Magnesium in PDB 3ggi: Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Protein crystallography data
The structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna, PDB code: 3ggi
was solved by
T.Maehigashi,
T.Moulaei,
D.Watkins,
S.Komeda,
L.D.Williams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.31 /
0.98
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
32.277,
25.204,
34.095,
90.00,
116.10,
90.00
|
R / Rfree (%)
|
11.8 /
14.4
|
Other elements in 3ggi:
The structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
(pdb code 3ggi). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Locating Monovalent Cations in One Turn of G/C Rich B-Dna, PDB code: 3ggi:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 1 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg21
b:8.5
occ:0.85
|
TL
|
A:TL102
|
1.8
|
14.1
|
0.1
|
O
|
A:HOH278
|
2.1
|
8.7
|
0.8
|
O
|
A:HOH280
|
2.1
|
8.6
|
0.8
|
O
|
A:HOH282
|
2.2
|
10.1
|
0.8
|
O
|
A:HOH281
|
2.2
|
10.4
|
0.8
|
O
|
A:HOH279
|
2.2
|
11.0
|
0.8
|
O
|
A:HOH277
|
2.2
|
12.4
|
0.8
|
O
|
A:HOH204
|
4.0
|
9.1
|
1.0
|
OP2
|
A:DA3
|
4.3
|
5.1
|
0.7
|
O6
|
A:DG4
|
4.3
|
5.8
|
1.0
|
N7
|
A:DA3
|
4.3
|
5.2
|
1.0
|
N7
|
A:DG4
|
4.4
|
6.3
|
1.0
|
O
|
A:HOH222
|
4.4
|
15.8
|
1.0
|
C8
|
A:DA3
|
4.8
|
5.1
|
1.0
|
O
|
A:HOH262
|
4.8
|
14.4
|
0.5
|
OP2
|
A:DA3
|
4.9
|
9.3
|
0.3
|
|
Magnesium binding site 2 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 2 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg22
b:8.2
occ:0.40
|
MG
|
A:MG22
|
0.0
|
8.2
|
0.4
|
O
|
A:HOH259
|
2.1
|
7.2
|
0.5
|
O
|
A:HOH284
|
2.2
|
8.9
|
0.4
|
O
|
A:HOH288
|
2.2
|
8.9
|
0.4
|
O
|
A:HOH283
|
2.2
|
9.4
|
0.4
|
O
|
A:HOH267
|
2.2
|
9.6
|
0.4
|
O
|
A:HOH285
|
2.2
|
9.7
|
0.4
|
O
|
A:HOH286
|
2.2
|
8.9
|
0.4
|
O
|
A:HOH287
|
2.2
|
6.9
|
0.4
|
TL
|
A:TL101
|
2.6
|
7.3
|
0.2
|
O
|
A:HOH283
|
3.1
|
11.4
|
0.5
|
O
|
A:HOH266
|
3.3
|
11.2
|
0.4
|
O
|
A:HOH286
|
3.3
|
10.1
|
0.5
|
O
|
A:HOH261
|
3.6
|
10.8
|
0.5
|
O
|
A:HOH208
|
4.1
|
11.6
|
1.0
|
TL
|
A:TL105
|
4.1
|
12.8
|
0.1
|
O
|
A:HOH227
|
4.3
|
12.5
|
0.5
|
MG
|
A:MG22
|
4.3
|
9.8
|
0.5
|
N7
|
A:DG9
|
4.6
|
6.0
|
1.0
|
O6
|
A:DG9
|
4.6
|
5.6
|
1.0
|
C2'
|
A:DT8
|
4.6
|
6.0
|
1.0
|
O
