Phosphorus in PDB 1a80: Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph
Protein crystallography data
The structure of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph, PDB code: 1a80
was solved by
S.Khurana,
D.B.Powers,
S.Anderson,
M.Blaber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
60.00 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.700,
55.800,
74.700,
90.00,
92.20,
90.00
|
R / Rfree (%)
|
19.1 /
28.8
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph
(pdb code 1a80). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the
Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph, PDB code: 1a80:
Jump to Phosphorus binding site number:
1;
2;
3;
Phosphorus binding site 1 out
of 3 in 1a80
Go back to
Phosphorus Binding Sites List in 1a80
Phosphorus binding site 1 out
of 3 in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P300
b:17.8
occ:1.00
|
PA
|
A:NDP300
|
0.0
|
17.8
|
1.0
|
O1A
|
A:NDP300
|
1.5
|
13.4
|
1.0
|
O2A
|
A:NDP300
|
1.5
|
13.2
|
1.0
|
O5B
|
A:NDP300
|
1.5
|
19.0
|
1.0
|
O3
|
A:NDP300
|
1.5
|
22.1
|
1.0
|
C5B
|
A:NDP300
|
2.7
|
21.9
|
1.0
|
PN
|
A:NDP300
|
2.9
|
15.9
|
1.0
|
O5D
|
A:NDP300
|
3.2
|
10.4
|
1.0
|
O2N
|
A:NDP300
|
3.5
|
11.2
|
1.0
|
CD
|
A:PRO189
|
3.7
|
8.1
|
1.0
|
C5D
|
A:NDP300
|
3.8
|
13.8
|
1.0
|
C4B
|
A:NDP300
|
3.9
|
22.4
|
1.0
|
O1N
|
A:NDP300
|
4.0
|
14.3
|
1.0
|
CA
|
A:GLN192
|
4.0
|
14.4
|
1.0
|
N
|
A:GLN192
|
4.1
|
13.2
|
1.0
|
CA
|
A:GLY188
|
4.1
|
8.1
|
1.0
|
N
|
A:LEU190
|
4.2
|
14.5
|
1.0
|
CB
|
A:LEU190
|
4.3
|
13.9
|
1.0
|
C
|
A:GLY188
|
4.4
|
14.2
|
1.0
|
O4B
|
A:NDP300
|
4.4
|
25.8
|
1.0
|
N
|
A:PRO189
|
4.4
|
10.1
|
1.0
|
CG
|
A:GLN192
|
4.4
|
24.2
|
1.0
|
N
|
A:LYS232
|
4.5
|
9.5
|
1.0
|
CG
|
A:PRO189
|
4.5
|
13.9
|
1.0
|
CA
|
A:LEU190
|
4.7
|
14.1
|
1.0
|
N
|
A:GLY188
|
4.8
|
6.8
|
1.0
|
CG
|
A:LEU190
|
4.8
|
17.4
|
1.0
|
CB
|
A:GLN192
|
4.8
|
14.9
|
1.0
|
C
|
A:LEU190
|
4.8
|
18.8
|
1.0
|
CD1
|
A:LEU190
|
4.9
|
15.8
|
1.0
|
O
|
A:HOH352
|
4.9
|
20.2
|
1.0
|
O
|
A:LYS232
|
4.9
|
16.2
|
1.0
|
CA
|
A:PRO231
|
4.9
|
14.1
|
1.0
|
|
Phosphorus binding site 2 out
of 3 in 1a80
Go back to
Phosphorus Binding Sites List in 1a80
Phosphorus binding site 2 out
of 3 in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P300
b:15.9
occ:1.00
|
PN
|
A:NDP300
|
0.0
|
15.9
|
1.0
|
O2N
|
A:NDP300
|
1.5
|
11.2
|
1.0
|
O1N
|
A:NDP300
|
1.5
|
14.3
|
1.0
|
O5D
|
A:NDP300
|
1.5
|
10.4
|
1.0
|
O3
|
A:NDP300
|
1.7
|
22.1
|
1.0
|
C5D
|
A:NDP300
|
2.5
|
13.8
|
1.0
|
PA
|
A:NDP300
|
2.9
|
17.8
|
1.0
|
O
|
A:HOH352
|
3.1
|
20.2
|
1.0
|
O2A
|
A:NDP300
|
3.4
|
13.2
|
1.0
|
O
|
A:HOH342
|
3.4
|
17.4
|
1.0
|
C4D
|
A:NDP300
|
3.5
|
18.5
|
1.0
