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Manganese in PDB 6yyx: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Methyl-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, 3-Methyl-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, 3-Methyl-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, 3-Methyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyx 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) 50.21 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.22, 86.591, 123.265, 90, 90, 90
R / Rfree (%) 16.2 / 19.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Methyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) (pdb code 6yyx). 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, 3-Methyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyx:

Manganese binding site 1 out of 1 in 6yyx

Go back to Manganese Binding Sites List in 6yyx
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Methyl-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, 3-Methyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:21.0
occ:1.00
 O01 A:Q1Z802 2.1 21.9 1.0
O B:HOH205 2.1 18.8 1.0
O02 A:Q1Z802 2.1 19.7 1.0
NE2 A:HIS725 2.2 18.8 1.0
NE2 A:HIS679 2.2 20.5 1.0
OD2 B:ASP103 2.7 36.4 1.0
C01 A:Q1Z802 2.8 19.5 1.0
C05 A:Q1Z802 2.8 21.9 1.0
CE1 A:HIS679 3.1 24.2 1.0
CD2 A:HIS725 3.1 17.9 1.0
CE1 A:HIS725 3.2 20.1 1.0
HE1 A:HIS679 3.2 29.1 1.0
CD2 A:HIS679 3.2 26.9 1.0
HD2 A:HIS725 3.3 21.5 1.0
HE1 A:HIS725 3.3 24.1 1.0
HD2 A:HIS679 3.5 32.3 1.0
HH11 A:ARG688 3.6 31.5 1.0
HB3 B:ASP103 3.6 30.4 1.0
CG B:ASP103 3.7 33.2 1.0
HB2 A:ASP721 3.9 27.0 1.0
HH12 A:ARG688 3.9 31.5 1.0
NH1 A:ARG688 4.1 26.2 1.0
O03 A:Q1Z802 4.1 19.5 1.0
CB B:ASP103 4.1 25.3 1.0
O B:ASP103 4.2 23.9 1.0
ND1 A:HIS679 4.2 20.8 1.0
ND1 A:HIS725 4.3 20.5 1.0
CG A:HIS725 4.3 17.7 1.0
CG A:HIS679 4.3 22.0 1.0
HH2 A:TRP625 4.3 26.2 1.0
C02 A:Q1Z802 4.3 15.3 1.0
OD2 A:ASP721 4.4 21.2 1.0
H06 A:Q1Z802 4.4 24.4 1.0
HA B:ASP103 4.4 25.4 1.0
HD13 A:LEU619 4.5 32.8 1.0
O B:HOH204 4.5 24.9 1.0
OD1 B:ASP103 4.6 26.6 1.0
HE2 A:PHE719 4.7 23.8 1.0
H01 A:Q1Z802 4.7 18.3 1.0
HZ A:PHE719 4.7 26.2 1.0
CA B:ASP103 4.7 21.1 1.0
C04 A:Q1Z802 4.8 20.3 1.0
CB A:ASP721 4.8 22.5 1.0
HD2 A:ARG688 4.9 30.6 1.0
C B:ASP103 4.9 26.6 1.0
HB2 B:ASP103 5.0 30.4 1.0
HD1 A:HIS679 5.0 24.9 1.0
H05 A:Q1Z802 5.0 24.4 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 07:56:31 2024

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