Nickel in PDB 6d3v: Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa
Protein crystallography data
The structure of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa, PDB code: 6d3v
was solved by
A.Hofmann,
M.Cross,
S.-Y.Park,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.30 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.265,
66.820,
75.165,
90.00,
119.60,
90.00
|
R / Rfree (%)
|
18.8 /
21.8
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa
(pdb code 6d3v). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the
Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa, PDB code: 6d3v:
Jump to Nickel binding site number:
1;
2;
3;
Nickel binding site 1 out
of 3 in 6d3v
Go back to
Nickel Binding Sites List in 6d3v
Nickel binding site 1 out
of 3 in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni303
b:34.5
occ:1.00
|
O
|
B:HOH422
|
2.1
|
32.5
|
1.0
|
O
|
A:HOH483
|
2.1
|
32.6
|
1.0
|
NE2
|
A:HIS0
|
2.2
|
28.9
|
1.0
|
NE2
|
B:HIS49
|
2.3
|
64.7
|
1.0
|
CE1
|
B:HIS49
|
3.0
|
44.3
|
1.0
|
CE1
|
A:HIS0
|
3.1
|
34.5
|
1.0
|
CD2
|
A:HIS0
|
3.3
|
47.4
|
1.0
|
CD2
|
B:HIS49
|
3.5
|
51.9
|
1.0
|
ND1
|
A:HIS0
|
4.3
|
32.0
|
1.0
|
ND1
|
B:HIS49
|
4.3
|
55.5
|
1.0
|
OG
|
B:SER50
|
4.3
|
40.6
|
1.0
|
O
|
B:HOH489
|
4.4
|
49.4
|
1.0
|
O
|
B:HOH493
|
4.4
|
40.7
|
1.0
|
CG
|
A:HIS0
|
4.4
|
29.1
|
1.0
|
O
|
B:HOH467
|
4.5
|
37.2
|
1.0
|
CG
|
B:HIS49
|
4.5
|
43.7
|
1.0
|
O
|
B:HOH503
|
4.7
|
40.1
|
1.0
|
|
Nickel binding site 2 out
of 3 in 6d3v
Go back to
Nickel Binding Sites List in 6d3v
Nickel binding site 2 out
of 3 in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni304
b:31.5
occ:1.00
|
OD2
|
A:ASP11
|
2.1
|
27.9
|
1.0
|
O
|
A:HOH410
|
2.2
|
28.9
|
1.0
|
OD1
|
A:ASP220
|
2.2
|
25.9
|
1.0
|
O
|
A:ASP13
|
2.3
|
27.2
|
1.0
|
O
|
A:HOH418
|
2.3
|
26.3
|
1.0
|
O
|
A:ACY301
|
2.4
|
37.7
|
1.0
|
CG
|
A:ASP11
|
3.0
|
39.9
|
1.0
|
CG
|
A:ASP220
|
3.2
|
30.0
|
1.0
|
OD1
|
A:ASP11
|
3.3
|
34.9
|
1.0
|
C
|
A:ACY301
|
3.4
|
39.0
|
1.0
|
C
|
A:ASP13
|
3.4
|
29.5
|
1.0
|
OD2
|
A:ASP220
|
3.5
|
30.6
|
1.0
|
O
|
A:HOH402
|
3.9
|
59.4
|
1.0
|
OXT
|
A:ACY301
|
4.1
|
37.3
|
1.0
|
OG
|
A:SER221
|
4.1
|
27.4
|
1.0
|
OD2
|
A:ASP224
|
4.1
|
27.8
|
1.0
|
N
|
A:ASP13
|
4.2
|
23.8
|
1.0
|
OG1
|
A:THR15
|
4.2
|
30.3
|
1.0
|
CH3
|
A:ACY301
