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Manganese in PDB 6yw1: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer), PDB code: 6yw1 was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.30 / 1.46
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 46.531, 46.531, 202.345, 90, 90, 120
R / Rfree (%) 16.4 / 17.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer) (pdb code 6yw1). 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 Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer), PDB code: 6yw1:

Manganese binding site 1 out of 1 in 6yw1

Go back to Manganese Binding Sites List in 6yw1
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with 2OG and Rapid- Derived Silent Allosteric Cyclic Peptide 3C (14-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:17.5
occ:1.00
 O5 A:AKG502 2.1 19.4 1.0
OD1 A:ASP315 2.1 22.1 1.0
O1 A:AKG502 2.1 21.7 1.0
O A:HOH652 2.2 19.6 1.0
NE2 A:HIS374 2.2 20.9 1.0
NE2 A:HIS313 2.2 23.9 1.0
C2 A:AKG502 2.8 21.2 1.0
C1 A:AKG502 2.8 22.5 1.0
CE1 A:HIS313 3.1 20.1 1.0
CE1 A:HIS374 3.1 17.4 1.0
CG A:ASP315 3.1 19.5 1.0
HE1 A:HIS313 3.2 24.1 1.0
CD2 A:HIS374 3.2 17.9 1.0
CD2 A:HIS313 3.2 20.8 1.0
HE1 A:HIS374 3.3 20.9 1.0
HD2 A:HIS374 3.4 21.5 1.0
HD2 A:HIS313 3.5 25.0 1.0
OD2 A:ASP315 3.5 17.9 1.0
HZ A:PHE366 4.0 19.6 1.0
O2 A:AKG502 4.1 22.8 1.0
O A:HOH634 4.1 27.6 1.0
HZ2 A:TRP389 4.1 22.7 1.0
ND1 A:HIS313 4.2 21.3 1.0
HA A:ASP315 4.2 23.6 1.0
ND1 A:HIS374 4.3 17.7 1.0
C3 A:AKG502 4.3 22.1 1.0
O A:HOH655 4.3 19.6 1.0
CG A:HIS374 4.3 17.6 1.0
CG A:HIS313 4.3 21.0 1.0
CB A:ASP315 4.5 18.3 1.0
H41 A:AKG502 4.5 24.9 1.0
H42 A:AKG502 4.6 24.9 1.0
HE2 A:TYR310 4.7 27.2 1.0
H31 A:AKG502 4.7 26.6 1.0
CE2 A:TYR310 4.7 22.7 1.0
C4 A:AKG502 4.8 20.7 1.0
CA A:ASP315 4.8 19.7 1.0
HG21 A:THR325 4.8 20.7 1.0
H32 A:AKG502 4.8 26.6 1.0
CZ A:PHE366 4.9 16.3 1.0
HH A:TYR310 4.9 28.2 1.0
H A:ASP315 4.9 23.1 1.0
HD1 A:HIS313 5.0 25.6 1.0
N A:ASP315 5.0 19.2 1.0
HE1 A:PHE366 5.0 21.3 1.0
HE1 A:TRP389 5.0 22.6 1.0

Reference:

R.Chowdhury, M.I.Abboud, T.E.Mcallister, B.Banerji, B.Bhushan, J.L.Sorensen, A.Kawamura, C.J.Schofield. Use of Cyclic Peptides to Induce Crystallization: Case Study with Prolyl Hydroxylase Domain 2. Sci Rep V. 10 21964 2020.
ISSN: ESSN 2045-2322
PubMed: 33319810
DOI: 10.1038/S41598-020-76307-8
Page generated: Sun Oct 6 07:55:22 2024

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