Atomistry » Manganese » PDB 7bmf-7d6g » 7bmj
Atomistry »
  Manganese »
    PDB 7bmf-7d6g »
      7bmj »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy