Sodium in PDB 6w1i: Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
Enzymatic activity of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
All present enzymatic activity of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).:
2.4.2.22;
Protein crystallography data
The structure of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B)., PDB code: 6w1i
was solved by
K.A.Satyshur,
B.W.Anderson,
J.L.Keck,
Midwest Center For Structuralgenomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
34.23 /
1.80
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.503,
115.902,
73.985,
90.00,
94.30,
90.00
|
|
R / Rfree (%)
|
16 /
20.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
(pdb code 6w1i). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B)., PDB code: 6w1i:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 1 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:17.1
occ:1.00
|
O
|
A:HOH429
|
2.3
|
16.5
|
1.0
|
|
O2'
|
A:G4P203
|
2.3
|
12.3
|
1.0
|
|
OD2
|
A:ASP125
|
2.3
|
11.5
|
1.0
|
|
O1C
|
A:G4P203
|
2.4
|
18.1
|
1.0
|
|
HO2'
|
A:G4P203
|
2.8
|
14.8
|
1.0
|
|
OD1
|
A:ASP125
|
2.9
|
15.8
|
1.0
|
|
CG
|
A:ASP125
|
2.9
|
16.1
|
1.0
|
|
O3'
|
A:G4P203
|
3.1
|
13.5
|
1.0
|
|
PC
|
A:G4P203
|
3.2
|
12.4
|
1.0
|
|
H1'
|
A:G4P203
|
3.2
|
17.4
|
1.0
|
|
HD2
|
A:PHE126
|
3.3
|
15.9
|
1.0
|
|
HB2
|
A:SER60
|
3.3
|
15.0
|
1.0
|
|
C2'
|
A:G4P203
|
3.5
|
13.2
|
1.0
|
|
O3D
|
A:G4P203
|
3.5
|
17.4
|
1.0
|
|
HB2
|
A:PHE126
|
3.5
|
14.6
|
1.0
|
|
HD21
|
A:ASN27
|
3.5
|
15.3
|
1.0
|
|
NA
|
A:NA202
|
3.5
|
12.7
|
1.0
|
|
O3C
|
A:G4P203
|
3.7
|
16.8
|
1.0
|
|
C3'
|
A:G4P203
|
3.9
|
16.9
|
1.0
|
|
ND2
|
A:ASN27
|
3.9
|
12.7
|
1.0
|
|
C1'
|
A:G4P203
|
3.9
|
14.5
|
1.0
|
|
HD22
|
A:ASN27
|
4.0
|
15.3
|
1.0
|
|
CB
|
A:SER60
|
4.0
|
12.5
|
1.0
|
|
PD
|
A:G4P203
|
4.1
|
14.3
|
1.0
|
|
CD2
|
A:PHE126
|
4.1
|
13.3
|
1.0
|
|
HB3
|
A:SER60
|
4.1
|
15.0
|
1.0
|
|
OG
|
A:SER60
|
4.2
|
11.7
|
1.0
|
|
O2D
|
A:G4P203
|
4.3
|
12.2
|
1.0
|
|
H2'
|
A:G4P203
|
4.3
|
15.8
|
1.0
|
|
O
|
A:HOH382
|
4.3
|
24.0
|
1.0
|
|
H
|
A:PHE126
|
4.3
|
13.9
|
1.0
|
|
CB
|
A:PHE126
|
4.4
|
12.2
|
1.0
|
|
