Nickel in PDB 6t8m: Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
Protein crystallography data
The structure of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum, PDB code: 6t8m
was solved by
R.Chowdhury,
M.A.Mcdonough,
T.Liu,
I.J.Clifton,
C.J.Schofield,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.92 /
2.02
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.216,
81.781,
379.210,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.8 /
25.7
|
Other elements in 6t8m:
The structure of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
(pdb code 6t8m). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the
Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum, PDB code: 6t8m:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
Nickel binding site 1 out
of 5 in 6t8m
Go back to
Nickel Binding Sites List in 6t8m
Nickel binding site 1 out
of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni501
b:22.3
occ:1.00
|
O2'
|
A:OGA503
|
1.9
|
34.8
|
1.0
|
NE2
|
A:HIS266
|
2.1
|
60.4
|
1.0
|
NE2
|
A:HIS191
|
2.1
|
51.6
|
1.0
|
O
|
A:HOH614
|
2.2
|
42.3
|
1.0
|
OD1
|
A:ASP193
|
2.2
|
40.9
|
1.0
|
O2
|
A:OGA503
|
2.2
|
33.0
|
1.0
|
C2
|
A:OGA503
|
2.5
|
36.8
|
1.0
|
C1
|
A:OGA503
|
2.7
|
32.6
|
1.0
|
CE1
|
A:HIS266
|
2.9
|
43.2
|
1.0
|
CE1
|
A:HIS191
|
3.0
|
53.6
|
1.0
|
CG
|
A:ASP193
|
3.1
|
39.6
|
1.0
|
CD2
|
A:HIS266
|
3.2
|
43.4
|
1.0
|
CD2
|
A:HIS191
|
3.2
|
48.3
|
1.0
|
OD2
|
A:ASP193
|
3.3
|
36.4
|
1.0
|
N1
|
A:OGA503
|
3.9
|
36.8
|
1.0
|
O1
|
A:OGA503
|
4.0
|
32.9
|
1.0
|
ND1
|
A:HIS266
|
4.0
|
41.5
|
1.0
|
ND1
|
A:HIS191
|
4.1
|
49.9
|
1.0
|
O
|
A:HOH641
|
4.2
|
27.9
|
1.0
|
CG
|
A:HIS266
|
4.2
|
44.1
|
1.0
|
CG
|
A:HIS191
|
4.3
|
56.0
|
1.0
|
O
|
A:HOH609
|
4.3
|
18.8
|
1.0
|
C4
|
A:OGA503
|
4.5
|
37.5
|
1.0
|
CB
|
A:ASP193
|
4.5
|
36.9
|
1.0
|
CZ2
|
A:TRP282
|
4.6
|
30.8
|
1.0
|
CE2
|
A:TYR188
|
4.8
|
40.0
|
1.0
|
CA
|
A:ASP193
|
4.9
|
34.9
|
1.0
|
N
|
A:ASP193
|
5.0
|
35.6
|
1.0
|
|
Nickel binding site 2 out
of 5 in 6t8m
Go back to
Nickel Binding Sites List in 6t8m
Nickel binding site 2 out
of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni504
b:52.2
occ:1.00
|
O
|
B:SER58
|
1.9
|
47.3
|
1.0
|
O
|
A:SER58
|
2.0
|
51.7
|
1.0
|
N
|
B:SER58
|
2.0
|
52.0
|
1.0
|
N
|
A:SER58
|
2.0
|
61.1
|
1.0
|
O
|
B:HOH439
|
2.3
|
55.5
|
1.0
|
C
|
B:SER58
|
2.5
|
43.4
|
1.0
|
C
|
A:SER58
|
2.6
|
53.1
|
1.0
|
CA
|
A:SER58
|
2.6
|
67.8
|
1.0
|
CA
|
B:SER58
|
2.7
|
56.6
|
1.0
|
CB
|
A:SER58
|
3.2
|
91.7
|
1.0
|
CB
|
B:SER58
|
3.7
|
75.5
|
1.0
|
O
|
A:HOH661
|
3.8
|
41.3
|
1.0
|
N
|
B:MET59
|
3.8
|
64.0
|
1.0
|
N
|
A:MET59
|
3.9
|
61.9
|
1.0
|
OG
|
A:SER58
|
4.2
|
0.9
|
1.0
|
CA
|
B:MET59
|
4.6
|
62.2
|
1.0
|
CA
|
A:MET59
|
4.7
|
60.1
|
1.0
|
OG
|
B:SER58
|
4.7
|
86.4
|
1.0
|
O
|
B:LYS60
|
4.8
|
52.7
|
1.0
|
N
|
B:LYS60
|
5.0
|
64.9
|
1.0
|
|
Nickel binding site 3 out
of 5 in 6t8m
Go back to
Nickel Binding Sites List in 6t8m
Nickel binding site 3 out
of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni301
b:38.5
occ:1.00
|
O2'
|
B:OGA303
|
1.9
|
43.5
|
1.0
|
OD1
|
B:ASP193
|
