Sodium in PDB 6riv: Crystal Structure of Alopecurus Myosuroides Gstf
Enzymatic activity of Crystal Structure of Alopecurus Myosuroides Gstf
All present enzymatic activity of Crystal Structure of Alopecurus Myosuroides Gstf:
2.5.1.18;
Protein crystallography data
The structure of Crystal Structure of Alopecurus Myosuroides Gstf, PDB code: 6riv
was solved by
A.C.Papageorgiou,
N.Poudel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.20 /
1.33
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.289,
50.708,
51.603,
97.74,
110.24,
110.96
|
R / Rfree (%)
|
13.1 /
16.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Alopecurus Myosuroides Gstf
(pdb code 6riv). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Crystal Structure of Alopecurus Myosuroides Gstf, PDB code: 6riv:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6riv
Go back to
Sodium Binding Sites List in 6riv
Sodium binding site 1 out
of 6 in the Crystal Structure of Alopecurus Myosuroides Gstf
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Alopecurus Myosuroides Gstf within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na504
b:32.3
occ:1.00
|
O
|
B:HOH650
|
2.8
|
33.3
|
1.0
|
N
|
B:ASN33
|
3.0
|
20.9
|
1.0
|
CA
|
B:VAL32
|
3.6
|
19.9
|
1.0
|
O
|
B:VAL31
|
3.8
|
22.5
|
1.0
|
C
|
B:VAL32
|
3.8
|
18.7
|
1.0
|
CB
|
B:ASN33
|
3.8
|
24.6
|
1.0
|
O
|
B:HOH686
|
3.9
|
31.6
|
1.0
|
CA
|
B:ASN33
|
4.0
|
22.2
|
1.0
|
CG1
|
B:VAL32
|
4.3
|
21.3
|
1.0
|
CB
|
B:VAL32
|
4.5
|
21.1
|
1.0
|
N
|
B:VAL32
|
4.6
|
19.5
|
1.0
|
C
|
B:VAL31
|
4.6
|
18.4
|
1.0
|
O
|
B:HOH752
|
4.8
|
37.9
|
1.0
|
O
|
B:ASN33
|
4.8
|
27.4
|
1.0
|
C
|
B:ASN33
|
4.9
|
24.6
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6riv
Go back to
Sodium Binding Sites List in 6riv
Sodium binding site 2 out
of 6 in the Crystal Structure of Alopecurus Myosuroides Gstf
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Alopecurus Myosuroides Gstf within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na505
b:38.0
occ:1.00
|
O
|
B:HOH638
|
2.3
|
28.3
|
1.0
|
OE2
|
B:GLU89
|
2.7
|
33.1
|
1.0
|
O
|
B:HOH679
|
2.9
|
21.4
|
1.0
|
NH2
|
A:ARG77
|
3.3
|
20.1
|
1.0
|
NH2
|
B:ARG77
|
3.5
|
19.2
|
1.0
|
CD
|
B:GLU89
|
3.6
|
29.1
|
1.0
|
CD2
|
B:LEU87
|
3.7
|
15.6
|
1.0
|
CD1
|
B:LEU87
|
3.8
|
16.1
|
1.0
|
CG
|
B:GLU89
|
3.8
|
23.2
|
1.0
|
OD1
|
B:ASP99
|
3.9
|
17.8
|
1.0
|
CB
|
B:LEU87
|
3.9
|
14.0
|
1.0
|
CD
|
B:LYS73
|
4.0
|
16.4
|
1.0
|
CG
|
B:LEU87
|
4.0
|
14.7
|
1.0
|
O
|
A:HOH617
|
4.2
|
28.0
|
1.0
|
OE2
|
A:GLU89
|
4.4
|
34.2
|
1.0
|
CZ
|
A:ARG77
|
4.4
|
17.8
|
1.0
|
CZ
|
B:ARG77
|
4.5
|
18.1
|
1.0
|
O
|
B:HOH695
|
4.7
|
23.6
|
1.0
|
O
|
A:HOH603
|
4.7
|
31.8
|
1.0
|
NE
|
B:ARG77
|
4.7
|
18.6
|
1.0
|
OE1
|
B:GLU89
|
4.7
|
37.6
|
1.0
|
CG
|
B:LYS73
|
4.7
|
14.3
|
1.0
|
OD2
|
B:ASP99
|
4.8
|
16.4
|
1.0
|
CG
|
B:ASP99
|
4.8
|
15.0
|
1.0
|
NH1
|
A:ARG77
|
4.9
|
17.5
|
1.0
|
O
|
B:LEU87
|
4.9
|
15.5
|
1.0
|
CA
|
B:LEU87
|
5.0
|
14.0
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6riv
Go back to
Sodium Binding Sites List in 6riv
Sodium binding site 3 out
of 6 in the Crystal Structure of Alopecurus Myosuroides Gstf
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Alopecurus Myosuroides Gstf within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na506