CB
|
A:ASP125
|
4.4
|
11.1
|
1.0
|
|
H3'
|
A:G4P203
|
4.4
|
20.2
|
1.0
|
|
HG
|
A:SER60
|
4.5
|
14.1
|
1.0
|
|
O
|
A:HOH381
|
4.5
|
20.8
|
1.0
|
|
N3
|
A:G4P203
|
4.6
|
14.0
|
1.0
|
|
O2C
|
A:G4P203
|
4.6
|
16.8
|
1.0
|
|
HB2
|
A:ASP125
|
4.7
|
13.3
|
1.0
|
|
CG
|
A:PHE126
|
4.7
|
13.1
|
1.0
|
|
O
|
A:HOH347
|
4.7
|
12.1
|
1.0
|
|
N
|
A:PHE126
|
4.7
|
11.6
|
1.0
|
|
CG
|
A:ASN27
|
4.8
|
16.8
|
1.0
|
|
HB3
|
A:ASP125
|
4.8
|
13.3
|
1.0
|
|
N9
|
A:G4P203
|
4.8
|
15.9
|
1.0
|
|
HB3
|
A:PHE126
|
4.9
|
14.6
|
1.0
|
|
C4
|
A:G4P203
|
5.0
|
13.0
|
1.0
|
|
C4'
|
A:G4P203
|
5.0
|
19.8
|
1.0
|
|
HN21
|
A:G4P203
|
5.0
|
17.3
|
1.0
|
|
O4'
|
A:G4P203
|
5.0
|
15.4
|
1.0
|
|
HE2
|
A:PHE126
|
5.0
|
17.6
|
1.0
|
|
Sodium binding site 2 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 2 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:12.7
occ:1.00
|
O1C
|
A:G4P203
|
2.3
|
18.1
|
1.0
|
|
OD1
|
A:ASP125
|
2.4
|
15.8
|
1.0
|
|
OD1
|
A:ASP124
|
2.4
|
15.2
|
1.0
|
|
O
|
A:HOH346
|
2.4
|
14.6
|
1.0
|
|
O
|
A:HOH347
|
2.5
|
12.1
|
1.0
|
|
CG
|
A:ASP124
|
3.3
|
20.3
|
1.0
|
|
H
|
A:ASP125
|
3.4
|
13.8
|
1.0
|
|
HG23
|
A:ILE57
|
3.4
|
18.8
|
1.0
|
|
CG
|
A:ASP125
|
3.5
|
16.1
|
1.0
|
|
OD2
|
A:ASP124
|
3.5
|
17.9
|
1.0
|
|
NA
|
A:NA201
|
3.5
|
17.1
|
1.0
|
|
O
|
A:HOH381
|
3.5
|
20.8
|
1.0
|
|
PC
|
A:G4P203
|
3.6
|
12.4
|
1.0
|
|
H
|
A:PHE126
|
3.9
|
13.9
|
1.0
|
|
HB2
|
A:SER60
|
3.9
|
15.0
|
1.0
|
|
O2'
|
A:G4P203
|
4.0
|
12.3
|
1.0
|
|
HO2'
|
A:G4P203
|
4.0
|
14.8
|
1.0
|
|
HG22
|
A:ILE57
|
4.0
|
18.8
|
1.0
|
|
CG2
|
A:ILE57
|
4.0
|
15.7
|
1.0
|
|
HG21
|
A:ILE57
|
4.0
|
18.8
|
1.0
|
|
OD2
|
A:ASP125
|
4.1
|
11.5
|
1.0
|
|
H
|
A:GLY61
|
4.1
|
13.1
|
1.0
|
|
O2C
|
A:G4P203
|
4.1
|
16.8
|
1.0
|
|
O2D
|
A:G4P203
|
4.1
|
12.2
|
1.0
|
|
N
|
A:ASP125
|
4.2
|
11.5
|
1.0
|
|
O
|
A:HOH353
|
4.4
|
25.5
|
1.0
|
|
O3'
|
A:G4P203
|
4.5
|
13.5
|
1.0
|
|
N
|
A:GLY61
|
4.5
|
10.9
|
1.0
|
|
HA3
|
A:GLY61
|
4.5
|
16.0
|
1.0
|
|
CB
|
A:ASP125
|
4.5
|
11.1
|
1.0
|
|
HB3
|
A:ASP125
|
4.6
|
13.3
|
1.0
|
|
HA
|
A:ASP124
|
4.6
|
15.4
|
1.0
|
|
CB
|
A:ASP124
|
4.6
|
13.5
|
1.0
|
|
N
|
A:PHE126
|
4.7
|
11.6
|
1.0
