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Manganese in PDB 6yvt: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253:
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253, PDB code: 6yvt was solved by R.Chowdhury, M.Demetriades, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.75 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.456, 103.018, 196.028, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 26.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253 (pdb code 6yvt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253, PDB code: 6yvt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6yvt

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Manganese binding site 1 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253


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 Md-253 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:36.4
occ:1.00
O26 A:PW2502 2.0 31.6 1.0
N18 A:PW2502 2.1 41.4 1.0
NE2 A:HIS313 2.1 37.0 1.0
OD1 A:ASP315 2.3 49.8 1.0
C20 A:PW2502 2.5 33.3 1.0
NE2 A:HIS374 2.5 31.8 1.0
C19 A:PW2502 2.6 40.0 1.0
O A:HOH605 2.8 25.4 1.0
CE1 A:HIS313 2.9 38.3 1.0
HE1 A:HIS313 2.9 46.0 1.0
C17 A:PW2502 3.2 40.8 1.0
CG A:ASP315 3.2 49.1 1.0
CD2 A:HIS313 3.3 40.5 1.0
H171 A:PW2502 3.4 49.0 1.0
CD2 A:HIS374 3.4 26.5 1.0
OD2 A:ASP315 3.4 49.0 1.0
HD2 A:HIS374 3.5 31.9 1.0
CE1 A:HIS374 3.6 32.6 1.0
HD2 A:HIS313 3.6 48.6 1.0
HE1 A:HIS374 3.7 39.2 1.0
N21 A:PW2502 3.9 33.7 1.0
C02 A:PW2502 4.0 38.4 1.0
HZ A:PHE366 4.0 40.3 1.0
ND1 A:HIS313 4.1 34.7 1.0
HZ2 A:TRP389 4.1 48.9 1.0
CG A:HIS313 4.3 40.1 1.0
HG11 C:VAL401 4.3 71.1 1.0
C04 A:PW2502 4.4 37.0 1.0
H211 A:PW2502 4.4 40.5 1.0
H222 A:PW2502 4.5 37.9 1.0
HA A:ASP315 4.5 65.9 1.0
CG A:HIS374 4.6 32.4 1.0
ND1 A:HIS374 4.6 34.4 1.0
C22 A:PW2502 4.7 31.6 1.0
CB A:ASP315 4.7 48.3 1.0
C03 A:PW2502 4.7 34.5 1.0
HG21 C:VAL401 4.7 66.4 1.0
H221 A:PW2502 4.8 37.9 1.0
HG21 A:THR325 4.8 48.6 1.0
HD1 A:HIS313 4.8 41.7 1.0
HE1 A:PHE366 4.8 42.1 1.0
HD11 A:ILE327 4.9 44.4 1.0
HG22 C:VAL401 4.9 66.4 1.0
CZ A:PHE366 4.9 33.5 1.0
O01 A:PW2502 4.9 36.0 1.0

