Magnesium in PDB 6puq: 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
Protein crystallography data
The structure of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn, PDB code: 6puq
was solved by
L.Sjekloca,
A.R.Ferre D'amare,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.50 /
1.56
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
28.298,
73.087,
42.518,
90.00,
91.86,
90.00
|
R / Rfree (%)
|
19.6 /
22.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
(pdb code 6puq). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn, PDB code: 6puq:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6puq
Go back to
Magnesium Binding Sites List in 6puq
Magnesium binding site 1 out
of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:28.9
occ:1.00
|
O4'
|
A:FMN301
|
2.6
|
22.2
|
1.0
|
OG1
|
A:THR99
|
2.9
|
19.8
|
1.0
|
OG
|
A:SER98
|
2.9
|
21.8
|
1.0
|
O5'
|
A:FMN301
|
3.3
|
20.0
|
1.0
|
CB
|
A:PHE187
|
3.3
|
18.5
|
1.0
|
CE2
|
A:PHE102
|
3.4
|
19.3
|
1.0
|
CG
|
A:PHE187
|
3.5
|
19.4
|
1.0
|
C4'
|
A:FMN301
|
3.6
|
20.9
|
1.0
|
CD2
|
A:PHE102
|
3.6
|
22.1
|
1.0
|
N
|
A:THR99
|
3.7
|
22.0
|
1.0
|
CA
|
A:THR99
|
3.9
|
21.6
|
1.0
|
CB
|
A:THR99
|
3.9
|
18.6
|
1.0
|
CD1
|
A:PHE187
|
4.0
|
21.9
|
1.0
|
C5'
|
A:FMN301
|
4.0
|
21.3
|
1.0
|
CB
|
A:SER98
|
4.0
|
22.4
|
1.0
|
CD2
|
A:PHE187
|
4.1
|
17.1
|
1.0
|
O2P
|
A:FMN301
|
4.1
|
20.2
|
1.0
|
CG1
|
A:VAL225
|
4.1
|
21.6
|
1.0
|
P
|
A:FMN301
|
4.2
|
21.7
|
1.0
|
C
|
A:SER98
|
4.2
|
18.3
|
1.0
|
O
|
A:HOH440
|
4.3
|
33.0
|
1.0
|
CB
|
A:PRO147
|
4.4
|
20.0
|
1.0
|
O1P
|
A:FMN301
|
4.5
|
23.9
|
1.0
|
CZ
|
A:PHE102
|
4.6
|
25.4
|
1.0
|
CG2
|
A:THR99
|
4.6
|
20.3
|
1.0
|
CA
|
A:SER98
|
4.7
|
20.1
|
1.0
|
CA
|
A:PHE187
|
4.8
|
17.8
|
1.0
|
O
|
A:SER98
|
4.8
|
19.6
|
1.0
|
CE1
|
A:PHE187
|
4.8
|
24.2
|
1.0
|
CE2
|
A:PHE187
|
4.9
|
17.0
|
1.0
|
C3'
|
A:FMN301
|
4.9
|
22.4
|
1.0
|
CG
|
A:PHE102
|
4.9
|
20.2
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6puq
Go back to
Magnesium Binding Sites List in 6puq
Magnesium binding site 2 out
of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:27.7
occ:1.00
|
OG
|
A:SER148
|
2.8
|
21.7
|
1.0
|
O
|
A:LEU146
|
2.8
|
17.4
|
1.0
|
O
|
A:PHE187
|
2.9
|
18.5
|
1.0
|
CA
|
A:CYS199
|
3.3
|
22.1
|
0.5
|
N
|
A:PHE187
|
3.3
|
16.3
|
1.0
|
N
|
A:SER148
|
3.3
|
18.1
|
1.0
|
CA
|
A:CYS199
|
3.3
|
22.0
|
0.5
|
CB
|
A:ALA202
|
3.4
|
17.7
|
1.0
|
CB
|
A:CYS199
|
3.4
|
22.3
|
0.5
|
C
|
A:PRO147
|
3.4
|
22.6
|
1.0
|
SG
|
A:CYS199
|
3.6
|
18.6
|
0.5
|
CB
|
A:SER148
|
3.6
|
22.6
|
