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

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-4-Hydroxy-2-Oxoglutarate 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-4-Hydroxy-2-Oxoglutarate and Factor X-Derived Peptide (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 D-4-Hydroxy-2-Oxoglutarate and Factor X-Derived Peptide (39MER-4SER), PDB code: 7ybb 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) 46.50 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.457, 123.608, 50.183, 90, 90, 90
R / Rfree (%) 19.5 / 21.9

Manganese Binding Sites:

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

Manganese binding site 1 out of 1 in 7ybb

Go back to Manganese Binding Sites List in 7ybb
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-4-Hydroxy-2-Oxoglutarate 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-4-Hydroxy-2-Oxoglutarate and Factor X-Derived Peptide (39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:17.3
occ:1.00
 O B:HOH206 2.0 11.8 1.0
O04 A:IO9802 2.1 15.3 1.0
O06 A:IO9802 2.1 17.0 1.0
NE2 A:HIS725 2.2 12.0 1.0
NE2 A:HIS679 2.2 12.5 1.0
C02 A:IO9802 2.7 20.3 1.0
C05 A:IO9802 2.8 15.6 1.0
CE1 A:HIS679 3.0 14.3 1.0
HE1 A:HIS679 3.0 17.6 1.0
CD2 A:HIS725 3.1 9.3 1.0
HB3 B:ASP103 3.2 17.2 1.0
HD2 A:HIS725 3.2 11.6 1.0
CE1 A:HIS725 3.2 15.2 1.0
CD2 A:HIS679 3.3 16.3 1.0
HE1 A:HIS725 3.5 18.6 1.0
HD2 A:HIS679 3.6 19.9 1.0
HH11 A:ARG688 3.8 23.0 1.0
HB2 A:ASP721 3.9 13.7 1.0
OD2 B:ASP103 4.0 30.5 1.0
CB B:ASP103 4.0 14.1 1.0
O03 A:IO9802 4.1 13.1 1.0
CG B:ASP103 4.1 16.2 1.0
ND1 A:HIS679 4.2 14.8 1.0
HH12 A:ARG688 4.2 23.0 1.0
O B:ASP103 4.2 14.0 1.0
CG A:HIS725 4.3 13.1 1.0
NH1 A:ARG688 4.3 18.8 1.0
ND1 A:HIS725 4.3 11.5 1.0
OD2 A:ASP721 4.3 13.6 1.0
C04 A:IO9802 4.3 14.7 1.0
CG A:HIS679 4.4 11.5 1.0
HH2 A:TRP625 4.5 23.8 1.0
HD13 A:LEU619 4.6 16.3 1.0
H06 A:IO9802 4.6 18.1 1.0
HA B:ASP103 4.6 7.5 1.0
HZ A:PHE719 4.6 20.2 1.0
HE2 A:PHE719 4.6 15.9 1.0
HB2 B:ASP103 4.7 17.2 1.0
H05 A:IO9802 4.8 18.1 1.0
CA B:ASP103 4.8 5.9 1.0
CB A:ASP721 4.8 11.0 1.0
O B:HOH201 4.8 16.5 1.0
HZ2 A:TRP625 4.9 15.9 1.0
HD1 A:HIS679 4.9 18.2 1.0
OD1 B:ASP103 4.9 14.5 1.0
C B:ASP103 4.9 11.8 1.0
HD2 A:ARG688 5.0 17.5 1.0

Reference:

Y.Nakashima, L.Brewitz, C.J.Schofield. Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with D-4-Hydroxy-2-Oxoglutarate and Factor X-Derived Peptide (39MER-4SER) To Be Published.
Page generated: Sun Aug 17 00:01:26 2025

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