b:36.9
occ:1.00
|
O
|
B:HOH710
|
2.5
|
25.4
|
1.0
|
O
|
B:HOH786
|
2.8
|
25.1
|
1.0
|
NH1
|
B:ARG153
|
3.1
|
19.6
|
1.0
|
O
|
B:HOH742
|
3.4
|
23.5
|
1.0
|
O
|
A:HOH802
|
3.5
|
26.8
|
1.0
|
CD
|
B:ARG153
|
3.5
|
15.2
|
1.0
|
CD
|
B:LYS156
|
3.7
|
23.5
|
1.0
|
CE
|
B:LYS156
|
3.9
|
21.3
|
1.0
|
CZ
|
B:ARG153
|
4.0
|
16.5
|
1.0
|
NZ
|
B:LYS156
|
4.0
|
23.8
|
1.0
|
NE
|
B:ARG153
|
4.2
|
15.8
|
1.0
|
O
|
B:HOH734
|
4.5
|
19.4
|
1.0
|
CA
|
B:ARG153
|
4.8
|
14.2
|
1.0
|
CG
|
B:ARG153
|
4.8
|
14.2
|
1.0
|
CG
|
B:LYS156
|
4.9
|
22.3
|
1.0
|
CB
|
B:ARG153
|
4.9
|
13.7
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6riv
Go back to
Sodium Binding Sites List in 6riv
Sodium binding site 4 out
of 6 in the Crystal Structure of Alopecurus Myosuroides Gstf
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Alopecurus Myosuroides Gstf within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:33.0
occ:1.00
|
O
|
A:HOH704
|
2.7
|
24.1
|
1.0
|
O
|
A:HOH683
|
2.8
|
21.6
|
1.0
|
O
|
A:HOH708
|
3.2
|
24.7
|
1.0
|
CB
|
A:ALA211
|
4.0
|
15.8
|
1.0
|
CG
|
A:LYS208
|
4.1
|
16.9
|
1.0
|
CE
|
A:MET202
|
4.1
|
26.3
|
1.0
|
CA
|
A:LYS208
|
4.2
|
15.5
|
1.0
|
CB
|
A:LYS208
|
4.4
|
16.7
|
1.0
|
NZ
|
A:LYS208
|
4.6
|
26.8
|
1.0
|
NA
|
A:NA504
|
4.6
|
31.4
|
1.0
|
O
|
A:HOH769
|
4.6
|
39.9
|
1.0
|
O
|
A:LYS208
|
4.6
|
16.5
|
1.0
|
O
|
A:MET202
|
4.7
|
17.6
|
1.0
|
CD
|
A:LYS208
|
4.8
|
21.2
|
1.0
|
C
|
A:LYS208
|
4.9
|
15.2
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6riv
Go back to
Sodium Binding Sites List in 6riv
Sodium binding site 5 out
of 6 in the Crystal Structure of Alopecurus Myosuroides Gstf
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Alopecurus Myosuroides Gstf within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:31.4
occ:1.00
|
O
|
A:HOH825
|
2.8
|
22.9
|
1.0
|
CE
|
A:MET202
|
3.8
|
26.3
|
1.0
|
O
|
A:HOH804
|
4.0
|
32.9
|
1.0
|
CE1
|
A:PHE177
|
4.2
|
18.2
|
1.0
|
O
|
A:HOH834
|
4.3
|
35.9
|
1.0
|
O
|
A:HOH818
|
4.5
|
32.0
|
1.0
|
NA
|
A:NA503
|
4.6
|
33.0
|
1.0
|
CZ
|
A:PHE177
|
4.6
|
19.5
|
1.0
|
O
|
A:HOH716
|
4.6
|
19.6
|
1.0
|
O
|
A:HOH769
|
4.7
|
39.9
|
1.0
|
O
|
A:HOH756
|
4.7
|
21.9
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6riv
Go back to
Sodium Binding Sites List in 6riv
Sodium binding site 6 out
of 6 in the Crystal Structure of Alopecurus Myosuroides Gstf
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of Alopecurus Myosuroides Gstf within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:36.5
occ:1.00
|
O
|
A:HOH790
|
2.8
|
31.7
|
1.0
|
O
|
A:HOH840
|
2.8
|
33.9
|
1.0
|
CD
|
A:LYS208
|
4.1
|
21.2
|
1.0
|
O
|
A:HOH823
|
4.2
|
25.1
|
1.0
|
CB
|
A:LYS208
|
4.2
|
16.7
|
1.0
|
O
|
A:HOH838
|
4.4
|
29.0
|
1.0
|
O
|
A:HOH704
|
4.5
|
24.1
|
1.0
|
O
|
A:HOH687
|
4.6
|
23.4
|
1.0
|
O
|
A:HOH816
|
4.6
|
32.4
|
1.0
|
CG
|
A:LYS208
|
4.7
|
16.9
|
1.0
|
O
|
A:HOH809
|
4.9
|
32.8
|
1.0
|
O
|
A:HOH708
|
4.9
|
24.7
|
1.0
|
|
Reference:
N.Georgakis,
N.Poudel,
A.C.Papageorgiou,
N.E.Labrou.
Comparative Structural and Functional Analysis of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops. Plant Physiol Biochem. V. 149 266 2020.
ISSN: ESSN 1873-2690
PubMed: 32088578
DOI: 10.1016/J.PLAPHY.2020.02.012
Page generated: Tue Oct 8 13:12:41 2024
|