|
|
O
|
A:ILE57
|
4.7
|
11.9
|
1.0
|
|
H3'
|
A:G4P203
|
4.7
|
20.2
|
1.0
|
|
O3C
|
A:G4P203
|
4.7
|
16.8
|
1.0
|
|
HB2
|
A:PHE126
|
4.8
|
14.6
|
1.0
|
|
HZ3
|
A:LYS81
|
4.8
|
27.1
|
1.0
|
|
H
|
A:SER60
|
4.8
|
10.8
|
1.0
|
|
CB
|
A:SER60
|
4.9
|
12.5
|
1.0
|
|
HB3
|
A:ASP124
|
4.9
|
16.2
|
1.0
|
|
CA
|
A:ASP125
|
4.9
|
9.8
|
1.0
|
|
CA
|
A:GLY61
|
5.0
|
13.3
|
1.0
|
|
C3'
|
A:G4P203
|
5.0
|
16.9
|
1.0
|
|
C2'
|
A:G4P203
|
5.0
|
13.2
|
1.0
|
|
PD
|
A:G4P203
|
5.0
|
14.3
|
1.0
|
|
Sodium binding site 3 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 3 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na201
b:21.8
occ:1.00
|
O2'
|
B:G4P203
|
2.2
|
18.1
|
1.0
|
|
O2C
|
B:G4P203
|
2.3
|
22.2
|
1.0
|
|
OD2
|
B:ASP125
|
2.4
|
15.9
|
1.0
|
|
O
|
B:HOH403
|
2.4
|
23.1
|
1.0
|
|
HO2'
|
B:G4P203
|
2.8
|
21.7
|
1.0
|
|
O3'
|
B:G4P203
|
2.9
|
23.4
|
1.0
|
|
OD1
|
B:ASP125
|
3.0
|
15.2
|
1.0
|
|
CG
|
B:ASP125
|
3.0
|
22.4
|
1.0
|
|
PC
|
B:G4P203
|
3.1
|
19.7
|
1.0
|
|
H1'
|
B:G4P203
|
3.1
|
24.6
|
1.0
|
|
HB2
|
B:SER60
|
3.3
|
16.8
|
1.0
|
|
C2'
|
B:G4P203
|
3.4
|
18.7
|
1.0
|
|
HD2
|
B:PHE126
|
3.4
|
22.4
|
1.0
|
|
O3D
|
B:G4P203
|
3.4
|
22.0
|
1.0
|
|
O3C
|
B:G4P203
|
3.5
|
21.5
|
1.0
|
|
NA
|
B:NA202
|
3.5
|
16.3
|
1.0
|
|
HD21
|
B:ASN27
|
3.6
|
22.7
|
1.0
|
|
HB2
|
B:PHE126
|
3.6
|
17.4
|
1.0
|
|
C3'
|
B:G4P203
|
3.7
|
29.3
|
1.0
|
|
C1'
|
B:G4P203
|
3.8
|
20.5
|
1.0
|
|
PD
|
B:G4P203
|
3.9
|
20.6
|
1.0
|
|
ND2
|
B:ASN27
|
4.0
|
18.9
|
1.0
|
|
CB
|
B:SER60
|
4.0
|
14.0
|
1.0
|
|
O1D
|
B:G4P203
|
4.1
|
20.5
|
1.0
|
|
HB3
|
B:SER60
|
4.1
|
16.8
|
1.0
|
|
O
|
B:HOH341
|
4.2
|
32.6
|
1.0
|
|
HD22
|
B:ASN27
|
4.2
|
22.7
|
1.0
|
|
H2'
|
B:G4P203
|
4.2
|
22.4
|
1.0
|
|
CD2
|
B:PHE126
|
4.2
|
18.7
|
1.0
|
|
OG
|
B:SER60
|
4.2
|
16.6
|
1.0
|
|
H
|
B:PHE126
|
4.3
|
18.9
|
1.0
|
|
H3'
|
B:G4P203
|
4.4
|
35.1
|
1.0
|
|
HG
|
B:SER60
|
4.4
|
19.9
|
1.0
|
|
O1C
|
B:G4P203
|
4.5
|
20.6
|
1.0
|
|
CB
|
B:ASP125
|
4.5
|
18.2
|
1.0
|
|
CB
|
B:PHE126
|
4.5
|
14.5
|
1.0
|
|
O
|
B:HOH356
|
4.6
|
27.2
|
1.0
|
|
N3
|
B:G4P203
|
4.7
|
18.4
|
1.0
|
|
O
|
B:HOH344
|
4.7
|
15.3
|
1.0
|
|
N9
|
B:G4P203