1.0
|
CB
|
A:CYS199
|
3.7
|
22.2
|
0.5
|
CA
|
A:GLY186
|
3.7
|
15.8
|
1.0
|
C
|
A:PHE187
|
3.7
|
19.9
|
1.0
|
CA
|
A:PRO147
|
3.7
|
19.9
|
1.0
|
C
|
A:LEU146
|
3.8
|
20.2
|
1.0
|
SG
|
A:CYS199
|
3.8
|
17.7
|
0.5
|
C
|
A:CYS199
|
3.8
|
22.8
|
0.5
|
N
|
A:ALA202
|
3.8
|
18.5
|
1.0
|
O
|
A:PRO147
|
3.9
|
21.3
|
1.0
|
C
|
A:GLY186
|
3.9
|
18.1
|
1.0
|
C
|
A:CYS199
|
3.9
|
22.8
|
0.5
|
O
|
A:CYS199
|
3.9
|
21.7
|
0.5
|
CA
|
A:SER148
|
4.0
|
19.8
|
1.0
|
O
|
A:CYS199
|
4.0
|
21.9
|
0.5
|
CA
|
A:PHE187
|
4.1
|
17.8
|
1.0
|
N
|
A:PRO147
|
4.2
|
17.6
|
1.0
|
CA
|
A:ALA202
|
4.2
|
17.9
|
1.0
|
N
|
A:CYS199
|
4.5
|
25.1
|
0.5
|
N
|
A:CYS199
|
4.5
|
25.1
|
0.5
|
N
|
A:GLY188
|
4.7
|
19.9
|
1.0
|
N
|
A:TYR200
|
4.8
|
18.8
|
1.0
|
N
|
A:GLN201
|
4.8
|
20.3
|
1.0
|
CB
|
A:LEU146
|
4.9
|
20.9
|
0.5
|
CA
|
A:LEU146
|
4.9
|
18.1
|
0.5
|
C
|
A:GLN201
|
4.9
|
18.6
|
1.0
|
CA
|
A:LEU146
|
4.9
|
18.0
|
0.5
|
CB
|
A:LEU146
|
4.9
|
20.9
|
0.5
|
O
|
A:GLY186
|
4.9
|
20.5
|
1.0
|
CA
|
A:GLY188
|
5.0
|
21.8
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6puq
Go back to
Magnesium Binding Sites List in 6puq
Magnesium binding site 3 out
of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:25.3
occ:1.00
|
O
|
A:ALA218
|
2.8
|
21.0
|
1.0
|
OD1
|
A:ASP206
|
2.9
|
19.4
|
1.0
|
N
|
A:VAL184
|
2.9
|
16.7
|
1.0
|
N
|
A:LEU220
|
3.3
|
19.6
|
1.0
|
O
|
A:HOH414
|
3.3
|
29.0
|
1.0
|
CA
|
A:LEU220
|
3.5
|
17.4
|
1.0
|
CA
|
A:ALA183
|
3.5
|
14.8
|
1.0
|
C
|
A:PRO219
|
3.6
|
18.1
|
1.0
|
C
|
A:ALA183
|
3.7
|
18.4
|
1.0
|
O
|
A:VAL184
|
3.8
|
16.1
|
1.0
|
CA
|
A:VAL184
|
3.9
|
16.5
|
1.0
|
CB
|
A:VAL184
|
3.9
|
14.1
|
1.0
|
O
|
A:PRO219
|
3.9
|
21.0
|
1.0
|
CG
|
A:ASP206
|
3.9
|
25.2
|
1.0
|
C
|
A:ALA218
|
4.0
|
24.3
|
1.0
|
CG
|
A:ARG216
|
4.0
|
20.4
|
1.0
|
CB
|
A:ALA183
|
4.0
|
20.8
|
1.0
|
CE2
|
A:PHE182
|
4.1
|
17.6
|
1.0
|
CD
|
A:ARG216
|
4.1
|
22.2
|
1.0
|
CB
|
A:LEU220
|
4.1
|
18.4
|
1.0
|
CG2
|
A:VAL184
|
4.2
|
14.8
|
1.0
|
CA
|
A:PRO219
|
4.3
|
22.6
|
1.0
|
C
|
A:VAL184
|
4.3
|
18.2
|
1.0
|
NE
|
A:ARG216
|
4.3
|
20.2
|
1.0
|
CD2
|
A:PHE182
|
4.5
|
18.2
|
1.0
|
N
|
A:PRO219
|
4.6
|
22.9
|
1.0
|
N
|
A:ALA183
|
4.7
|
17.3
|
1.0
|
CB
|
A:ASP206
|
4.7
|
18.8
|
1.0
|
OD2
|
A:ASP206
|
4.7
|
26.7
|
1.0
|
C
|
A:LEU220
|
4.7
|
19.7
|
1.0
|
O
|
A:PHE182
|
4.7
|
18.1
|
1.0
|
CZ
|
A:PHE182
|
4.9
|
15.1
|
1.0
|
O
|
A:ALA183
|
4.9
|
16.5
|
1.0
|
CD1
|
A:LEU220
|
4.9
|
16.2
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6puq
Go back to
Magnesium Binding Sites List in 6puq
Magnesium binding site 4 out