Manganese binding site 2 out of 6 in 6yvt

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Manganese binding site 2 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:29.4
occ:1.00
N18 B:PW2502 2.1 37.4 1.0
O26 B:PW2502 2.3 38.0 1.0
O B:HOH607 2.3 36.5 1.0
OD1 B:ASP315 2.3 32.3 1.0
NE2 B:HIS313 2.3 42.9 1.0
NE2 B:HIS374 2.3 32.0 1.0
C19 B:PW2502 2.9 36.3 1.0
C20 B:PW2502 2.9 38.0 1.0
CE1 B:HIS313 3.0 41.1 1.0
HE1 B:HIS313 3.0 49.4 1.0
C17 B:PW2502 3.1 39.3 1.0
H171 B:PW2502 3.1 47.2 1.0
CD2 B:HIS374 3.2 35.4 1.0
CG B:ASP315 3.2 38.6 1.0
HD2 B:HIS374 3.3 42.5 1.0
CE1 B:HIS374 3.4 34.1 1.0
OD2 B:ASP315 3.4 37.2 1.0
CD2 B:HIS313 3.5 39.8 1.0
HE1 B:HIS374 3.6 41.0 1.0
HD2 B:HIS313 3.8 47.8 1.0
HG11 F:VAL401 3.9 57.9 1.0
HZ B:PHE366 4.0 36.6 1.0
HZ2 B:TRP389 4.1 48.2 1.0
C02 B:PW2502 4.2 37.9 1.0
N21 B:PW2502 4.2 43.0 1.0
ND1 B:HIS313 4.2 41.7 1.0
C04 B:PW2502 4.3 41.1 1.0
HG21 F:VAL401 4.4 57.9 1.0
O B:HOH604 4.4 31.7 1.0
CG B:HIS374 4.4 36.6 1.0
ND1 B:HIS374 4.5 37.3 1.0
CG B:HIS313 4.5 36.9 1.0
HA B:ASP315 4.5 44.4 1.0
HG13 F:VAL401 4.6 57.9 1.0
CB B:ASP315 4.6 40.5 1.0
CG1 F:VAL401 4.7 48.2 1.0
H222 B:PW2502 4.7 49.1 1.0
HG21 B:THR325 4.8 53.8 1.0
H211 B:PW2502 4.8 51.7 1.0
C03 B:PW2502 4.8 38.5 1.0
CZ B:PHE366 4.9 30.4 1.0
HE1 B:PHE366 4.9 42.2 1.0
C22 B:PW2502 4.9 40.9 1.0
HD1 B:HIS313 5.0 50.1 1.0
CA B:ASP315 5.0 37.0 1.0

Manganese binding site 3 out of 6 in 6yvt

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Manganese binding site 3 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:32.4
occ:1.00
O C:HOH607 1.9 26.4 1.0
OD1 C:ASP315 2.2 38.0 1.0
NE2 C:HIS313 2.2 35.1 1.0
N18 C:PW2502 2.2 41.1 1.0
O26 C:PW2502 2.4 37.0 1.0
NE2 C:HIS374 2.4 41.7 1.0
CE1 C:HIS313 3.0 34.7 1.0
HE1 C:HIS313 3.0 41.7 1.0
C19 C:PW2502 3.0 36.2 1.0
C20 C:PW2502 3.0 32.5 1.0
CD2 C:HIS374 3.2 32.1 1.0
C17 C:PW2502 3.2 34.8 1.0
HD2 C:HIS374 3.2 38.5 1.0
CG C:ASP315 3.2 35.6 1.0
H171 C:PW2502 3.2 41.8 1.0
CD2 C:HIS313 3.4 36.7 1.0
CE1 C:HIS374 3.4 36.6 1.0
OD2 C:ASP315 3.5 30.4 1.0
HD2 C:HIS313 3.7 44.1 1.0
HE1 C:HIS374 3.7 44.0 1.0
HZ2 C:TRP389 4.1 44.3 1.0
HG11 D:VAL401 4.1 51.8 1.0
ND1 C:HIS313 4.2 34.6 1.0
HZ C:PHE366 4.2 49.7 1.0
HA C:ASP315 4.3 40.7 1.0
C02 C:PW2502 4.3 36.8 1.0
O C:HOH603 4.4 30.2 1.0
CG C:HIS374 4.4 31.2 1.0
CG C:HIS313 4.4 35.6 1.0
N21 C:PW2502 4.4 37.2 1.0
C04 C:PW2502 4.5 34.1 1.0
ND1 C:HIS374 4.5 35.8 1.0
HG22 D:VAL401 4.5 54.3 1.0
HG21 C:THR325 4.6 38.1 1.0
CB C:ASP315 4.6 40.6 1.0
HE2 C:PHE366 4.7 47.1 1.0
H222 C:PW2502 4.8 37.5 1.0
CA C:ASP315 4.8 33.8 1.0
H C:ASP315 4.9 41.4 1.0
HG21 D:VAL401 4.9 54.3 1.0
HD1 C:HIS313 4.9 41.5 1.0
HD11 C:ILE327 4.9 41.5 1.0
C03 C:PW2502 5.0 36.1 1.0
H211 C:PW2502 5.0 44.8 1.0
CZ C:PHE366 5.0 41.4 1.0
CZ2 C:TRP389 5.0 36.9 1.0
N C:ASP315 5.0 34.5 1.0