|
C3D
|
A:NDP300
|
3.5
|
17.0
|
1.0
|
O5B
|
A:NDP300
|
3.7
|
19.0
|
1.0
|
O1A
|
A:NDP300
|
3.7
|
13.4
|
1.0
|
O3D
|
A:NDP300
|
3.9
|
16.4
|
1.0
|
CG
|
A:GLN192
|
4.0
|
24.2
|
1.0
|
C5B
|
A:NDP300
|
4.1
|
21.9
|
1.0
|
CA
|
A:GLY188
|
4.1
|
8.1
|
1.0
|
NE2
|
A:GLN192
|
4.1
|
21.1
|
1.0
|
N
|
A:GLY188
|
4.2
|
6.8
|
1.0
|
O4D
|
A:NDP300
|
4.3
|
19.1
|
1.0
|
C6N
|
A:NDP300
|
4.3
|
18.3
|
1.0
|
CD2
|
A:PHE22
|
4.5
|
15.1
|
1.0
|
CB
|
A:LYS232
|
4.5
|
10.9
|
1.0
|
CD
|
A:GLN192
|
4.6
|
34.1
|
1.0
|
CD
|
A:PRO189
|
4.6
|
8.1
|
1.0
|
C2D
|
A:NDP300
|
4.9
|
18.4
|
1.0
|
CB
|
A:GLN192
|
4.9
|
14.9
|
1.0
|
CA
|
A:GLN192
|
5.0
|
14.4
|
1.0
|
|
Phosphorus binding site 3 out
of 3 in 1a80
Go back to
Phosphorus Binding Sites List in 1a80
Phosphorus binding site 3 out
of 3 in the Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Native 2,5-Diketo-D-Gluconic Acid Reductase A From Corynbacterium Sp. Complexed with Nadph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P300
b:17.7
occ:1.00
|
P2B
|
A:NDP300
|
0.0
|
17.7
|
1.0
|
O2B
|
A:NDP300
|
1.5
|
20.6
|
1.0
|
O3X
|
A:NDP300
|
1.5
|
20.2
|
1.0
|
O2X
|
A:NDP300
|
1.5
|
12.0
|
1.0
|
O1X
|
A:NDP300
|
1.5
|
16.1
|
1.0
|
C2B
|
A:NDP300
|
2.5
|
25.1
|
1.0
|
O
|
A:HOH406
|
3.1
|
54.8
|
1.0
|
OG
|
A:SER233
|
3.4
|
31.9
|
1.0
|
O
|
A:HOH396
|
3.4
|
36.5
|
1.0
|
NH1
|
A:ARG238
|
3.4
|
23.6
|
1.0
|
C3B
|
A:NDP300
|
3.5
|
25.4
|
1.0
|
C1B
|
A:NDP300
|
3.6
|
23.9
|
1.0
|
N
|
A:VAL234
|
3.7
|
17.2
|
1.0
|
CA
|
A:SER233
|
3.7
|
17.6
|
1.0
|
O3B
|
A:NDP300
|
3.8
|
27.7
|
1.0
|
CG2
|
A:VAL234
|
3.9
|
18.9
|
1.0
|
CB
|
A:SER233
|
3.9
|
22.0
|
1.0
|
N9A
|
A:NDP300
|
4.1
|
20.2
|
1.0
|
NZ
|
A:LYS232
|
4.2
|
25.0
|
1.0
|
C
|
A:SER233
|
4.2
|
20.2
|
1.0
|
NE
|
A:ARG235
|
4.3
|
64.6
|
1.0
|
CZ
|
A:ARG235
|
4.4
|
89.5
|
1.0
|
CD
|
A:ARG235
|
4.5
|
35.7
|
1.0
|
CD
|
A:ARG238
|
4.5
|
21.3
|
1.0
|
O
|
A:LYS232
|
4.6
|
16.2
|
1.0
|
CZ
|
A:ARG238
|
4.6
|
38.5
|
1.0
|
NH1
|
A:ARG235
|
4.6
|
80.1
|
1.0
|
C8A
|
A:NDP300
|
4.7
|
21.4
|
1.0
|
C4A
|
A:NDP300
|
4.7
|
21.9
|
1.0
|
NH2
|
A:ARG235
|
4.8
|
73.4
|
1.0
|
CA
|
A:VAL234
|
4.8
|
16.5
|
1.0
|
O4B
|
A:NDP300
|
4.8
|
25.8
|
1.0
|
C4B
|
A:NDP300
|
4.8
|
22.4
|
1.0
|
N
|
A:SER233
|
4.8
|
17.4
|
1.0
|
N
|
A:ARG235
|
4.8
|
19.5
|
1.0
|
CG
|
A:ARG235
|
4.9
|
23.5
|
1.0
|
CB
|
A:VAL234
|
5.0
|
19.1
|
1.0
|
N3A
|
A:NDP300
|
5.0
|
24.3
|
1.0
|
|
Reference:
S.Khurana,
D.B.Powers,
S.Anderson,
M.Blaber.
Crystal Structure of 2,5-Diketo-D-Gluconic Acid Reductase A Complexed with Nadph at 2.1-A Resolution. Proc.Natl.Acad.Sci.Usa V. 95 6768 1998.
ISSN: ISSN 0027-8424
PubMed: 9618487
DOI: 10.1073/PNAS.95.12.6768
Page generated: Fri Sep 25 12:25:26 2020
|