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Manganese in PDB 6yyw: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER)

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER)

All present enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER):
1.14.11.16; 3.4.21.6;

Protein crystallography data

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyw was solved by Y.Nakashima, L.Brewitz, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.64 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.439, 90.951, 123.605, 90, 90, 90
R / Rfree (%) 18.8 / 22.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) (pdb code 6yyw). 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 Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyw:

Manganese binding site 1 out of 1 in 6yyw

Go back to Manganese Binding Sites List in 6yyw
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:37.2
occ:1.00
 NE2 A:HIS725 2.1 49.3 1.0
O A:HOH917 2.1 42.5 1.0
O2 A:AKG802 2.2 46.9 1.0
NE2 A:HIS679 2.2 40.4 1.0
O5 A:AKG802 2.2 41.8 1.0
OD2 B:ASP103 2.4 57.1 1.0
C2 A:AKG802 2.8 43.1 1.0
C1 A:AKG802 2.8 44.1 1.0
CE1 A:HIS725 3.0 47.0 1.0
CE1 A:HIS679 3.0 46.9 1.0
CD2 A:HIS725 3.1 47.5 1.0
HE1 A:HIS679 3.1 56.2 1.0
HE1 A:HIS725 3.2 56.4 1.0
HD2 A:HIS725 3.3 57.0 1.0
CD2 A:HIS679 3.3 47.4 1.0
HD2 A:HIS679 3.6 56.9 1.0
HH11 A:ARG688 3.6 51.0 1.0
CG B:ASP103 3.7 57.5 1.0
HB2 A:ASP721 3.8 50.5 1.0
HB3 B:ASP103 3.9 51.9 1.0
O1 A:AKG802 4.1 46.2 1.0
HH12 A:ARG688 4.1 51.0 1.0
ND1 A:HIS725 4.1 42.6 1.0
NH1 A:ARG688 4.2 42.5 1.0
ND1 A:HIS679 4.2 42.9 1.0
CG A:HIS725 4.2 39.9 1.0
O B:ASP103 4.2 45.5 1.0
OD2 A:ASP721 4.2 46.5 1.0
CB B:ASP103 4.3 43.3 1.0
HH2 A:TRP625 4.3 56.2 1.0
C3 A:AKG802 4.3 39.0 1.0
CG A:HIS679 4.4 52.2 1.0
HD13 A:LEU619 4.5 55.4 1.0
HZ A:PHE719 4.6 58.5 1.0
HA B:ASP103 4.6 46.1 1.0
H31 A:AKG802 4.6 46.8 1.0
OD1 B:ASP103 4.7 53.2 1.0
CB A:ASP721 4.7 42.0 1.0
HE2 A:PHE719 4.8 49.9 1.0
H32 A:AKG802 4.8 46.8 1.0
CA B:ASP103 4.9 38.4 1.0
HD1 A:HIS725 4.9 51.1 1.0
HD3 A:ARG688 4.9 51.6 1.0
HD1 A:HIS679 4.9 51.5 1.0
CG A:ASP721 5.0 44.1 1.0

Reference:

L.Brewitz, Y.Nakashima, C.J.Schofield. Synthesis of 2-Oxoglutarate Derivatives and Their Evaluation As Cosubstrates and Inhibitors of Human Aspartate/Asparagine-Beta-Hydroxylase Chem Sci V. 12 1327 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC04301J
Page generated: Sun Oct 6 07:56:22 2024

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