Magnesium in PDB 9dtc: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
Enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
All present enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2):
3.6.1.13;
Protein crystallography data
The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2), PDB code: 9dtc
was solved by
Seattle Structural Genomics Center For Infectious Disease,
Seattlestructural Genomics Center For Infectious Disease (Ssgcid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.71 /
1.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.426,
79.749,
91.982,
90,
90,
90
|
R / Rfree (%)
|
16.2 /
18.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
(pdb code 9dtc). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2), PDB code: 9dtc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 9dtc
Go back to
Magnesium Binding Sites List in 9dtc
Magnesium binding site 1 out
of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:24.3
occ:1.00
|
OE2
|
A:GLU116
|
2.1
|
19.3
|
1.0
|
O
|
A:HOH505
|
2.2
|
35.0
|
1.0
|
O
|
A:HOH406
|
2.2
|
22.6
|
1.0
|
O
|
A:HOH476
|
2.2
|
32.4
|
1.0
|
OE1
|
A:GLU112
|
2.2
|
26.0
|
1.0
|
OE2
|
A:GLU164
|
2.3
|
30.4
|
1.0
|
CD
|
A:GLU116
|
3.0
|
19.0
|
1.0
|
CD
|
A:GLU112
|
3.2
|
24.9
|
1.0
|
CD
|
A:GLU164
|
3.3
|
34.5
|
1.0
|
MG
|
A:MG304
|
3.3
|
20.9
|
1.0
|
CG
|
A:GLU116
|
3.4
|
17.9
|
1.0
|
O
|
A:HOH411
|
3.4
|
30.8
|
1.0
|
OE2
|
A:GLU112
|
3.6
|
25.7
|
1.0
|
OE1
|
A:GLU164
|
3.6
|
29.4
|
1.0
|
O
|
A:HOH401
|
3.7
|
20.3
|
1.0
|
O1A
|
A:AR6301
|
3.7
|
80.9
|
0.8
|
O
|
A:ALA96
|
4.0
|
17.9
|
1.0
|
OE1
|
A:GLU116
|
4.2
|
19.8
|
1.0
|
OE1
|
A:GLU115
|
4.3
|
33.6
|
1.0
|
CG
|
A:GLU112
|
4.5
|
21.3
|
1.0
|
CG
|
A:GLU164
|
4.6
|
27.3
|
1.0
|
O1P
|
A:AMP302
|
4.8
|
34.9
|
0.2
|
O
|
A:HOH432
|
4.8
|
29.1
|
0.8
|
CB
|
A:GLU112
|
4.8
|
18.9
|
1.0
|
CB
|
A:GLU116
|
4.9
|
18.1
|
1.0
|
O1B
|
A:AR6301
|
4.9
|
32.4
|
0.8
|
O2P
|
A:AMP302
|
4.9
|
36.6
|
0.2
|
O
|
A:HOH428
|
5.0
|
26.2
|
1.0
|
CD1
|
A:ILE166
|
5.0
|
19.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 9dtc
Go back to
Magnesium Binding Sites List in 9dtc