|
4.2
|
37.8
|
1.0
|
CA
|
A:ASP13
|
4.2
|
24.4
|
1.0
|
CB
|
A:ASP11
|
4.3
|
29.7
|
1.0
|
OD2
|
A:ASP14
|
4.3
|
37.8
|
1.0
|
O
|
A:HOH420
|
4.4
|
33.5
|
1.0
|
CB
|
A:ASP14
|
4.4
|
29.7
|
1.0
|
CB
|
A:ASP13
|
4.5
|
27.9
|
1.0
|
N
|
A:ASP14
|
4.5
|
26.3
|
1.0
|
CB
|
A:ASP220
|
4.5
|
24.6
|
1.0
|
C
|
A:LEU12
|
4.7
|
23.0
|
1.0
|
N
|
A:THR15
|
4.7
|
24.8
|
1.0
|
C
|
A:ASP14
|
4.7
|
24.4
|
1.0
|
CA
|
A:ASP14
|
4.8
|
23.1
|
1.0
|
N
|
A:LEU12
|
4.8
|
23.3
|
1.0
|
N
|
A:ASP220
|
4.9
|
25.8
|
1.0
|
CG
|
A:ASP14
|
4.9
|
47.7
|
1.0
|
N
|
A:SER221
|
4.9
|
21.3
|
1.0
|
|
Nickel binding site 3 out
of 3 in 6d3v
Go back to
Nickel Binding Sites List in 6d3v
Nickel binding site 3 out
of 3 in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni301
b:31.4
occ:1.00
|
OD2
|
B:ASP11
|
2.0
|
28.9
|
1.0
|
O
|
B:HOH408
|
2.1
|
26.6
|
1.0
|
OD1
|
B:ASP220
|
2.2
|
28.0
|
1.0
|
O
|
B:ASP13
|
2.2
|
26.2
|
1.0
|
O
|
B:HOH423
|
2.2
|
26.9
|
1.0
|
O
|
B:ACY302
|
2.3
|
38.9
|
1.0
|
CG
|
B:ASP11
|
3.0
|
37.0
|
1.0
|
CG
|
B:ASP220
|
3.2
|
25.4
|
1.0
|
OD1
|
B:ASP11
|
3.3
|
31.4
|
1.0
|
C
|
B:ACY302
|
3.3
|
39.1
|
1.0
|
C
|
B:ASP13
|
3.4
|
30.7
|
1.0
|
OD2
|
B:ASP220
|
3.5
|
28.0
|
1.0
|
O
|
B:HOH402
|
4.0
|
51.1
|
1.0
|
OXT
|
B:ACY302
|
4.1
|
37.9
|
1.0
|
OG
|
B:SER221
|
4.1
|
26.6
|
1.0
|
N
|
B:ASP13
|
4.1
|
24.1
|
1.0
|
OD2
|
B:ASP224
|
4.1
|
27.5
|
1.0
|
OG1
|
B:THR15
|
4.2
|
28.7
|
1.0
|
CA
|
B:ASP13
|
4.2
|
24.8
|
1.0
|
CH3
|
B:ACY302
|
4.2
|
35.7
|
1.0
|
O
|
B:HOH409
|
4.3
|
37.1
|
1.0
|
OD2
|
B:ASP14
|
4.3
|
37.4
|
1.0
|
CB
|
B:ASP11
|
4.3
|
27.4
|
1.0
|
CB
|
B:ASP14
|
4.4
|
30.1
|
1.0
|
CB
|
B:ASP13
|
4.4
|
27.9
|
1.0
|
N
|
B:ASP14
|
4.4
|
26.0
|
1.0
|
CB
|
B:ASP220
|
4.5
|
25.7
|
1.0
|
C
|
B:LEU12
|
4.7
|
24.6
|
1.0
|
N
|
B:THR15
|
4.7
|
24.0
|
1.0
|
C
|
B:ASP14
|
4.7
|
25.1
|
1.0
|
CA
|
B:ASP14
|
4.7
|
23.9
|
1.0
|
N
|
B:LEU12
|
4.8
|
24.3
|
1.0
|
CG
|
B:ASP14
|
4.9
|
44.1
|
1.0
|
N
|
B:ASP220
|
4.9
|
24.5
|
1.0
|
N
|
B:SER221
|
5.0
|
22.2
|
1.0
|
|
Reference:
M.Cross,
S.Biberacher,
S.Y.Park,
S.Rajan,
P.Korhonen,
R.B.Gasser,
J.S.Kim,
M.J.Coster,
A.Hofmann.
Trehalose 6-Phosphate Phosphatases of Pseudomonas Aeruginosa. Faseb J. V. 32 5470 2018.
ISSN: ESSN 1530-6860
PubMed: 29688811
DOI: 10.1096/FJ.201800500R
Page generated: Thu Oct 10 08:21:37 2024
|