Manganese binding site 4 out of 6 in 6yvt

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Manganese binding site 4 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:26.8
occ:1.00
NE2 D:HIS313 2.0 37.1 1.0
OD1 D:ASP315 2.2 30.4 1.0
O D:HOH606 2.3 26.9 1.0
N18 D:PW2502 2.3 35.5 1.0
O26 D:PW2502 2.3 31.7 1.0
NE2 D:HIS374 2.3 29.4 1.0
CE1 D:HIS313 2.7 30.9 1.0
HE1 D:HIS313 2.7 37.2 1.0
C20 D:PW2502 3.0 31.7 1.0
C19 D:PW2502 3.0 33.1 1.0
CE1 D:HIS374 3.2 29.7 1.0
CD2 D:HIS313 3.2 32.5 1.0
C17 D:PW2502 3.2 38.8 1.0
CD2 D:HIS374 3.3 32.2 1.0
H171 D:PW2502 3.3 46.6 1.0
CG D:ASP315 3.3 36.3 1.0
HE1 D:HIS374 3.3 35.7 1.0
HD2 D:HIS374 3.5 38.7 1.0
HD2 D:HIS313 3.6 39.1 1.0
OD2 D:ASP315 3.7 37.1 1.0
HG11 A:VAL401 3.8 43.1 1.0
HZ D:PHE366 3.9 32.8 1.0
ND1 D:HIS313 3.9 32.1 1.0
CG D:HIS313 4.2 29.7 1.0
HA D:ASP315 4.3 41.8 1.0
ND1 D:HIS374 4.3 28.0 1.0
HG13 A:VAL401 4.4 43.1 1.0
HG21 A:VAL401 4.4 41.7 1.0
CG D:HIS374 4.4 33.1 1.0
C02 D:PW2502 4.4 34.5 1.0
N21 D:PW2502 4.4 31.9 1.0
HZ2 D:TRP389 4.4 34.1 1.0
C04 D:PW2502 4.5 33.6 1.0
CG1 A:VAL401 4.6 35.9 1.0
CB D:ASP315 4.6 34.0 1.0
HD1 D:HIS313 4.6 38.5 1.0
H222 D:PW2502 4.7 43.5 1.0
CZ D:PHE366 4.8 27.3 1.0
CA D:ASP315 4.8 34.8 1.0
H D:ASP315 4.9 42.8 1.0
N D:ASP315 4.9 35.6 1.0
HG21 D:THR325 5.0 36.7 1.0

Manganese binding site 5 out of 6 in 6yvt

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Manganese binding site 5 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn501

b:31.4
occ:1.00
NE2 E:HIS313 2.0 41.0 1.0
NE2 E:HIS374 2.3 37.3 1.0
O26 E:PW2502 2.3 28.4 1.0
OD1 E:ASP315 2.4 32.0 1.0
O E:HOH609 2.4 32.4 1.0
N18 E:PW2502 2.4 34.2 1.0
CE1 E:HIS313 2.7 40.7 1.0
HE1 E:HIS313 2.7 48.9 1.0
C20 E:PW2502 3.0 33.5 1.0
CE1 E:HIS374 3.1 33.3 1.0
C19 E:PW2502 3.2 35.4 1.0
CD2 E:HIS313 3.2 40.9 1.0
CD2 E:HIS374 3.2 31.6 1.0
HE1 E:HIS374 3.2 40.0 1.0
C17 E:PW2502 3.4 32.0 1.0
H171 E:PW2502 3.4 38.5 1.0
CG E:ASP315 3.4 35.9 1.0
HD2 E:HIS374 3.5 38.0 1.0
HD2 E:HIS313 3.5 49.1 1.0
HG11 B:VAL401 3.7 55.7 1.0
ND1 E:HIS313 3.8 41.4 1.0
OD2 E:ASP315 3.9 32.5 1.0
CG E:HIS313 4.1 40.9 1.0
ND1 E:HIS374 4.2 29.1 1.0
HG21 B:VAL401 4.2 58.8 1.0
HZ E:PHE366 4.2 46.4 1.0
HA E:ASP315 4.3 47.4 1.0
CG E:HIS374 4.3 27.2 1.0
HZ2 E:TRP389 4.3 48.3 1.0
N21 E:PW2502 4.4 28.6 1.0
C02 E:PW2502 4.5 32.9 1.0
HD1 E:HIS313 4.6 49.8 1.0
CG1 B:VAL401 4.6 46.3 1.0
HG13 B:VAL401 4.6 55.7 1.0
O E:HOH607 4.7 33.1 1.0
CB E:ASP315 4.7 39.0 1.0
C04 E:PW2502 4.7 31.8 1.0
CA E:ASP315 4.8 39.5 1.0
H E:ASP315 4.8 36.4 1.0
HE1 E:PHE366 4.9 39.0 1.0
H222 E:PW2502 4.9 33.0 1.0
N E:ASP315 4.9 30.3 1.0
HD1 E:HIS374 4.9 34.9 1.0
HG21 E:THR325 5.0 41.6 1.0