Magnesium binding site 2 out
of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:20.9
occ:1.00
|
O2B
|
A:AR6301
|
2.1
|
17.5
|
0.8
|
OE2
|
A:GLU116
|
2.2
|
19.3
|
1.0
|
O
|
A:HOH401
|
2.2
|
20.3
|
1.0
|
O
|
A:HOH406
|
2.2
|
22.6
|
1.0
|
O
|
A:HOH428
|
2.2
|
26.2
|
1.0
|
O
|
A:ALA96
|
2.3
|
17.9
|
1.0
|
O1A
|
A:AR6301
|
3.1
|
80.9
|
0.8
|
CD
|
A:GLU116
|
3.1
|
19.0
|
1.0
|
PB
|
A:AR6301
|
3.3
|
24.7
|
0.8
|
O2P
|
A:AMP302
|
3.3
|
36.6
|
0.2
|
MG
|
A:MG303
|
3.3
|
24.3
|
1.0
|
OE1
|
A:GLU116
|
3.4
|
19.8
|
1.0
|
C
|
A:ALA96
|
3.4
|
16.3
|
1.0
|
O1B
|
A:AR6301
|
3.6
|
32.4
|
0.8
|
OE2
|
A:GLU164
|
3.8
|
30.4
|
1.0
|
NH2
|
A:ARG79
|
4.0
|
17.3
|
1.0
|
O3A
|
A:AR6301
|
4.1
|
40.4
|
0.8
|
PA
|
A:AR6301
|
4.2
|
103.8
|
0.8
|
N
|
A:ALA96
|
4.2
|
15.5
|
1.0
|
CA
|
A:ALA96
|
4.3
|
15.3
|
1.0
|
OE1
|
A:GLU112
|
4.3
|
26.0
|
1.0
|
N
|
A:GLY97
|
4.4
|
15.8
|
1.0
|
O
|
A:HOH410
|
4.4
|
24.3
|
1.0
|
CA
|
A:GLY97
|
4.4
|
16.3
|
1.0
|
NE2
|
A:GLN77
|
4.5
|
22.3
|
1.0
|
CG
|
A:GLU116
|
4.5
|
17.9
|
1.0
|
CB
|
A:ALA96
|
4.6
|
15.1
|
1.0
|
OE1
|
A:GLN77
|
4.6
|
22.5
|
1.0
|
P
|
A:AMP302
|
4.6
|
25.0
|
0.2
|
O5D
|
A:AR6301
|
4.6
|
22.6
|
0.8
|
O1P
|
A:AMP302
|
4.8
|
34.9
|
0.2
|
C5D
|
A:AR6301
|
4.9
|
27.2
|
0.8
|
O
|
A:HOH505
|
4.9
|
35.0
|
1.0
|
CD
|
A:GLU112
|
4.9
|
24.9
|
1.0
|
CD
|
A:GLN77
|
5.0
|
19.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 9dtc
Go back to
Magnesium Binding Sites List in 9dtc
Magnesium binding site 3 out
of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:21.1
occ:1.00
|
O1B
|
B:AR6301
|
2.2
|
11.6
|
0.6
|
OE2
|
B:GLU116
|
2.2
|
16.1
|
1.0
|
O
|
B:HOH437
|
2.2
|
20.7
|
1.0
|
O
|
B:ALA96
|
2.3
|
15.7
|
1.0
|
O
|
B:HOH463
|
2.4
|
25.6
|
1.0
|
O
|
B:HOH401
|
2.4
|
17.7
|
1.0
|
O3P
|
B:AMP302
|
3.0
|
108.8
|
0.4
|
CD
|
B:GLU116
|
3.1
|
16.2
|
1.0
|
OE1
|
B:GLU116
|
3.3
|
18.3
|
1.0
|
PB
|
B:AR6301
|
3.4
|
23.1
|
0.6
|
MG
|
B:MG304
|
3.4
|
20.6
|
1.0
|
C
|
B:ALA96
|
3.5
|
14.0
|
1.0
|
O3A
|
B:AR6301
|
3.5
|
17.8
|
0.6
|
OE2
|
B:GLU164
|
4.0
|
30.4
|
1.0
|
NH2
|
B:ARG79
|
4.0
|
18.3
|
1.0
|
P
|
B:AMP302
|
4.0
|
31.0
|
0.4
|
O
|