2.0
|
44.3
|
1.0
|
NE2
|
B:HIS266
|
2.2
|
41.5
|
1.0
|
O2
|
B:OGA303
|
2.2
|
44.0
|
1.0
|
NE2
|
B:HIS191
|
2.3
|
53.1
|
1.0
|
O
|
B:HOH406
|
2.4
|
39.3
|
1.0
|
C2
|
B:OGA303
|
2.6
|
43.7
|
1.0
|
C1
|
B:OGA303
|
2.7
|
42.4
|
1.0
|
CG
|
B:ASP193
|
2.9
|
42.1
|
1.0
|
CE1
|
B:HIS191
|
3.0
|
53.8
|
1.0
|
OD2
|
B:ASP193
|
3.1
|
42.7
|
1.0
|
CD2
|
B:HIS266
|
3.1
|
41.8
|
1.0
|
CE1
|
B:HIS266
|
3.2
|
39.9
|
1.0
|
CD2
|
B:HIS191
|
3.3
|
53.6
|
1.0
|
N1
|
B:OGA303
|
3.9
|
42.6
|
1.0
|
O1
|
B:OGA303
|
4.0
|
43.6
|
1.0
|
ND1
|
B:HIS191
|
4.2
|
54.6
|
1.0
|
CB
|
B:ASP193
|
4.3
|
39.7
|
1.0
|
ND1
|
B:HIS266
|
4.3
|
42.1
|
1.0
|
CG
|
B:HIS266
|
4.3
|
40.5
|
1.0
|
O
|
B:HOH417
|
4.3
|
37.0
|
1.0
|
CG
|
B:HIS191
|
4.3
|
54.3
|
1.0
|
O
|
B:HOH422
|
4.5
|
29.3
|
1.0
|
C4
|
B:OGA303
|
4.5
|
40.6
|
1.0
|
CA
|
B:ASP193
|
4.7
|
36.5
|
1.0
|
N
|
B:ASP193
|
4.7
|
34.4
|
1.0
|
CE2
|
B:TYR188
|
4.9
|
44.2
|
1.0
|
CZ2
|
B:TRP282
|
4.9
|
35.5
|
1.0
|
CZ
|
B:PHE259
|
4.9
|
42.0
|
1.0
|
|
Nickel binding site 4 out
of 5 in 6t8m
Go back to
Nickel Binding Sites List in 6t8m
Nickel binding site 4 out
of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni301
b:52.4
occ:1.00
|
OD2
|
C:ASP193
|
1.8
|
69.4
|
1.0
|
O2'
|
C:OGA303
|
1.8
|
65.3
|
1.0
|
NE2
|
C:HIS266
|
2.0
|
86.6
|
1.0
|
O1
|
C:OGA303
|
2.1
|
74.6
|
1.0
|
NE2
|
C:HIS191
|
2.4
|
51.7
|
1.0
|
C2
|
C:OGA303
|
2.5
|
69.9
|
1.0
|
O
|
C:HOH417
|
2.6
|
54.1
|
1.0
|
C1
|
C:OGA303
|
2.7
|
71.3
|
1.0
|
CG
|
C:ASP193
|
2.8
|
70.6
|
1.0
|
CD2
|
C:HIS266
|
2.8
|
51.1
|
1.0
|
OD1
|
C:ASP193
|
3.1
|
73.4
|
1.0
|
CE1
|
C:HIS266
|
3.2
|
49.5
|
1.0
|
CE1
|
C:HIS191
|
3.2
|
52.8
|
1.0
|
CD2
|
C:HIS191
|
3.3
|
52.0
|
1.0
|
N1
|
C:OGA303
|
3.9
|
65.9
|
1.0
|
O2
|
C:OGA303
|
3.9
|
74.2
|
1.0
|
CG
|
C:HIS266
|
4.1
|
51.3
|
1.0
|
CB
|
C:ASP193
|
4.1
|
65.0
|
1.0
|
O
|
C:HOH414
|
4.1
|
38.7
|
1.0
|
ND1
|
C:HIS266
|
4.2
|
50.2
|
1.0
|
ND1
|
C:HIS191
|
4.3
|
54.0
|
1.0
|
CG
|
C:HIS191
|
4.4
|
53.5
|
1.0
|
O
|
C:HOH407
|
4.4
|
39.6
|
1.0
|
C4
|
C:OGA303
|
4.5
|
65.3
|
1.0
|
N
|
C:ASP193
|
4.6
|
47.3
|
1.0
|
CA
|
C:ASP193
|
4.7
|
52.8
|
1.0
|
CZ2
|
C:TRP282
|
4.9
|
48.1
|
1.0
|
CE2
|
C:TYR188
|
5.0
|
54.8
|
1.0
|
CZ
|
C:PHE259
|
5.0
|
52.2
|
1.0
|
|
Nickel binding site 5 out
of 5 in 6t8m
Go back to
Nickel Binding Sites List in 6t8m
Nickel binding site 5 out
of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni305
b:83.2
occ:0.50
|
N
|
C:SER58
|
1.9
|
1.0
|
1.0
|
O
|
C:SER58
|
1.9
|
0.0
|
1.0
|
C
|
C:SER58
|
2.6
|
0.5
|
1.0
|
CA
|
C:SER58
|
2.6
|
0.6
|
1.0
|
CB
|
C:SER58
|
3.3
|
0.0
|
1.0
|
N
|
C:MET59
|
3.9
|
0.9
|
1.0
|
OG
|
C:SER58
|
4.5
|
0.3
|
1.0
|
CA
|
C:MET59
|
4.7
|
0.8
|
1.0
|
|
Reference:
T.Liu,
M.I.Abboud,
R.Chowdhury,
A.Tumber,
A.P.Hardy,
K.Lippl,
C.T.Lohans,
E.Pires,
J.Wickens,
M.A.Mcdonough,
C.M.West,
C.J.Schofield.
Biochemical and Biophysical Analyses of Hypoxia Sensing Prolyl Hydroxylases From Dictyostelium Discoideum and Toxoplasma Gondii. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32934009
DOI: 10.1074/JBC.RA120.013998
Page generated: Thu Oct 10 08:53:39 2024
|