|
A:HOH287
|
4.6
|
8.2
|
0.5
|
|
Magnesium binding site 3 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 3 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg22
b:9.8
occ:0.50
|
MG
|
A:MG22
|
0.0
|
9.8
|
0.5
|
O
|
A:HOH287
|
2.2
|
8.2
|
0.5
|
O
|
A:HOH286
|
2.2
|
10.1
|
0.5
|
O
|
A:HOH284
|
2.2
|
8.6
|
0.5
|
O
|
A:HOH285
|
2.2
|
11.4
|
0.5
|
O
|
A:HOH283
|
2.2
|
11.4
|
0.5
|
O
|
A:HOH288
|
2.2
|
12.4
|
0.5
|
O
|
A:HOH284
|
2.8
|
8.9
|
0.4
|
TL
|
A:TL104
|
2.9
|
11.7
|
0.1
|
O
|
A:HOH285
|
3.6
|
9.7
|
0.4
|
TL
|
A:TL105
|
3.9
|
12.8
|
0.1
|
O
|
A:HOH266
|
4.1
|
11.2
|
0.4
|
MG
|
A:MG22
|
4.3
|
8.2
|
0.4
|
O
|
A:HOH288
|
4.6
|
8.9
|
0.4
|
TL
|
A:TL101
|
4.9
|
7.3
|
0.2
|
|
Magnesium binding site 4 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 4 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg23
b:9.2
occ:0.60
|
O
|
A:HOH292
|
2.2
|
10.3
|
0.6
|
O
|
A:HOH289
|
2.2
|
8.5
|
0.6
|
O
|
A:HOH290
|
2.2
|
11.3
|
0.6
|
O
|
A:HOH291
|
2.2
|
10.0
|
0.6
|
O
|
A:HOH293
|
2.2
|
10.8
|
0.6
|
O
|
A:HOH294
|
2.2
|
12.0
|
0.6
|
O
|
A:HOH245
|
3.2
|
8.8
|
0.2
|
O
|
A:HOH245
|
3.9
|
10.6
|
0.2
|
OP1
|
A:DT8
|
3.9
|
9.7
|
0.7
|
O
|
A:HOH216
|
4.1
|
12.8
|
1.0
|
OP2
|
A:DT8
|
4.2
|
7.7
|
0.3
|
O
|
A:HOH227
|
4.3
|
12.5
|
0.5
|
O
|
A:HOH252
|
4.5
|
11.8
|
0.8
|
OP2
|
A:DT8
|
4.6
|
9.0
|
0.7
|
P
|
A:DT8
|
4.7
|
7.5
|
0.7
|
O
|
A:HOH258
|
4.9
|
12.2
|
0.5
|
|
Magnesium binding site 5 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 5 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg24
b:10.0
occ:0.35
|
MG
|
A:MG24
|
0.0
|
10.0
|
0.3
|
O
|
A:HOH241
|
1.4
|
7.5
|
0.1
|
O
|
A:HOH295
|
1.6
|
5.7
|
0.1
|
O
|
A:HOH241
|
2.1
|
7.3
|
0.3
|
O
|
A:HOH297
|
2.2
|
9.9
|
0.3
|
O
|
A:HOH300
|
2.2
|
11.2
|
0.3
|
O
|
A:HOH299
|
2.2
|
10.3
|
0.3
|
O
|
A:HOH295
|
2.2
|
11.3
|
0.3
|
O
|
A:HOH298
|
2.2
|
9.4
|
0.3
|
O
|
A:HOH296
|
2.2
|
10.6
|
0.3
|
O
|
A:HOH300
|
2.2
|
9.9
|
0.3
|
O
|
A:HOH299
|
2.4
|
5.5
|
0.1
|
O
|
A:HOH240
|
2.5
|
11.6
|
0.3
|
O
|
A:HOH240
|
2.6
|
8.8
|
0.3
|
MG
|
A:MG24
|
2.6
|
5.0
|
0.1
|
O
|
A:HOH297
|
2.7
|
5.1
|
0.1
|
O
|
A:HOH275
|
3.0
|
10.3
|
0.2
|
O
|
A:HOH297
|
3.2
|
10.7
|
0.3
|
O
|
A:HOH274
|
3.4
|
7.3
|
0.2
|
O
|
A:HOH264
|
3.7
|
14.8