B:HOH414
|
4.1
|
29.8
|
1.0
|
N
|
B:ALA96
|
4.1
|
13.4
|
1.0
|
O2P
|
B:AMP302
|
4.2
|
36.7
|
0.4
|
CA
|
B:ALA96
|
4.3
|
13.5
|
1.0
|
OE1
|
B:GLU112
|
4.3
|
20.2
|
1.0
|
NE2
|
B:GLN77
|
4.4
|
21.6
|
1.0
|
C5D
|
B:AR6301
|
4.4
|
23.0
|
0.6
|
O2B
|
B:AR6301
|
4.4
|
27.3
|
0.6
|
N
|
B:GLY97
|
4.4
|
14.2
|
1.0
|
O5D
|
B:AR6301
|
4.5
|
33.1
|
0.6
|
OE1
|
B:GLN77
|
4.5
|
23.4
|
1.0
|
CG
|
B:GLU116
|
4.5
|
16.2
|
1.0
|
CB
|
B:ALA96
|
4.6
|
15.1
|
1.0
|
CA
|
B:GLY97
|
4.6
|
14.7
|
1.0
|
O1P
|
B:AMP302
|
4.7
|
26.6
|
0.4
|
O4D
|
B:AR6301
|
4.8
|
131.6
|
0.6
|
CD
|
B:GLU112
|
4.9
|
19.5
|
1.0
|
CD
|
B:GLN77
|
4.9
|
19.8
|
1.0
|
O
|
B:HOH560
|
4.9
|
27.7
|
1.0
|
CZ
|
B:ARG79
|
5.0
|
19.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 9dtc
Go back to
Magnesium Binding Sites List in 9dtc
Magnesium binding site 4 out
of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:20.6
occ:1.00
|
O
|
B:HOH421
|
2.1
|
23.6
|
1.0
|
O
|
B:HOH560
|
2.1
|
27.7
|
1.0
|
OE1
|
B:GLU112
|
2.1
|
20.2
|
1.0
|
OE2
|
B:GLU116
|
2.1
|
16.1
|
1.0
|
O
|
B:HOH401
|
2.2
|
17.7
|
1.0
|
OE2
|
B:GLU164
|
2.3
|
30.4
|
1.0
|
CD
|
B:GLU116
|
3.1
|
16.2
|
1.0
|
CD
|
B:GLU112
|
3.1
|
19.5
|
1.0
|
CD
|
B:GLU164
|
3.3
|
27.9
|
1.0
|
MG
|
B:MG303
|
3.4
|
21.1
|
1.0
|
OE2
|
B:GLU112
|
3.4
|
22.6
|
1.0
|
CG
|
B:GLU116
|
3.4
|
16.2
|
1.0
|
OE1
|
B:GLU164
|
3.6
|
25.8
|
1.0
|
O
|
B:HOH412
|
3.7
|
32.6
|
1.0
|
O
|
B:HOH437
|
3.7
|
20.7
|
1.0
|
O3P
|
B:AMP302
|
4.0
|
108.8
|
0.4
|
O
|
B:ALA96
|
4.0
|
15.7
|
1.0
|
O
|
B:HOH477
|
4.2
|
43.3
|
1.0
|
OE1
|
B:GLU116
|
4.2
|
18.3
|
1.0
|
OE1
|
B:GLU115
|
4.3
|
26.7
|
1.0
|
CG
|
B:GLU112
|
4.4
|
17.0
|
1.0
|
O3A
|
B:AR6301
|
4.5
|
17.8
|
0.6
|
CG
|
B:GLU164
|
4.7
|
28.5
|
1.0
|
O2P
|
B:AMP302
|
4.7
|
36.7
|
0.4
|
O
|
B:HOH482
|
4.7
|
27.3
|
1.0
|
CB
|
B:GLU112
|
4.8
|
16.4
|
1.0
|
P
|
B:AMP302
|
4.9
|
31.0
|
0.4
|
CB
|
B:GLU116
|
4.9
|
14.6
|
1.0
|
|
Reference:
M.R.Mian,
L.Liu,
S.Lovell,
G.W.Buchko,
K.P.Battaile.
Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Adp Ribose Bound, Orthrhombic FORM2) To Be Published.
Page generated: Thu Oct 31 22:27:19 2024
|