of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg305
b:38.9
occ:1.00
|
OG
|
A:SER153
|
2.5
|
30.9
|
1.0
|
O
|
A:ILE151
|
2.7
|
38.2
|
1.0
|
NE2
|
A:GLN201
|
3.0
|
25.8
|
1.0
|
O
|
A:TYR149
|
3.1
|
31.1
|
1.0
|
OD2
|
A:ASP156
|
3.3
|
42.1
|
1.0
|
OD1
|
A:ASP156
|
3.4
|
40.2
|
1.0
|
CB
|
A:SER153
|
3.4
|
29.7
|
1.0
|
CG
|
A:ASP156
|
3.5
|
38.6
|
1.0
|
N
|
A:SER153
|
3.5
|
33.8
|
1.0
|
OE1
|
A:GLN201
|
3.5
|
27.7
|
1.0
|
CD
|
A:GLN201
|
3.6
|
22.6
|
1.0
|
CB
|
A:TYR149
|
3.7
|
24.6
|
1.0
|
C
|
A:ILE151
|
3.9
|
41.1
|
1.0
|
CA
|
A:SER153
|
3.9
|
27.2
|
1.0
|
C
|
A:TYR149
|
4.0
|
35.0
|
1.0
|
C
|
A:GLU152
|
4.0
|
38.8
|
1.0
|
N
|
A:ASP156
|
4.2
|
24.9
|
1.0
|
CA
|
A:GLU152
|
4.2
|
41.2
|
1.0
|
CA
|
A:TYR149
|
4.3
|
22.9
|
1.0
|
OH
|
A:TYR200
|
4.3
|
28.2
|
1.0
|
CB
|
A:ILE155
|
4.4
|
24.6
|
1.0
|
O
|
A:SER153
|
4.4
|
26.9
|
1.0
|
C
|
A:SER153
|
4.4
|
34.0
|
1.0
|
N
|
A:TYR149
|
4.4
|
24.3
|
1.0
|
N
|
A:GLU152
|
4.6
|
38.8
|
1.0
|
CB
|
A:ASP156
|
4.6
|
30.2
|
1.0
|
O
|
A:GLU152
|
4.7
|
45.9
|
1.0
|
CD1
|
A:ILE155
|
4.8
|
36.0
|
1.0
|
CA
|
A:ASP156
|
4.8
|
24.5
|
1.0
|
N
|
A:ILE151
|
4.9
|
34.0
|
1.0
|
N
|
A:ILE155
|
4.9
|
27.6
|
1.0
|
C
|
A:ILE155
|
4.9
|
25.1
|
1.0
|
CA
|
A:ILE155
|
5.0
|
25.4
|
1.0
|
CG
|
A:TYR149
|
5.0
|
27.5
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6puq
Go back to
Magnesium Binding Sites List in 6puq
Magnesium binding site 5 out
of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg306
b:42.4
occ:1.00
|
OD2
|
A:ASP125
|
2.3
|
45.6
|
1.0
|
O
|
A:HOH459
|
2.7
|
37.5
|
1.0
|
N
|
A:THR94
|
2.9
|
20.4
|
1.0
|
OG
|
A:SER93
|
2.9
|
42.8
|
1.0
|
OD1
|
A:ASN123
|
2.9
|
21.0
|
1.0
|
CG
|
A:ASP125
|
3.0
|
37.8
|
1.0
|
O
|
A:THR94
|
3.2
|
27.0
|
1.0
|
CA
|
A:SER93
|
3.3
|
20.1
|
1.0
|
C
|
A:SER93
|
3.6
|
21.8
|
1.0
|
OD1
|
A:ASP125
|
3.6
|
48.1
|
1.0
|
CB
|
A:ASP125
|
3.7
|
23.3
|
1.0
|
CB
|
A:SER93
|
3.7
|
24.5
|
1.0
|
CG
|
A:ASN123
|
3.7
|
20.8
|
1.0
|
ND2
|
A:ASN123
|
3.7
|
24.7
|
1.0
|
CA
|
A:THR94
|
4.0
|
20.8
|
1.0
|
C
|
A:THR94
|
4.0
|
27.7
|
1.0
|
OG
|
A:SER154
|
4.3
|
38.0
|
1.0
|
CG2
|
A:THR94
|
4.3
|
22.2
|
1.0
|
N
|
A:ASP125
|
4.3
|
20.7
|
1.0
|
O
|
A:TYR92
|
4.6
|
17.7
|
1.0
|
N
|
A:SER93
|
4.6
|
20.5
|
1.0
|
CB
|
A:THR94
|
4.6
|
23.5
|
1.0
|
CA
|
A:ASP125
|
4.7
|
23.1
|
1.0
|
O
|
A:SER93
|
4.8
|
17.6
|
1.0
|
|
Reference:
L.Sjekloca,
A.R.Ferre D'amare.
Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn To Be Published.
Page generated: Tue Oct 1 15:18:44 2024
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