Nickel in PDB 5erl: Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro
Protein crystallography data
The structure of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro, PDB code: 5erl
was solved by
B.Selvaraj,
Y.Lindqvist,
V.Siitonen,
M.Metsa-Ketela,
G.Schneider,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.80 /
2.85
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.324,
117.784,
160.964,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
22.4
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro
(pdb code 5erl). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the
Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro, PDB code: 5erl:
Jump to Nickel binding site number:
1;
2;
3;
4;
Nickel binding site 1 out
of 4 in 5erl
Go back to
Nickel Binding Sites List in 5erl
Nickel binding site 1 out
of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni300
b:12.0
occ:1.00
|
O2
|
A:SIN301
|
1.9
|
12.3
|
1.0
|
OD2
|
A:ASP132
|
1.9
|
50.1
|
1.0
|
NE2
|
A:HIS130
|
2.0
|
48.7
|
1.0
|
O
|
A:HOH401
|
2.0
|
35.0
|
1.0
|
NE2
|
A:HIS213
|
2.1
|
46.2
|
1.0
|
CG
|
A:ASP132
|
2.7
|
50.1
|
1.0
|
C1
|
A:SIN301
|
2.7
|
13.9
|
1.0
|
CE1
|
A:HIS130
|
2.7
|
48.5
|
1.0
|
OD1
|
A:ASP132
|
2.8
|
50.2
|
1.0
|
CE1
|
A:HIS213
|
3.0
|
46.2
|
1.0
|
O1
|
A:SIN301
|
3.1
|
11.8
|
1.0
|
CD2
|
A:HIS130
|
3.1
|
49.7
|
1.0
|
CD2
|
A:HIS213
|
3.2
|
45.6
|
1.0
|
ND1
|
A:HIS130
|
3.9
|
49.6
|
1.0
|
C2
|
A:SIN301
|
4.1
|
14.0
|
1.0
|
CB
|
A:ASP132
|
4.1
|
50.7
|
1.0
|
CG
|
A:HIS130
|
4.1
|
50.5
|
1.0
|
ND1
|
A:HIS213
|
4.2
|
46.5
|
1.0
|
O
|
A:HOH407
|
4.3
|
40.4
|
1.0
|
CG
|
A:HIS213
|
4.3
|
45.9
|
1.0
|
NE2
|
A:HIS207
|
4.3
|
48.3
|
1.0
|
C3
|
A:SIN301
|
4.6
|
13.7
|
1.0
|
CE1
|
A:HIS207
|
4.8
|
49.1
|
1.0
|
CA
|
A:ASP132
|
5.0
|
52.1
|
1.0
|
|
Nickel binding site 2 out
of 4 in 5erl
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Nickel Binding Sites List in 5erl
Nickel binding site 2 out
of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni300
b:18.2
occ:1.00
|
O1
|
B:SIN301
|
1.9
|
14.8
|
1.0
|
O
|
B:HOH401
|
1.9
|
52.4
|
1.0
|
OD2
|
B:ASP132
|
2.0
|
72.1
|
1.0
|
NE2
|
B:HIS130
|
2.0
|
67.5
|
1.0
|
NE2
|
B:HIS213
|
2.0
|
64.2
|
1.0
|
CE1
|
B:HIS130
|
2.7
|
66.8
|
1.0
|
CG
|
B:ASP132
|
2.8
|
72.4
|
1.0
|
C1
|
B:SIN301
|
2.9
|
13.9
|
1.0
|
CE1
|
B:HIS213
|
2.9
|
62.6
|
1.0
|
OD1
|
B:ASP132
|
3.0
|
73.5
|
1.0
|
CD2
|
B:HIS213
|
3.2
|
62.3
|
1.0
|
CD2
|
B:HIS130
|
3.2
|
67.8
|
1.0
|
O2
|
B:SIN301
|
3.3
|
13.4
|
1.0
|
ND1
|
B:HIS130
|
3.9
|
66.7
|
1.0
|
ND1
|
B:HIS213
|
4.1
|
61.0
|
1.0
|
CB
|
B:ASP132
|
4.2
|
72.2
|
1.0
|
C2
|
B:SIN301
|
4.2
|
13.5
|
1.0
|
CG
|
B:HIS130
|
4.2
|
66.9
|
1.0
|
CG
|
B:HIS213