|
4.7
|
18.6
|
1.0
|
|
CG
|
B:ASN27
|
4.8
|
22.6
|
1.0
|
|
HB2
|
B:ASP125
|
4.8
|
21.8
|
1.0
|
|
C4'
|
B:G4P203
|
4.8
|
33.0
|
1.0
|
|
O4'
|
B:G4P203
|
4.8
|
27.3
|
1.0
|
|
N
|
B:PHE126
|
4.8
|
15.8
|
1.0
|
|
CG
|
B:PHE126
|
4.8
|
13.1
|
1.0
|
|
HB3
|
B:ASP125
|
4.9
|
21.8
|
1.0
|
|
O
|
B:HOH306
|
4.9
|
18.1
|
1.0
|
|
H4'
|
B:G4P203
|
4.9
|
39.7
|
1.0
|
|
C4
|
B:G4P203
|
5.0
|
14.4
|
1.0
|
|
Sodium binding site 4 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 4 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na202
b:16.3
occ:1.00
|
O2C
|
B:G4P203
|
2.2
|
22.2
|
1.0
|
|
O
|
B:HOH306
|
2.3
|
18.1
|
1.0
|
|
OD1
|
B:ASP125
|
2.4
|
15.2
|
1.0
|
|
OD1
|
B:ASP124
|
2.4
|
16.8
|
1.0
|
|
O
|
B:HOH344
|
2.5
|
15.3
|
1.0
|
|
CG
|
B:ASP124
|
3.2
|
24.0
|
1.0
|
|
H
|
B:ASP125
|
3.3
|
15.8
|
1.0
|
|
OD2
|
B:ASP124
|
3.4
|
22.7
|
1.0
|
|
CG
|
B:ASP125
|
3.4
|
22.4
|
1.0
|
|
HG23
|
B:ILE57
|
3.4
|
21.0
|
1.0
|
|
NA
|
B:NA201
|
3.5
|
21.8
|
1.0
|
|
PC
|
B:G4P203
|
3.6
|
19.7
|
1.0
|
|
O
|
B:HOH356
|
3.7
|
27.2
|
1.0
|
|
HB2
|
B:SER60
|
3.9
|
16.8
|
1.0
|
|
H
|
B:PHE126
|
3.9
|
18.9
|
1.0
|
|
O2'
|
B:G4P203
|
3.9
|
18.1
|
1.0
|
|
HO2'
|
B:G4P203
|
3.9
|
21.7
|
1.0
|
|
OD2
|
B:ASP125
|
4.0
|
15.9
|
1.0
|
|
CG2
|
B:ILE57
|
4.0
|
17.5
|
1.0
|
|
HG22
|
B:ILE57
|
4.0
|
21.0
|
1.0
|
|
O1D
|
B:G4P203
|
4.1
|
20.5
|
1.0
|
|
HG21
|
B:ILE57
|
4.1
|
21.0
|
1.0
|
|
H
|
B:GLY61
|
4.1
|
16.5
|
1.0
|
|
O1C
|
B:G4P203
|
4.1
|
20.6
|
1.0
|
|
N
|
B:ASP125
|
4.2
|
13.2
|
1.0
|
|
O
|
B:HOH305
|
4.3
|
31.1
|
1.0
|
|
O3'
|
B:G4P203
|
4.4
|
23.4
|
1.0
|
|
N
|
B:GLY61
|
4.5
|
13.8
|
1.0
|
|
CB
|
B:ASP125
|
4.5
|
18.2
|
1.0
|
|
HA3
|
B:GLY61
|
4.5
|
18.1
|
1.0
|
|
HB3
|
B:ASP125
|
4.5
|
21.8
|
1.0
|
|
CB
|
B:ASP124
|
4.5
|
17.3
|
1.0
|
|
HZ3
|
B:LYS81
|
4.6
|
29.1
|
1.0
|
|
HA
|
B:ASP124
|
4.6
|
18.7
|
1.0
|
|
O
|
B:ILE57
|
4.7
|
11.8
|
1.0
|
|
N
|
B:PHE126
|
4.7
|
15.8
|
1.0
|
|
O3C
|
B:G4P203
|
4.7
|
21.5
|
1.0
|
|
H
|
B:SER60
|
4.7
|
14.4
|
1.0
|
|
CB
|
B:SER60
|
4.8
|
14.0
|
1.0
|
|
H3'
|
B:G4P203
|
4.8
|
35.1
|
1.0
|
|
HB3
|
B:ASP124
|
4.8
|
20.8
|
1.0
|
|
HB2
|
B:PHE126
|
4.8
|
17.4
|
1.0
|
|
CA
|
