Nickel in PDB 4xca: Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound
Protein crystallography data
The structure of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound, PDB code: 4xca
was solved by
K.M.Mcculloch,
E.K.Mccranie,
M.Sarwar,
J.L.Mathieu,
B.L.Gitschlag,
Y.Du,
B.O.Bachmann,
T.M.Iverson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.71 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.399,
112.044,
177.803,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
23.6
|
Other elements in 4xca:
The structure of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound
(pdb code 4xca). 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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound, PDB code: 4xca:
Jump to Nickel binding site number:
1;
2;
3;
4;
Nickel binding site 1 out
of 4 in 4xca
Go back to
Nickel Binding Sites List in 4xca
Nickel binding site 1 out
of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound
 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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni301
b:30.1
occ:1.00
|
O
|
A:HOH458
|
1.9
|
20.4
|
1.0
|
O
|
A:HOH459
|
2.1
|
31.8
|
1.0
|
NE2
|
A:HIS206
|
2.1
|
24.9
|
1.0
|
NE2
|
A:HIS102
|
2.2
|
21.4
|
1.0
|
O5
|
A:AKG302
|
2.2
|
27.1
|
1.0
|
O1
|
A:AKG302
|
2.3
|
32.4
|
1.0
|
C2
|
A:AKG302
|
2.9
|
31.6
|
1.0
|
C1
|
A:AKG302
|
3.0
|
30.0
|
1.0
|
CD2
|
A:HIS206
|
3.0
|
20.6
|
1.0
|
CE1
|
A:HIS102
|
3.1
|
25.4
|
1.0
|
CE1
|
A:HIS206
|
3.2
|
18.8
|
1.0
|
CD2
|
A:HIS102
|
3.2
|
25.7
|
1.0
|
O
|
A:HOH530
|
4.0
|
43.6
|
1.0
|
OE1
|
A:GLU202
|
4.1
|
33.6
|
1.0
|
OE2
|
A:GLU202
|
4.1
|
27.0
|
1.0
|
CG
|
A:HIS206
|
4.2
|
26.2
|
1.0
|
O2
|
A:AKG302
|
4.2
|
31.2
|
1.0
|
ND1
|
A:HIS206
|
4.2
|
19.3
|
1.0
|
ND1
|
A:HIS102
|
4.3
|
27.7
|
1.0
|
CG
|
A:HIS102
|
4.3
|
25.0
|
1.0
|
C3
|
A:AKG302
|
4.4
|
25.9
|
1.0
|
NZ
|
A:LYS137
|
4.5
|
23.6
|
1.0
|
CD
|
A:GLU202
|
4.6
|
24.9
|
1.0
|
CD2
|
A:LEU200
|
4.8
|
24.5
|
1.0
|
C4
|
A:AKG302
|
4.9
|
25.4
|
1.0
|
CD2
|
A:LEU99
|
5.0
|
23.5
|
1.0
|
|
Nickel binding site 2 out
of 4 in 4xca
Go back to
Nickel Binding Sites List in 4xca
Nickel binding site 2 out
of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound
 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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni301
b:32.3
occ:1.00
|
O
|
B:HOH462
|
1.9
|
29.8
|
1.0
|
O5
|
B:AKG302
|
2.1
|
35.0
|
1.0
|
O
|
B:HOH463
|
2.1
|
33.6
|
1.0
|
NE2
|
B:HIS102
|
2.2
|
32.4
|
1.0
|
NE2
|
B:HIS206
|
2.2
|
33.0
|
1.0
|
O1
|
B:AKG302
|
2.2
|
40.7
|
1.0
|
C2
|
B:AKG302
|
2.8
|
37.6
|
1.0
|
C1
|
B:AKG302
|
2.8
|
37.4
|
1.0
|
CE1
|
B:HIS102
|
3.0
|
31.3
|
1.0
|
CD2
|
B:HIS206
|
3.0
|
27.5
|
1.0
|
CD2
|
B:HIS102
|
3.1
|
31.4
|
1.0
|
CE1
|
B:HIS206
|
3.2
|
25.3
|
1.0
|
O2
|
B:AKG302
|
4.1
|
40.6
|
1.0
|
OE1
|
B:GLU202
|
4.1
|
36.9
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
31.0
|
1.0
|
CG
|
B:HIS206
|
4.2
|
26.8
|
1.0
|
CG
|
B:HIS102
|
4.2
|
27.6
|
1.0
|
OE2
|
B:GLU202
|
4.2
|
32.2
|
1.0
|
C3
|
B:AKG302
|
4.2
|
31.3
|
