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Manganese in PDB 6z6q: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Ethyl-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-Ethyl-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-Ethyl-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-Ethyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6z6q 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) 46.00 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.62, 91.371, 122.701, 90, 90, 90
R / Rfree (%) 20.8 / 23.2

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-Ethyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) (pdb code 6z6q). 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-Ethyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6z6q:

Manganese binding site 1 out of 1 in 6z6q

Go back to Manganese Binding Sites List in 6z6q
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Ethyl-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-Ethyl-2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:37.8
occ:1.00
 O09 A:QA81003 1.9 42.4 1.0
O A:HOH1135 2.0 36.6 1.0
NE2 A:HIS725 2.2 55.1 1.0
O12 A:QA81003 2.2 49.5 1.0
NE2 A:HIS679 2.3 36.8 1.0
C08 A:QA81003 2.7 46.1 1.0
C10 A:QA81003 2.9 47.8 1.0
OD2 B:ASP103 2.9 40.7 0.6
CD2 A:HIS725 3.1 54.2 1.0
CE1 A:HIS679 3.1 37.4 1.0
CE1 A:HIS725 3.1 54.9 1.0
HE1 A:HIS679 3.3 44.8 1.0
HD2 A:HIS725 3.3 65.0 1.0
CD2 A:HIS679 3.3 37.6 1.0
HB3 B:ASP103 3.3 45.1 0.4
HE1 A:HIS725 3.3 65.8 1.0
HD2 A:HIS679 3.5 45.1 1.0
HB3 B:ASP103 3.7 45.0 0.6
H011 A:QA81003 3.7 65.8 1.0
CG B:ASP103 3.8 39.0 0.6
HH11 A:ARG688 3.8 39.4 1.0
O B:ASP103 3.9 36.3 0.4
HB2 A:ASP721 3.9 44.1 1.0
O B:ASP103 4.1 36.3 0.6
HH12 A:ARG688 4.1 39.4 1.0
O11 A:QA81003 4.1 48.8 1.0
H013 A:QA81003 4.2 65.8 1.0
CB B:ASP103 4.2 37.6 0.6
C03 A:QA81003 4.2 49.3 1.0
CB B:ASP103 4.2 37.6 0.4
NH1 A:ARG688 4.2 32.9 1.0
ND1 A:HIS679 4.2 38.7 1.0
ND1 A:HIS725 4.3 56.0 1.0
OD2 A:ASP721 4.3 35.7 1.0
CG A:HIS725 4.3 54.4 1.0
C01 A:QA81003 4.3 54.8 1.0
CG A:HIS679 4.3 38.4 1.0
HA B:ASP103 4.4 43.5 0.4
HA B:ASP103 4.4 43.4 0.6
HH2 A:TRP625 4.4 41.2 1.0
H021 A:QA81003 4.5 62.9 1.0
HD13 A:LEU619 4.5 40.2 1.0
C02 A:QA81003 4.6 52.5 1.0
HE2 A:PHE719 4.6 47.1 1.0
H031 A:QA81003 4.7 59.1 1.0
HZ A:PHE719 4.7 45.6 1.0
OD1 B:ASP103 4.7 39.0 0.6
CG B:ASP103 4.7 38.8 0.4
CA B:ASP103 4.7 36.2 0.4
CA B:ASP103 4.7 36.1 0.6
C B:ASP103 4.8 35.8 0.4
OD1 B:ASP103 4.8 35.5 0.4
C B:ASP103 4.8 35.7 0.6
CB A:ASP721 4.8 36.8 1.0
HB2 B:ASP103 4.9 45.1 0.4
HD2 A:ARG688 5.0 42.9 1.0
H042 A:QA81003 5.0 59.9 1.0
HD1 A:HIS679 5.0 46.4 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 07:56:57 2024

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