B:ASP125
|
4.9
|
14.4
|
1.0
|
|
CA
|
B:GLY61
|
4.9
|
15.1
|
1.0
|
|
C2'
|
B:G4P203
|
4.9
|
18.7
|
1.0
|
|
C3'
|
B:G4P203
|
4.9
|
29.3
|
1.0
|
|
HA2
|
B:GLY61
|
5.0
|
18.1
|
1.0
|
|
HB3
|
B:SER60
|
5.0
|
16.8
|
1.0
|
|
PD
|
B:G4P203
|
5.0
|
20.6
|
1.0
|
|
CA
|
B:ASP124
|
5.0
|
15.6
|
1.0
|
|
Sodium binding site 5 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 5 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na201
b:18.6
occ:1.00
|
HO2'
|
C:G4P203
|
2.2
|
22.1
|
1.0
|
|
O2'
|
C:G4P203
|
2.2
|
18.4
|
1.0
|
|
O2C
|
C:G4P203
|
2.3
|
14.5
|
1.0
|
|
O
|
C:HOH396
|
2.3
|
16.8
|
1.0
|
|
OD2
|
C:ASP125
|
2.3
|
12.9
|
1.0
|
|
OD1
|
C:ASP125
|
2.9
|
17.5
|
1.0
|
|
CG
|
C:ASP125
|
3.0
|
14.2
|
1.0
|
|
PC
|
C:G4P203
|
3.2
|
16.3
|
1.0
|
|
HD2
|
C:PHE126
|
3.2
|
19.2
|
1.0
|
|
O3'
|
C:G4P203
|
3.2
|
13.7
|
1.0
|
|
HB2
|
C:SER60
|
3.3
|
16.1
|
1.0
|
|
H1'
|
C:G4P203
|
3.3
|
23.9
|
1.0
|
|
HB2
|
C:PHE126
|
3.4
|
16.7
|
1.0
|
|
C2'
|
C:G4P203
|
3.4
|
18.3
|
1.0
|
|
HD21
|
C:ASN27
|
3.4
|
16.7
|
1.0
|
|
O1D
|
C:G4P203
|
3.5
|
14.3
|
1.0
|
|
NA
|
C:NA202
|
3.5
|
15.7
|
1.0
|
|
O3C
|
C:G4P203
|
3.7
|
16.9
|
1.0
|
|
ND2
|
C:ASN27
|
3.8
|
13.9
|
1.0
|
|
HD22
|
C:ASN27
|
3.8
|
16.7
|
1.0
|
|
C3'
|
C:G4P203
|
3.9
|
17.1
|
1.0
|
|
CB
|
C:SER60
|
3.9
|
13.4
|
1.0
|
|
HB3
|
C:SER60
|
4.0
|
16.1
|
1.0
|
|
C1'
|
C:G4P203
|
4.0
|
19.9
|
1.0
|
|
CD2
|
C:PHE126
|
4.1
|
16.0
|
1.0
|
|
PD
|
C:G4P203
|
4.1
|
16.2
|
1.0
|
|
OG
|
C:SER60
|
4.1
|
13.2
|
1.0
|
|
H
|
C:PHE126
|
4.2
|
13.9
|
1.0
|
|
H2'
|
C:G4P203
|
4.2
|
22.0
|
1.0
|
|
O
|
C:HOH357
|
4.2
|
23.5
|
1.0
|
|
O2D
|
C:G4P203
|
4.3
|
16.9
|
1.0
|
|
CB
|
C:PHE126
|
4.4
|
13.9
|
1.0
|
|
H3'
|
C:G4P203
|
4.4
|
20.5
|
1.0
|
|
HG
|
C:SER60
|
4.4
|
15.9
|
1.0
|
|
CB
|
C:ASP125
|
4.4
|
11.6
|
1.0
|
|
O
|
C:HOH365
|
4.5
|
19.3
|
1.0
|
|
N3
|
C:G4P203
|
4.5
|
14.5
|
1.0
|
|
O1C
|
C:G4P203
|
4.6
|
14.1
|
1.0
|
|
CG
|
C:PHE126
|
4.7
|
12.7
|
1.0
|
|
N
|
C:PHE126
|
4.7
|
11.6
|
1.0
|
|
HB2
|
C:ASP125
|
4.7
|
14.0
|
1.0
|
|
O
|
C:HOH368
|
4.7
|
12.7
|
1.0
|
|
CG
|
C:ASN27
|
4.7
|
17.3
|
1.0
|
|
HB3
|
C:ASP125
|
4.8
|
14.0
|
1.0
|
|
N9
|
C:G4P203
|
4.8
|
