Atomistry » Manganese » PDB 6wj4-6z6r » 6yyw
Atomistry »
  Manganese »
    PDB 6wj4-6z6r »
      6yyw »

Manganese in PDB 6yyw: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER)

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, 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, 2-Oxoglutarate, 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, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyw 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) 29.64 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.439, 90.951, 123.605, 90, 90, 90
R / Rfree (%) 18.8 / 22.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) (pdb code 6yyw). 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, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER), PDB code: 6yyw:

Manganese binding site 1 out of 1 in 6yyw

Go back to Manganese Binding Sites List in 6yyw
Manganese binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 2-Oxoglutarate, 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, 2-Oxoglutarate, and Factor X Substrate Peptide Fragment(39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:37.2
occ:1.00
 NE2 A:HIS725 2.1 49.3 1.0
O A:HOH917 2.1 42.5 1.0
O2 A:AKG802 2.2 46.9 1.0
NE2 A:HIS679 2.2 40.4 1.0
O5 A:AKG802 2.2 41.8 1.0
OD2 B:ASP103 2.4 57.1 1.0
C2 A:AKG802 2.8 43.1 1.0
C1 A:AKG802 2.8 44.1 1.0
CE1 A:HIS725 3.0 47.0 1.0
CE1 A:HIS679 3.0 46.9 1.0
CD2 A:HIS725 3.1 47.5 1.0
HE1 A:HIS679 3.1 56.2 1.0
HE1 A:HIS725 3.2 56.4 1.0
HD2 A:HIS725 3.3 57.0 1.0
CD2 A:HIS679 3.3 47.4 1.0
HD2 A:HIS679 3.6 56.9 1.0
HH11 A:ARG688 3.6 51.0 1.0
CG B:ASP103 3.7 57.5 1.0
HB2 A:ASP721 3.8 50.5 1.0
HB3 B:ASP103 3.9 51.9 1.0
O1 A:AKG802 4.1 46.2 1.0
HH12 A:ARG688 4.1 51.0 1.0
ND1 A:HIS725 4.1 42.6 1.0
NH1 A:ARG688 4.2 42.5 1.0
ND1 A:HIS679 4.2 42.9 1.0
CG A:HIS725 4.2 39.9 1.0
O B:ASP103 4.2 45.5 1.0
OD2 A:ASP721 4.2 46.5 1.0
CB B:ASP103 4.3 43.3 1.0
HH2 A:TRP625 4.3 56.2 1.0
C3 A:AKG802 4.3 39.0 1.0
CG A:HIS679 4.4 52.2 1.0
HD13 A:LEU619 4.5 55.4 1.0
HZ A:PHE719 4.6 58.5 1.0
HA B:ASP103 4.6 46.1 1.0
H31 A:AKG802 4.6 46.8 1.0
OD1 B:ASP103 4.7 53.2 1.0
CB A:ASP721 4.7 42.0 1.0
HE2 A:PHE719 4.8 49.9 1.0
H32 A:AKG802 4.8 46.8 1.0
CA B:ASP103 4.9 38.4 1.0
HD1 A:HIS725 4.9 51.1 1.0
HD3 A:ARG688 4.9 51.6 1.0
HD1 A:HIS679 4.9 51.5 1.0
CG A:ASP721 5.0 44.1 1.0

Reference:

L.Brewitz, Y.Nakashima, C.J.Schofield. Synthesis of 2-Oxoglutarate Derivatives and Their Evaluation As Cosubstrates and Inhibitors of Human Aspartate/Asparagine-Beta-Hydroxylase Chem Sci V. 12 1327 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC04301J
Page generated: Sun Oct 6 07:56:22 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy