Manganese in PDB 6yw4: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog) and A Rapid-Derived Silent Allosteric Cyclic Peptide 3C (14- Mer)

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

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog) and A 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 N-Oxalylglycine (Nog) and A Rapid-Derived Silent Allosteric Cyclic Peptide 3C (14- Mer), PDB code: 6yw4 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) 39.61 / 1.53
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 46.622, 46.622, 203.711, 90, 90, 120
R / Rfree (%) 16.2 / 17.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog) and A Rapid-Derived Silent Allosteric Cyclic Peptide 3C (14- Mer) (pdb code 6yw4). 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 N-Oxalylglycine (Nog) and A Rapid-Derived Silent Allosteric Cyclic Peptide 3C (14- Mer), PDB code: 6yw4:

Manganese binding site 1 out of 1 in 6yw4

Go back to Manganese Binding Sites List in 6yw4
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog) and A 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 N-Oxalylglycine (Nog) and A Rapid-Derived Silent Allosteric Cyclic Peptide 3C (14- Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:17.1
occ:1.00
 O1 A:OGA502 2.1 21.1 1.0
O2' A:OGA502 2.1 18.5 1.0
OD1 A:ASP315 2.1 17.5 1.0
NE2 A:HIS313 2.1 19.7 1.0
NE2 A:HIS374 2.2 17.7 1.0
O A:HOH621 2.2 17.8 1.0
C1 A:OGA502 2.8 20.4 1.0
C2 A:OGA502 2.9 16.8 1.0
CE1 A:HIS313 3.0 20.5 1.0
HE1 A:HIS313 3.1 24.6 1.0
CD2 A:HIS374 3.1 20.0 1.0
CE1 A:HIS374 3.1 17.7 1.0
CG A:ASP315 3.2 20.6 1.0
CD2 A:HIS313 3.2 19.8 1.0
HD2 A:HIS374 3.3 24.0 1.0
HE1 A:HIS374 3.3 21.2 1.0
OD2 A:ASP315 3.4 19.0 1.0
HD2 A:HIS313 3.5 23.8 1.0
HZ A:PHE366 4.0 20.3 1.0
N1 A:OGA502 4.1 19.6 1.0
O A:HOH614 4.1 26.4 1.0
O2 A:OGA502 4.1 23.6 1.0
HZ2 A:TRP389 4.2 26.9 1.0
ND1 A:HIS313 4.2 21.7 1.0
ND1 A:HIS374 4.2 19.3 1.0
CG A:HIS374 4.3 19.3 1.0
CG A:HIS313 4.3 22.1 1.0
O A:HOH666 4.3 23.0 1.0
HA A:ASP315 4.3 23.6 1.0
H4C2 A:OGA502 4.5 23.3 1.0
CB A:ASP315 4.5 18.5 1.0
H4C1 A:OGA502 4.6 23.3 1.0
C4 A:OGA502 4.7 19.4 1.0
HE2 A:TYR310 4.7 25.5 1.0
CE2 A:TYR310 4.8 21.3 1.0
H1 A:OGA502 4.8 23.6 1.0
CA A:ASP315 4.8 19.7 1.0
HG21 A:THR325 4.8 20.9 1.0
CZ A:PHE366 4.9 16.9 1.0
H A:ASP315 4.9 22.8 1.0
HD1 A:HIS313 4.9 26.1 1.0
HE1 A:PHE366 4.9 21.3 1.0
N A:ASP315 5.0 19.0 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: Mon Jan 25 15:36:10 2021

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