17.8
|
1.0
|
|
HB3
|
C:PHE126
|
4.9
|
16.7
|
1.0
|
|
C4
|
C:G4P203
|
4.9
|
13.1
|
1.0
|
|
HE2
|
C:PHE126
|
5.0
|
19.4
|
1.0
|
|
CE2
|
C:PHE126
|
5.0
|
16.2
|
1.0
|
|
HN21
|
C:G4P203
|
5.0
|
17.0
|
1.0
|
|
Sodium binding site 6 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 6 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na202
b:15.7
occ:1.00
|
O2C
|
C:G4P203
|
2.3
|
14.5
|
1.0
|
|
OD1
|
C:ASP125
|
2.3
|
17.5
|
1.0
|
|
OD1
|
C:ASP124
|
2.4
|
16.0
|
1.0
|
|
O
|
C:HOH317
|
2.4
|
14.8
|
1.0
|
|
O
|
C:HOH368
|
2.5
|
12.7
|
1.0
|
|
CG
|
C:ASP124
|
3.3
|
20.5
|
1.0
|
|
H
|
C:ASP125
|
3.3
|
15.7
|
1.0
|
|
OD2
|
C:ASP124
|
3.5
|
20.9
|
1.0
|
|
CG
|
C:ASP125
|
3.5
|
14.2
|
1.0
|
|
NA
|
C:NA201
|
3.5
|
18.6
|
1.0
|
|
HG23
|
C:ILE57
|
3.6
|
19.1
|
1.0
|
|
PC
|
C:G4P203
|
3.7
|
16.3
|
1.0
|
|
O
|
C:HOH365
|
3.8
|
19.3
|
1.0
|
|
HB2
|
C:SER60
|
3.8
|
16.1
|
1.0
|
|
H
|
C:PHE126
|
3.8
|
13.9
|
1.0
|
|
HG22
|
C:ILE57
|
3.9
|
19.1
|
1.0
|
|
O2'
|
C:G4P203
|
4.0
|
18.4
|
1.0
|
|
CG2
|
C:ILE57
|
4.0
|
15.9
|
1.0
|
|
H
|
C:GLY61
|
4.0
|
15.5
|
1.0
|
|
HG21
|
C:ILE57
|
4.1
|
19.1
|
1.0
|
|
OD2
|
C:ASP125
|
4.1
|
12.9
|
1.0
|
|
O1C
|
C:G4P203
|
4.1
|
14.1
|
1.0
|
|
O2D
|
C:G4P203
|
4.1
|
16.9
|
1.0
|
|
N
|
C:ASP125
|
4.2
|
13.1
|
1.0
|
|
N
|
C:GLY61
|
4.4
|
12.9
|
1.0
|
|
O
|
C:HOH319
|
4.5
|
34.2
|
1.0
|
|
HA3
|
C:GLY61
|
4.5
|
16.7
|
1.0
|
|
CB
|
C:ASP125
|
4.5
|
11.6
|
1.0
|
|
HB3
|
C:ASP125
|
4.5
|
14.0
|
1.0
|
|
H3'
|
C:G4P203
|
4.6
|
20.5
|
1.0
|
|
HO2'
|
C:G4P203
|
4.6
|
22.1
|
1.0
|
|
CB
|
C:ASP124
|
4.6
|
13.1
|
1.0
|
|
HA
|
C:ASP124
|
4.6
|
14.6
|
1.0
|
|
O3'
|
C:G4P203
|
4.6
|
13.7
|
1.0
|
|
N
|
C:PHE126
|
4.7
|
11.6
|
1.0
|
|
O
|
C:ILE57
|
4.7
|
12.5
|
1.0
|
|
CB
|
C:SER60
|
4.7
|
13.4
|
1.0
|
|
H
|
C:SER60
|
4.7
|
11.5
|
1.0
|
|
O3C
|
C:G4P203
|
4.8
|
16.9
|
1.0
|
|
HB2
|
C:PHE126
|
4.8
|
16.7
|
1.0
|
|
HZ3
|
C:LYS81
|
4.8
|
30.9
|
1.0
|
|
CA
|
C:ASP125
|
4.9
|
12.4
|
1.0
|
|
HB3
|
C:SER60
|
4.9
|
16.1
|
1.0
|
|
CA
|
C:GLY61
|
4.9
|
13.9
|
1.0
|
|
HB3
|
C:ASP124
|
4.9
|
15.7
|
1.0
|
|
HA2
|
C:GLY61
|
4.9
|
16.7
|
1.0
|
|
C3'
|
C:G4P203
|
4.9
|
17.1
|
1.0
|
|
C2'
|
C:G4P203
