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Manganese in PDB 7bmj: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-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, 5-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, 5-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, 5-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER), PDB code: 7bmj 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) 46.26 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.35, 59.48, 95.54, 104.26, 91.51, 92.76
R / Rfree (%) 22.1 / 25.1

Other elements in 7bmj:

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) (pdb code 7bmj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER), PDB code: 7bmj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7bmj

Go back to Manganese Binding Sites List in 7bmj
Manganese binding site 1 out of 2 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-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, 5-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:54.2
occ:1.00
 OD2 B:ASP103 2.0 60.5 0.5
NE2 A:HIS725 2.1 43.9 1.0
O B:HOH202 2.2 36.1 1.0
O03 A:U4Q802 2.2 37.6 1.0
N13 A:U4Q802 2.3 39.5 1.0
NE2 A:HIS679 2.4 50.0 1.0
C02 A:U4Q802 3.0 38.0 1.0
CE1 A:HIS725 3.0 43.4 1.0
C04 A:U4Q802 3.0 39.8 1.0
CD2 A:HIS725 3.1 40.8 1.0
HE1 A:HIS725 3.1 52.0 1.0
CG B:ASP103 3.1 52.7 0.5
HB3 B:ASP103 3.2 61.2 0.5
C12 A:U4Q802 3.3 41.2 1.0
CE1 A:HIS679 3.3 51.1 1.0
HD2 A:HIS725 3.3 49.0 1.0
CD2 A:HIS679 3.3 50.0 1.0
H121 A:U4Q802 3.4 49.4 1.0
HE1 A:HIS679 3.5 61.3 1.0
HD2 A:HIS679 3.5 60.0 1.0
HH11 A:ARG688 3.5 52.7 1.0
HB3 B:ASP103 3.7 61.3 0.5
HB2 A:ASP721 3.8 51.0 1.0
CB B:ASP103 4.0 51.1 0.5
CB B:ASP103 4.0 51.0 0.5
OD1 B:ASP103 4.0 52.0 0.5
CG B:ASP103 4.1 52.6 0.5
HH12 A:ARG688 4.1 52.7 1.0
ND1 A:HIS725 4.1 43.1 1.0
NH1 A:ARG688 4.1 44.0 1.0
O B:ASP103 4.2 52.3 0.5
O B:ASP103 4.2 52.2 0.5
O01 A:U4Q802 4.2 38.0 1.0
CG A:HIS725 4.2 41.0 1.0
HA B:ASP103 4.2 59.3 0.5
HA B:ASP103 4.2 59.3 0.5
C05 A:U4Q802 4.3 39.7 1.0
OD2 A:ASP721 4.4 44.1 1.0
OD2 B:ASP103 4.4 54.9 0.5
ND1 A:HIS679 4.4 50.6 1.0
OD1 B:ASP103 4.4 50.2 0.5
HH2 A:TRP625 4.4 53.7 1.0
CG A:HIS679 4.4 49.6 1.0
HE2 A:PHE719 4.5 49.6 1.0
C10 A:U4Q802 4.5 39.0 1.0
CA B:ASP103 4.6 49.4 0.5
CA B:ASP103 4.6 49.5 0.5
HD2 A:ARG688 4.7 56.3 1.0
CB A:ASP721 4.7 42.5 1.0
HZ A:PHE719 4.7 48.5 1.0
HB2 B:ASP103 4.8 61.2 0.5
HB2 B:ASP103 4.8 61.3 0.5
HD13 A:LEU619 4.8 64.0 1.0
C B:ASP103 4.8 51.2 0.5
C B:ASP103 4.8 51.2 0.5
HD1 A:HIS725 4.9 51.7 1.0
O B:HOH201 4.9 47.1 1.0
HB3 A:ASP721 5.0 51.0 1.0
C06 A:U4Q802 5.0 39.1 1.0

Manganese binding site 2 out of 2 in 7bmj

Go back to Manganese Binding Sites List in 7bmj
Manganese binding site 2 out of 2 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-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 2 of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 5-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn801

b:71.2
occ:1.00
 O C:HOH983 2.0 38.6 1.0
NE2 C:HIS725 2.1 38.9 1.0
O01 C:U4Q802 2.2 35.0 1.0
NE2 C:HIS679 2.3 40.6 1.0
O C:HOH927 2.3 41.2 1.0
N13 C:U4Q802 2.4 39.3 1.0
C02 C:U4Q802 3.0 38.2 1.0
CE1 C:HIS725 3.0 39.7 1.0
C04 C:U4Q802 3.0 38.7 1.0
HE1 C:HIS725 3.1 47.7 1.0
CE1 C:HIS679 3.2 40.9 1.0
CD2 C:HIS725 3.2 38.0 1.0
CD2 C:HIS679 3.3 43.0 1.0
HE1 C:HIS679 3.3 49.0 1.0
C12 C:U4Q802 3.4 37.0 1.0
HH12 C:ARG688 3.4 61.0 1.0
HD2 C:HIS725 3.4 45.6 1.0
H121 C:U4Q802 3.5 44.4 1.0
HD2 C:HIS679 3.5 51.5 1.0
HH11 C:ARG688 4.0 61.0 1.0
NH1 C:ARG688 4.0 50.9 1.0
HB2 C:ASP721 4.0 52.1 1.0
ND1 C:HIS725 4.2 39.8 1.0
O03 C:U4Q802 4.2 36.3 1.0
O C:HOH1049 4.2 56.3 1.0
CG C:HIS725 4.3 38.3 1.0
ND1 C:HIS679 4.3 44.1 1.0
OD1 C:ASP721 4.4 46.1 1.0
C05 C:U4Q802 4.4 36.6 1.0
CG C:HIS679 4.4 45.5 1.0
O C:HOH966 4.5 47.4 1.0
HD13 C:LEU619 4.5 60.9 1.0
C10 C:U4Q802 4.6 37.7 1.0
O C:HOH1066 4.7 57.0 1.0
HD2 C:ARG688 4.8 53.4 1.0
HZ C:PHE719 4.8 48.2 1.0
HE2 C:PHE719 4.8 48.0 1.0
HD3 C:ARG688 4.9 53.4 1.0
CB C:ASP721 4.9 43.4 1.0
HD1 C:HIS725 4.9 47.7 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: Sun Oct 6 08:10:20 2024

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