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

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with (S)-4-Hydroxy-4-Methyl-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 (S)-4-Hydroxy-4-Methyl-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 (S)-4-Hydroxy-4-Methyl-2-Oxoglutarate and Factor X- Derived Peptide (39MER-4SER), PDB code: 7ybc 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) 43.60 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.372, 87.049, 124.396, 90, 90, 90
R / Rfree (%) 17.8 / 19.9

Manganese Binding Sites:

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

Manganese binding site 1 out of 1 in 7ybc

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

b:27.9
occ:1.00
 O01 A:IOW803 2.2 29.1 1.0
O B:HOH201 2.2 25.1 1.0
NE2 A:HIS725 2.2 25.4 1.0
O03 A:IOW803 2.3 31.8 1.0
NE2 A:HIS679 2.3 25.3 1.0
O A:HOH949 2.4 41.7 1.0
C01 A:IOW803 2.9 33.4 1.0
C02 A:IOW803 2.9 34.1 1.0
CE1 A:HIS679 3.1 27.4 1.0
CD2 A:HIS725 3.1 25.5 1.0
HE1 A:HIS679 3.2 32.9 1.0
HD2 A:HIS725 3.2 30.6 1.0
CE1 A:HIS725 3.3 27.1 1.0
CD2 A:HIS679 3.3 26.0 1.0
HB3 B:ASP103 3.4 42.8 1.0
HE1 A:HIS725 3.5 32.5 1.0
HD2 A:HIS679 3.6 31.2 1.0
HH11 A:ARG688 3.7 34.9 1.0
HB2 A:ASP721 3.9 31.7 1.0
HH12 A:ARG688 4.0 34.9 1.0
O02 A:IOW803 4.1 30.6 1.0
H06 A:IOW803 4.1 38.2 1.0
NH1 A:ARG688 4.2 29.0 1.0
O B:ASP103 4.2 34.7 1.0
ND1 A:HIS679 4.3 25.6 1.0
CG A:HIS725 4.3 25.8 1.0
CB B:ASP103 4.3 35.7 1.0
ND1 A:HIS725 4.4 26.3 1.0
CG A:HIS679 4.4 23.7 1.0
OD2 A:ASP721 4.4 26.6 1.0
C03 A:IOW803 4.4 32.4 1.0
HZ A:PHE719 4.5 34.8 1.0
HE2 A:PHE719 4.6 32.1 1.0
O A:HOH945 4.6 39.3 1.0
HD13 A:LEU619 4.7 32.7 1.0
HA B:ASP103 4.7 41.7 1.0
HH2 A:TRP625 4.7 38.3 1.0
CB A:ASP721 4.8 26.4 1.0
OD1 B:ASP103 4.8 38.9 1.0
H02 A:IOW803 4.8 38.9 1.0
CG B:ASP103 4.8 41.1 1.0
CA B:ASP103 4.9 34.9 1.0
HD3 A:ARG688 4.9 40.7 1.0
HB2 B:ASP103 4.9 42.8 1.0
C06 A:IOW803 5.0 31.8 1.0
C B:ASP103 5.0 34.9 1.0
HD1 A:HIS679 5.0 30.8 1.0
H03 A:IOW803 5.0 38.9 1.0

Reference:

Y.Nakashima, L.Brewitz, C.J.Schofield. Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with (S)-4-Hydroxy-4-Methyl-2-Oxoglutarate and Factor X-Derived Peptide (39MER-4SER) To Be Published.
Page generated: Sun Oct 6 11:08:41 2024

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