|
4.2
|
60.3
|
1.0
|
NE2
|
B:HIS207
|
4.2
|
63.3
|
1.0
|
C3
|
B:SIN301
|
4.6
|
13.2
|
1.0
|
CE1
|
B:HIS207
|
4.7
|
63.9
|
1.0
|
|
Nickel binding site 3 out
of 4 in 5erl
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Nickel Binding Sites List in 5erl
Nickel binding site 3 out
of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni300
b:16.2
occ:1.00
|
O2
|
C:SIN301
|
1.9
|
14.1
|
1.0
|
OD2
|
C:ASP132
|
1.9
|
77.5
|
1.0
|
O
|
C:HOH401
|
2.0
|
49.9
|
1.0
|
NE2
|
C:HIS213
|
2.0
|
69.4
|
1.0
|
NE2
|
C:HIS130
|
2.0
|
74.9
|
1.0
|
C1
|
C:SIN301
|
2.7
|
13.0
|
1.0
|
CG
|
C:ASP132
|
2.7
|
78.9
|
1.0
|
CE1
|
C:HIS130
|
2.8
|
75.4
|
1.0
|
CE1
|
C:HIS213
|
2.8
|
68.0
|
1.0
|
O1
|
C:SIN301
|
2.9
|
11.4
|
1.0
|
OD1
|
C:ASP132
|
2.9
|
81.9
|
1.0
|
CD2
|
C:HIS213
|
3.2
|
68.6
|
1.0
|
CD2
|
C:HIS130
|
3.2
|
75.7
|
1.0
|
ND1
|
C:HIS130
|
3.9
|
76.4
|
1.0
|
ND1
|
C:HIS213
|
4.0
|
67.1
|
1.0
|
C2
|
C:SIN301
|
4.0
|
13.1
|
1.0
|
CB
|
C:ASP132
|
4.1
|
76.4
|
1.0
|
CG
|
C:HIS130
|
4.2
|
76.6
|
1.0
|
CG
|
C:HIS213
|
4.2
|
67.1
|
1.0
|
NE2
|
C:HIS207
|
4.2
|
62.1
|
1.0
|
C3
|
C:SIN301
|
4.5
|
13.1
|
1.0
|
CE1
|
C:HIS207
|
4.8
|
62.5
|
1.0
|
CA
|
C:ASP132
|
4.9
|
76.6
|
1.0
|
|
Nickel binding site 4 out
of 4 in 5erl
Go back to
Nickel Binding Sites List in 5erl
Nickel binding site 4 out
of 4 in the Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of the Epimerase Snon in Complex with NI2+, Succinate and Nogalamycin Ro within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni300
b:17.2
occ:1.00
|
O1
|
D:SIN301
|
1.9
|
14.7
|
1.0
|
OD2
|
D:ASP132
|
1.9
|
86.8
|
1.0
|
NE2
|
D:HIS213
|
2.0
|
79.2
|
1.0
|
O
|
D:HOH403
|
2.0
|
59.6
|
1.0
|
NE2
|
D:HIS130
|
2.1
|
83.9
|
1.0
|
CG
|
D:ASP132
|
2.7
|
87.9
|
1.0
|
C1
|
D:SIN301
|
2.8
|
13.4
|
1.0
|
CE1
|
D:HIS130
|
2.8
|
84.3
|
1.0
|
CE1
|
D:HIS213
|
2.8
|
76.4
|
1.0
|
O2
|
D:SIN301
|
2.9
|
12.8
|
1.0
|
OD1
|
D:ASP132
|
3.0
|
90.1
|
1.0
|
CD2
|
D:HIS213
|
3.1
|
78.2
|
1.0
|
CD2
|
D:HIS130
|
3.3
|
82.9
|
1.0
|
ND1
|
D:HIS130
|
4.0
|
83.9
|
1.0
|
ND1
|
D:HIS213
|
4.0
|
74.3
|
1.0
|
NE2
|
D:HIS207
|
4.1
|
78.3
|
1.0
|
CB
|
D:ASP132
|
4.1
|
85.1
|
1.0
|
CG
|
D:HIS213
|
4.2
|
75.1
|
1.0
|
C2
|
D:SIN301
|
4.2
|
12.9
|
1.0
|
CG
|
D:HIS130
|
4.2
|
83.1
|
1.0
|
C3
|
D:SIN301
|
4.6
|
12.6
|
1.0
|
CE1
|
D:HIS207
|
4.6
|
80.1
|
1.0
|
O
|
D:HOH401
|
5.0
|
50.5
|
1.0
|
|
Reference:
V.Siitonen,
B.Selvaraj,
L.Niiranen,
Y.Lindqvist,
G.Schneider,
M.Metsa-Ketela.
Divergent Non-Heme Iron Enzymes in the Nogalamycin Biosynthetic Pathway. Proc.Natl.Acad.Sci.Usa V. 113 5251 2016.
ISSN: ESSN 1091-6490
PubMed: 27114534
DOI: 10.1073/PNAS.1525034113
Page generated: Thu Oct 10 06:21:31 2024
|