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Manganese in PDB 6yyy: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 4,4-Dimethyl-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, 4,4-Dimethyl-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, 4,4-Dimethyl-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, 4,4-Dimethyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyy 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) 71.34 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.815, 50.318, 86.603, 90, 90, 90
R / Rfree (%) 20.9 / 24.4

Manganese Binding Sites:

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

Manganese binding site 1 out of 1 in 6yyy

Go back to Manganese Binding Sites List in 6yyy
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 4,4-Dimethyl-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, 4,4-Dimethyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:30.9
occ:1.00
 O02 A:Q1W802 2.3 43.7 1.0
O01 A:Q1W802 2.3 34.1 1.0
NE2 A:HIS725 2.3 30.3 1.0
O A:HOH908 2.3 38.6 1.0
NE2 A:HIS679 2.4 34.4 1.0
HD2 A:HIS725 2.8 39.8 1.0
CD2 A:HIS725 2.9 33.2 1.0
C01 A:Q1W802 2.9 40.9 1.0
C02 A:Q1W802 3.0 46.3 1.0
HB3 B:ASP103 3.1 47.0 1.0
HH21 A:ARG688 3.3 38.3 1.0
CD2 A:HIS679 3.3 33.6 1.0
HD2 A:HIS679 3.4 40.4 1.0
CE1 A:HIS679 3.4 33.3 1.0
CE1 A:HIS725 3.5 37.4 1.0
HH22 A:ARG688 3.6 38.3 1.0
HE1 A:HIS679 3.6 39.9 1.0
NH2 A:ARG688 3.8 31.9 1.0
HE1 A:HIS725 3.9 44.9 1.0
O03 A:Q1W802 4.0 33.7 1.0
O B:ASP103 4.0 33.2 1.0
CB B:ASP103 4.0 39.2 1.0
HB2 A:ASP721 4.1 47.9 1.0
CG A:HIS725 4.2 30.1 1.0
OD2 B:ASP103 4.2 49.9 1.0
HZ A:PHE719 4.2 44.3 1.0
CG B:ASP103 4.3 43.5 1.0
HA B:ASP103 4.3 42.5 1.0
ND1 A:HIS725 4.4 35.0 1.0
CG A:HIS679 4.5 37.5 1.0
ND1 A:HIS679 4.5 35.1 1.0
C03 A:Q1W802 4.5 33.1 1.0
H09 A:Q1W802 4.5 57.6 1.0
CA B:ASP103 4.6 35.4 1.0
H01 A:Q1W802 4.7 39.8 1.0
HD13 A:LEU619 4.7 47.2 1.0
HB2 B:ASP103 4.7 47.0 1.0
HE2 A:PHE719 4.8 35.1 1.0
C B:ASP103 4.8 34.6 1.0
HD3 A:ARG688 4.8 63.1 1.0
OD2 A:ASP721 4.9 41.8 1.0
H07 A:Q1W802 4.9 57.6 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 07:56:39 2024

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