen Glycosyltransferase Activity Int J Mol Sci 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS241311213
Page generated: Sun Oct 6 13:30:11 2024

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