Manganese binding site 6 out of 6 in 6yvt

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Manganese binding site 6 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Md-253 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn501

b:36.7
occ:1.00
N18 F:PW2502 2.1 39.4 1.0
O26 F:PW2502 2.1 39.3 1.0
NE2 F:HIS374 2.3 33.9 1.0
OD1 F:ASP315 2.3 39.8 1.0
NE2 F:HIS313 2.4 35.1 1.0
O F:HOH605 2.6 30.8 1.0
C20 F:PW2502 2.8 37.9 1.0
C19 F:PW2502 2.8 39.3 1.0
C17 F:PW2502 3.1 37.5 1.0
H171 F:PW2502 3.2 45.0 1.0
CG F:ASP315 3.3 35.5 1.0
CE1 F:HIS313 3.3 34.8 1.0
CD2 F:HIS374 3.3 31.7 1.0
CE1 F:HIS374 3.3 34.3 1.0
HE1 F:HIS313 3.3 41.8 1.0
HD2 F:HIS374 3.4 38.1 1.0
CD2 F:HIS313 3.5 35.7 1.0
OD2 F:ASP315 3.5 38.5 1.0
HE1 F:HIS374 3.5 41.2 1.0
HD2 F:HIS313 3.7 42.9 1.0
HG11 E:VAL401 3.9 59.0 1.0
HZ F:PHE366 3.9 44.5 1.0
HZ2 F:TRP389 4.1 48.8 1.0
C02 F:PW2502 4.1 35.8 1.0
N21 F:PW2502 4.2 37.2 1.0
C04 F:PW2502 4.4 37.1 1.0
ND1 F:HIS374 4.4 39.0 1.0
HA F:ASP315 4.4 50.5 1.0
ND1 F:HIS313 4.4 34.3 1.0
CG F:HIS374 4.4 37.0 1.0
HG21 E:VAL401 4.5 42.9 1.0
CG F:HIS313 4.6 35.8 1.0
HG21 F:THR325 4.6 36.0 1.0
H222 F:PW2502 4.6 42.0 1.0
CB F:ASP315 4.6 36.9 1.0
HG13 E:VAL401 4.7 59.0 1.0
CG1 E:VAL401 4.7 49.1 1.0
H211 F:PW2502 4.8 44.7 1.0
C03 F:PW2502 4.8 40.4 1.0
CZ F:PHE366 4.8 37.0 1.0
C22 F:PW2502 4.9 35.0 1.0
CA F:ASP315 5.0 42.0 1.0
CZ2 F:TRP389 5.0 40.6 1.0
H F:ASP315 5.0 59.8 1.0

Reference:

M.Demetriades, I.K.Leung, R.Chowdhury, M.C.Chan, M.A.Mcdonough, K.K.Yeoh, Y.M.Tian, T.D.Claridge, P.J.Ratcliffe, E.C.Woon, C.J.Schofield. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew.Chem.Int.Ed.Engl. V. 51 6672 2012.
ISSN: ESSN 1521-3773
PubMed: 22639232
DOI: 10.1002/ANIE.201202000
Page generated: Sun Oct 6 07:54:57 2024

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