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Manganese in PDB 7yb8: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER)

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER)

All present enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER):
1.14.11.16;

Protein crystallography data

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER), PDB code: 7yb8 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) 50.78 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.879, 91.063, 122.351, 90, 90, 90
R / Rfree (%) 21.9 / 24.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER) (pdb code 7yb8). 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 D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER), PDB code: 7yb8:

Manganese binding site 1 out of 1 in 7yb8

Go back to Manganese Binding Sites List in 7yb8
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (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 D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1003

b:66.1
occ:1.00
 HO3 A:2HG1004 1.8 105.6 1.0
NE2 A:HIS725 2.0 55.3 1.0
O3 A:2HG1004 2.0 87.5 1.0
O B:HOH202 2.1 61.4 1.0
O2 A:2HG1004 2.1 111.5 1.0
NE2 A:HIS679 2.3 39.5 1.0
C1 A:2HG1004 2.8 111.0 1.0
CE1 A:HIS725 2.8 49.5 1.0
C2 A:2HG1004 2.8 98.6 1.0
HE1 A:HIS725 3.0 60.1 1.0
CE1 A:HIS679 3.0 38.6 1.0
CD2 A:HIS725 3.1 48.5 1.0
HE1 A:HIS679 3.1 47.0 1.0
HD2 A:HIS725 3.3 58.9 1.0
HB3 B:ASP103 3.3 50.0 1.0
CD2 A:HIS679 3.3 39.2 1.0
H2 A:2HG1004 3.4 118.9 1.0
HD2 A:HIS679 3.6 47.7 1.0
HH11 A:ARG688 3.7 47.1 1.0
HB2 A:ASP721 3.9 42.6 1.0
O1 A:2HG1004 4.0 115.1 1.0
ND1 A:HIS725 4.0 48.8 1.0
O B:ASP103 4.0 32.4 1.0
HH12 A:ARG688 4.1 47.1 1.0
C3 A:2HG1004 4.1 93.9 1.0
H3A A:2HG1004 4.1 113.3 1.0
CG A:HIS725 4.1 46.8 1.0
NH1 A:ARG688 4.1 38.7 1.0
ND1 A:HIS679 4.2 39.7 1.0
CB B:ASP103 4.3 41.1 1.0
CG A:HIS679 4.4 38.5 1.0
H3 A:2HG1004 4.4 113.3 1.0
OD2 A:ASP721 4.4 37.8 1.0
HA B:ASP103 4.5 46.3 1.0
HE1 A:PHE719 4.5 53.4 1.0
HH2 A:TRP625 4.6 44.7 1.0
HD13 A:LEU619 4.6 40.8 1.0
HZ A:PHE719 4.7 54.7 1.0
OD2 B:ASP103 4.7 47.0 1.0
HD1 A:HIS725 4.8 59.2 1.0
CB A:ASP721 4.8 35.0 1.0
CA B:ASP103 4.8 38.1 1.0
C B:ASP103 4.8 33.9 1.0
CG B:ASP103 4.8 47.4 1.0
HB2 B:ASP103 4.9 50.0 1.0
HD2 A:ARG688 4.9 49.4 1.0
HD1 A:HIS679 4.9 48.3 1.0

Reference:

Y.Nakashima, L.Brewitz, C.J.Schofield. Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-2-Hydroxyglutarate and Factor X-Derived Peptide (39MER-4SER) To Be Published.
Page generated: Sun Aug 17 00:01:05 2025

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