1.0
|
ND1
|
B:HIS206
|
4.2
|
28.3
|
1.0
|
NZ
|
B:LYS137
|
4.3
|
36.1
|
1.0
|
CD
|
B:GLU202
|
4.6
|
37.0
|
1.0
|
CD2
|
B:LEU200
|
4.7
|
25.9
|
1.0
|
C4
|
B:AKG302
|
4.9
|
34.5
|
1.0
|
CD2
|
B:LEU99
|
4.9
|
35.1
|
1.0
|
|
Nickel binding site 3 out
of 4 in 4xca
Go back to
Nickel Binding Sites List in 4xca
Nickel binding site 3 out
of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound
 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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni301
b:35.6
occ:1.00
|
O
|
C:HOH492
|
1.9
|
26.1
|
1.0
|
O
|
C:HOH493
|
2.1
|
30.9
|
1.0
|
NE2
|
C:HIS206
|
2.1
|
23.6
|
1.0
|
NE2
|
C:HIS102
|
2.2
|
34.7
|
1.0
|
O5
|
C:AKG302
|
2.3
|
27.6
|
1.0
|
O2
|
C:AKG302
|
2.4
|
46.5
|
1.0
|
CD2
|
C:HIS206
|
3.0
|
21.9
|
1.0
|
C2
|
C:AKG302
|
3.0
|
38.0
|
1.0
|
C1
|
C:AKG302
|
3.1
|
38.0
|
1.0
|
CE1
|
C:HIS102
|
3.1
|
23.7
|
1.0
|
CE1
|
C:HIS206
|
3.1
|
24.6
|
1.0
|
CD2
|
C:HIS102
|
3.3
|
27.0
|
1.0
|
OE1
|
C:GLU202
|
4.0
|
27.5
|
1.0
|
ND1
|
C:HIS206
|
4.2
|
23.8
|
1.0
|
CG
|
C:HIS206
|
4.2
|
24.6
|
1.0
|
ND1
|
C:HIS102
|
4.3
|
28.3
|
1.0
|
O1
|
C:AKG302
|
4.3
|
39.8
|
1.0
|
CG
|
C:HIS102
|
4.4
|
25.5
|
1.0
|
OE2
|
C:GLU202
|
4.4
|
39.3
|
1.0
|
C3
|
C:AKG302
|
4.5
|
28.4
|
1.0
|
NZ
|
C:LYS137
|
4.6
|
28.6
|
1.0
|
CD
|
C:GLU202
|
4.7
|
33.5
|
1.0
|
CD2
|
C:LEU99
|
4.9
|
26.7
|
1.0
|
|
Nickel binding site 4 out
of 4 in 4xca
Go back to
Nickel Binding Sites List in 4xca
Nickel binding site 4 out
of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound
 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 Hygx From Streptomyces Hygroscopicus with Nickel and 2-Oxoglutarate Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni301
b:27.4
occ:1.00
|
O
|
D:HOH495
|
2.1
|
22.1
|
1.0
|
O1
|
D:AKG302
|
2.1
|
36.5
|
1.0
|
NE2
|
D:HIS206
|
2.2
|
22.2
|
1.0
|
NE2
|
D:HIS102
|
2.2
|
32.0
|
1.0
|
O5
|
D:AKG302
|
2.2
|
27.9
|
1.0
|
O
|
D:HOH496
|
2.2
|
33.1
|
1.0
|
C1
|
D:AKG302
|
2.8
|
32.9
|
1.0
|
C2
|
D:AKG302
|
2.9
|
29.5
|
1.0
|
CD2
|
D:HIS206
|
3.1
|
22.1
|
1.0
|
CE1
|
D:HIS102
|
3.1
|
26.8
|
1.0
|
CE1
|
D:HIS206
|
3.2
|
19.1
|
1.0
|
CD2
|
D:HIS102
|
3.2
|
33.6
|
1.0
|
O2
|
D:AKG302
|
4.0
|
31.6
|
1.0
|
OE1
|
D:GLU202
|
4.2
|
32.2
|
1.0
|
ND1
|
D:HIS102
|
4.2
|
26.5
|
1.0
|
NZ
|
D:LYS137
|
4.2
|
27.7
|
1.0
|
CG
|
D:HIS206
|
4.2
|
22.5
|
1.0
|
ND1
|
D:HIS206
|
4.2
|
25.2
|
1.0
|
OE2
|
D:GLU202
|
4.3
|
27.3
|
1.0
|
CG
|
D:HIS102
|
4.3
|
26.2
|
1.0
|
O
|
D:HOH523
|
4.4
|
39.5
|
1.0
|
C3
|
D:AKG302
|
4.4
|
24.3
|
1.0
|
CD
|
D:GLU202
|
4.7
|
28.0
|
1.0
|
CD2
|
D:LEU200
|
4.7
|
24.9
|
1.0
|
CD2
|
D:LEU99
|
4.8
|
18.7
|
1.0
|
C4
|
D:AKG302
|
5.0
|
25.1
|
1.0
|
|
Reference:
K.M.Mcculloch,
E.K.Mccranie,
J.A.Smith,
M.Sarwar,
J.L.Mathieu,
B.L.Gitschlag,
Y.Du,
B.O.Bachmann,
T.M.Iverson.
Oxidative Cyclizations in Orthosomycin Biosynthesis Expand the Known Chemistry of An Oxygenase Superfamily. Proc.Natl.Acad.Sci.Usa V. 112 11547 2015.
ISSN: ESSN 1091-6490
PubMed: 26240321
DOI: 10.1073/PNAS.1500964112
Page generated: Wed Oct 9 19:21:02 2024
|