|
5.0
|
18.3
|
1.0
|
|
Sodium binding site 7 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 7 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na201
b:24.8
occ:1.00
|
O2'
|
D:G4P203
|
2.2
|
25.9
|
1.0
|
|
HO2'
|
D:G4P203
|
2.2
|
31.1
|
1.0
|
|
OD2
|
D:ASP125
|
2.3
|
16.2
|
1.0
|
|
O2C
|
D:G4P203
|
2.3
|
21.9
|
1.0
|
|
O
|
D:HOH402
|
2.4
|
26.4
|
1.0
|
|
OD1
|
D:ASP125
|
2.8
|
21.8
|
1.0
|
|
CG
|
D:ASP125
|
2.9
|
21.9
|
1.0
|
|
O3'
|
D:G4P203
|
3.2
|
18.4
|
1.0
|
|
O2D
|
D:G4P203
|
3.2
|
24.3
|
1.0
|
|
HB2
|
D:SER60
|
3.2
|
18.6
|
1.0
|
|
PC
|
D:G4P203
|
3.2
|
20.0
|
1.0
|
|
HD21
|
D:ASN27
|
3.3
|
27.4
|
1.0
|
|
H1'
|
D:G4P203
|
3.3
|
24.7
|
1.0
|
|
C2'
|
D:G4P203
|
3.4
|
16.9
|
1.0
|
|
HD2
|
D:PHE126
|
3.4
|
22.1
|
1.0
|
|
NA
|
D:NA202
|
3.5
|
17.6
|
1.0
|
|
HB2
|
D:PHE126
|
3.5
|
19.2
|
1.0
|
|
O3C
|
D:G4P203
|
3.7
|
22.4
|
1.0
|
|
ND2
|
D:ASN27
|
3.7
|
22.9
|
1.0
|
|
HD22
|
D:ASN27
|
3.9
|
27.4
|
1.0
|
|
C3'
|
D:G4P203
|
3.9
|
20.1
|
1.0
|
|
PD
|
D:G4P203
|
3.9
|
19.7
|
1.0
|
|
CB
|
D:SER60
|
3.9
|
15.5
|
1.0
|
|
C1'
|
D:G4P203
|
4.0
|
20.6
|
1.0
|
|
HB3
|
D:SER60
|
4.1
|
18.6
|
1.0
|
|
O
|
D:HOH314
|
4.1
|
33.4
|
1.0
|
|
OG
|
D:SER60
|
4.1
|
16.0
|
1.0
|
|
H2'
|
D:G4P203
|
4.1
|
20.2
|
1.0
|
|
O3D
|
D:G4P203
|
4.2
|
16.6
|
1.0
|
|
H
|
D:PHE126
|
4.2
|
17.2
|
1.0
|
|
HG
|
D:SER60
|
4.3
|
19.2
|
1.0
|
|
CD2
|
D:PHE126
|
4.3
|
18.4
|
1.0
|
|
O
|
D:HOH381
|
4.3
|
21.0
|
1.0
|
|
H3'
|
D:G4P203
|
4.4
|
24.1
|
1.0
|
|
CB
|
D:ASP125
|
4.4
|
16.2
|
1.0
|
|
CB
|
D:PHE126
|
4.5
|
16.0
|
1.0
|
|
O
|
D:HOH336
|
4.6
|
16.4
|
1.0
|
|
O1C
|
D:G4P203
|
4.6
|
19.9
|
1.0
|
|
HB2
|
D:ASP125
|
4.6
|
19.5
|
1.0
|
|
N3
|
D:G4P203
|
4.7
|
18.0
|
1.0
|
|
CG
|
D:ASN27
|
4.7
|
25.8
|
1.0
|
|
N
|
D:PHE126
|
4.7
|
14.3
|
1.0
|
|
HB3
|
D:ASP125
|
4.8
|
19.5
|
1.0
|
|
N9
|
D:G4P203
|
4.8
|
25.0
|
1.0
|
|
CG
|
D:PHE126
|
4.9
|
16.4
|
1.0
|
|
H
|
D:SER60
|
4.9
|
13.3
|
1.0
|
|
C4
|
D:G4P203
|
5.0
|
15.5
|
1.0
|
|
Sodium binding site 8 out
of 8 in 6w1i
Go back to
Sodium Binding Sites List in 6w1i
Sodium binding site 8 out
of 8 in the Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B).
