Manganese in PDB 7bmi: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, 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-Fluoropyridine-2,4-Dicarboxylic Acid, 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-Fluoropyridine-2,4-Dicarboxylic Acid, 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-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER), PDB code: 7bmi 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) 46.06 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.702, 91.274, 122.629, 90, 90, 90
R / Rfree (%) 18.9 / 22

Other elements in 7bmi:

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) also contains other interesting chemical elements:

Fluorine (F) 1 atom

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-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) (pdb code 7bmi). 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-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER), PDB code: 7bmi:

Manganese binding site 1 out of 1 in 7bmi

Go back to Manganese Binding Sites List in 7bmi
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, 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-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:32.5
occ:1.00
 O A:HOH965 2.0 31.7 1.0
O11 A:U4B802 2.2 32.5 1.0
NE2 A:HIS725 2.2 40.5 1.0
N07 A:U4B802 2.3 31.9 1.0
NE2 A:HIS679 2.3 32.2 1.0
OD1 B:ASP103 2.6 35.9 0.5
C09 A:U4B802 2.9 31.0 1.0
C08 A:U4B802 3.0 30.8 1.0
CE1 A:HIS725 3.1 36.5 1.0
CE1 A:HIS679 3.2 33.0 1.0
CD2 A:HIS725 3.2 36.1 1.0
HE1 A:HIS679 3.3 39.8 1.0
HE1 A:HIS725 3.3 44.0 1.0
CD2 A:HIS679 3.3 33.3 1.0
C06 A:U4B802 3.3 31.9 1.0
HD2 A:HIS725 3.4 43.5 1.0
HB3 B:ASP103 3.4 41.4 0.5
H061 A:U4B802 3.5 38.5 1.0
HD2 A:HIS679 3.5 40.1 1.0
HH11 A:ARG688 3.5 38.9 1.0
CG B:ASP103 3.6 38.7 0.5
HB2 A:ASP721 3.9 40.2 1.0
HB3 B:ASP103 3.9 41.6 0.5
HH12 A:ARG688 4.1 38.9 1.0
O10 A:U4B802 4.1 31.2 1.0
NH1 A:ARG688 4.1 32.3 1.0
O B:ASP103 4.2 33.1 0.5
ND1 A:HIS725 4.3 37.9 1.0
OD2 A:ASP721 4.3 32.1 1.0
ND1 A:HIS679 4.3 34.2 1.0
CB B:ASP103 4.3 34.5 0.5
CB B:ASP103 4.3 34.3 0.5
CG A:HIS725 4.3 36.9 1.0
O B:ASP103 4.3 33.3 0.5
C12 A:U4B802 4.4 31.4 1.0
CG A:HIS679 4.4 33.4 1.0
OD2 B:ASP103 4.4 42.5 0.5
HZ A:PHE719 4.5 44.5 1.0
HH2 A:TRP625 4.5 37.0 1.0
HE2 A:PHE719 4.6 46.1 1.0
C05 A:U4B802 4.6 30.9 1.0
HA B:ASP103 4.6 40.2 0.5
HA B:ASP103 4.6 40.2 0.5
HD13 A:LEU619 4.7 36.9 1.0
HD2 A:ARG688 4.7 40.0 1.0
CB A:ASP721 4.7 33.4 1.0
O B:HOH202 4.8 38.7 1.0
HB2 B:ASP103 4.9 41.4 0.5
CG B:ASP103 4.9 41.4 0.5
CA B:ASP103 4.9 33.4 0.5
CA B:ASP103 4.9 33.4 0.5
C04 A:U4B802 5.0 30.5 1.0

Reference:

L.Brewitz, Y.Nakashima, A.Tumber, E.Salah, C.J.Schofield. Fluorinated Derivatives of Pyridine-2,4-Dicarboxylate Are Potent Inhibitors of Human 2-Oxoglutarate Dependent Oxygenases J Fluor Chem V. 247 09804 2021.
DOI: 10.1016/J.JFLUCHEM.2021.109804
Page generated: Mon Jul 12 15:20:01 2021

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