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Re-Interpretation of Ppgpp (G4P) Electron Density in the Deposited Crystal Structure of Xanthine Phosphoribosyltransferase (Xprt) (1Y0B). within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na202
b:17.6
occ:1.00
|
OD1
|
D:ASP125
|
2.3
|
21.8
|
1.0
|
|
O2C
|
D:G4P203
|
2.3
|
21.9
|
1.0
|
|
OD1
|
D:ASP124
|
2.3
|
16.9
|
1.0
|
|
O
|
D:HOH336
|
2.4
|
16.4
|
1.0
|
|
O
|
D:HOH321
|
2.4
|
16.9
|
1.0
|
|
CG
|
D:ASP124
|
3.2
|
19.0
|
1.0
|
|
H
|
D:ASP125
|
3.3
|
18.9
|
1.0
|
|
OD2
|
D:ASP124
|
3.4
|
18.1
|
1.0
|
|
CG
|
D:ASP125
|
3.4
|
21.9
|
1.0
|
|
HG23
|
D:ILE57
|
3.5
|
17.5
|
1.0
|
|
NA
|
D:NA201
|
3.5
|
24.8
|
1.0
|
|
O
|
D:HOH381
|
3.5
|
21.0
|
1.0
|
|
PC
|
D:G4P203
|
3.6
|
20.0
|
1.0
|
|
HB2
|
D:SER60
|
3.8
|
18.6
|
1.0
|
|
H
|
D:PHE126
|
3.8
|
17.2
|
1.0
|
|
O2'
|
D:G4P203
|
3.9
|
25.9
|
1.0
|
|
HG22
|
D:ILE57
|
3.9
|
17.5
|
1.0
|
|
H
|
D:GLY61
|
4.0
|
16.2
|
1.0
|
|
CG2
|
D:ILE57
|
4.0
|
14.6
|
1.0
|
|
HG21
|
D:ILE57
|
4.0
|
17.5
|
1.0
|
|
OD2
|
D:ASP125
|
4.1
|
16.2
|
1.0
|
|
O3D
|
D:G4P203
|
4.1
|
16.6
|
1.0
|
|
N
|
D:ASP125
|
4.1
|
15.7
|
1.0
|
|
O1C
|
D:G4P203
|
4.1
|
19.9
|
1.0
|
|
O
|
D:HOH326
|
4.3
|
28.1
|
1.0
|
|
N
|
D:GLY61
|
4.4
|
13.5
|
1.0
|
|
CB
|
D:ASP125
|
4.5
|
16.2
|
1.0
|
|
HB3
|
D:ASP125
|
4.5
|
19.5
|
1.0
|
|
HO2'
|
D:G4P203
|
4.5
|
31.1
|
1.0
|
|
HA3
|
D:GLY61
|
4.5
|
14.7
|
1.0
|
|
H3'
|
D:G4P203
|
4.5
|
24.1
|
1.0
|
|
CB
|
D:ASP124
|
4.5
|
13.8
|
1.0
|
|
HA
|
D:ASP124
|
4.6
|
17.9
|
1.0
|
|
O3'
|
D:G4P203
|
4.6
|
18.4
|
1.0
|
|
H
|
D:SER60
|
4.7
|
13.3
|
1.0
|
|
N
|
D:PHE126
|
4.7
|
14.3
|
1.0
|
|
HZ1
|
D:LYS81
|
4.7
|
25.7
|
1.0
|
|
O
|
D:ILE57
|
4.7
|
10.7
|
1.0
|
|
CB
|
D:SER60
|
4.7
|
15.5
|
1.0
|
|
O3C
|
D:G4P203
|
4.7
|
22.4
|
1.0
|
|
HB2
|
D:PHE126
|
4.8
|
19.2
|
1.0
|
|
HB3
|
D:ASP124
|
4.8
|
16.6
|
1.0
|
|
CA
|
D:ASP125
|
4.8
|
14.7
|
1.0
|
|
C2'
|
D:G4P203
|
4.9
|
16.9
|
1.0
|
|
C3'
|
D:G4P203
|
4.9
|
20.1
|
1.0
|
|
CA
|
D:GLY61
|
4.9
|
12.3
|
1.0
|
|
PD
|
D:G4P203
|
4.9
|
19.7
|
1.0
|
|
HA2
|
D:GLY61
|
4.9
|
14.7
|
1.0
|
|
CA
|
D:ASP124
|
5.0
|
14.9
|
1.0
|
|
HB3
|
D:SER60
|
5.0
|
18.6
|
1.0
|
|
Reference:
B.W.Anderson,
A.Hao,
K.A.Satyshur,
J.L.Keck,
J.D.Wang.
Molecular Mechanism of Regulation of the Purine Salvage Enzyme Xprt By the Alarmones Pppgpp, Ppgpp, and Pgpp. J.Mol.Biol. V. 432 4108 2020.
ISSN: ESSN 1089-8638
PubMed: 32446804
DOI: 10.1016/J.JMB.2020.05.013
Page generated: Tue Oct 8 14:31:25 2024
|