|
0.5
|
MG
|
A:MG24
|
3.7
|
10.0
|
0.3
|
O
|
A:HOH239
|
3.8
|
15.0
|
0.4
|
O
|
A:HOH276
|
4.0
|
7.0
|
0.2
|
O
|
A:HOH298
|
4.0
|
5.5
|
0.1
|
TL
|
A:TL106
|
4.1
|
14.7
|
0.1
|
O
|
A:HOH269
|
4.1
|
8.5
|
0.2
|
O
|
A:HOH300
|
4.2
|
5.4
|
0.1
|
O4'
|
A:DC6
|
4.2
|
6.8
|
0.7
|
O
|
A:HOH295
|
4.2
|
11.1
|
0.3
|
N2
|
A:DG5
|
4.2
|
6.3
|
0.7
|
C4'
|
A:DC6
|
4.3
|
7.1
|
0.7
|
O
|
A:HOH273
|
4.3
|
11.0
|
0.2
|
O
|
A:HOH296
|
4.4
|
11.1
|
0.3
|
O
|
A:HOH296
|
4.5
|
5.2
|
0.1
|
N2
|
A:DG4
|
4.5
|
6.5
|
1.0
|
N3
|
A:DG5
|
4.7
|
5.4
|
0.7
|
C5'
|
A:DC6
|
4.8
|
7.2
|
0.7
|
N2
|
A:DG5
|
4.9
|
7.6
|
0.3
|
C2
|
A:DG5
|
4.9
|
5.2
|
0.7
|
|
Magnesium binding site 6 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 6 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg24
b:5.0
occ:0.15
|
MG
|
A:MG24
|
0.0
|
5.0
|
0.1
|
O
|
A:HOH300
|
0.9
|
11.2
|
0.3
|
MG
|
A:MG24
|
1.3
|
10.0
|
0.3
|
O
|
A:HOH297
|
1.4
|
10.7
|
0.3
|
O
|
A:HOH300
|
1.7
|
9.9
|
0.3
|
TL
|
A:TL106
|
1.9
|
14.7
|
0.1
|
O
|
A:HOH276
|
2.0
|
7.0
|
0.2
|
O
|
A:HOH274
|
2.1
|
7.3
|
0.2
|
O
|
A:HOH299
|
2.2
|
5.5
|
0.1
|
O
|
A:HOH297
|
2.2
|
5.1
|
0.1
|
O
|
A:HOH298
|
2.2
|
5.5
|
0.1
|
O
|
A:HOH296
|
2.2
|
5.2
|
0.1
|
O
|
A:HOH300
|
2.2
|
5.4
|
0.1
|
O
|
A:HOH295
|
2.2
|
5.7
|
0.1
|
O
|
A:HOH296
|
2.3
|
11.1
|
0.3
|
MG
|
A:MG24
|
2.6
|
10.0
|
0.3
|
O
|
A:HOH295
|
2.8
|
11.1
|
0.3
|
O
|
A:HOH296
|
2.8
|
10.6
|
0.3
|
O
|
A:HOH241
|
2.9
|
7.3
|
0.3
|
O
|
A:HOH299
|
3.2
|
10.0
|
0.3
|
O
|
A:HOH239
|
3.3
|
15.0
|
0.4
|
O
|
A:HOH298
|
3.3
|
11.0
|
0.3
|
O
|
A:HOH298
|
3.4
|
9.4
|
0.3
|
O
|
A:HOH240
|
3.4
|
11.6
|
0.3
|
O
|
A:HOH297
|
3.4
|
9.9
|
0.3
|
O
|
A:HOH241
|
3.4
|
7.5
|
0.1
|
O
|
A:HOH265
|
3.7
|
11.1
|
0.4
|
O
|
A:HOH240
|
3.7
|
8.8
|
0.3
|
O
|
A:HOH295
|
3.9
|
11.3
|
0.3
|
N2
|
A:DG4
|
4.6
|
6.5
|
1.0
|
O
|
A:HOH234
|
4.6
|
9.2
|
0.3
|
O
|
A:HOH299
|
4.7
|
10.3
|
0.3
|
O
|
A:HOH234
|
4.7
|
10.1
|
0.7
|
|
Magnesium binding site 7 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 7 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg24
b:10.0
occ:0.30
|
MG
|
A:MG24
|
0.0
|
10.0
|
0.3
|
O
|
A:HOH298
|
1.3
|
5.5
|
0.1
|
MG
|
A:MG24
|
1.3
|
5.0
|
0.1
|
O
|
A:HOH274
|
1.7
|
7.3
|
0.2
|
O
|
A:HOH296
|
1.8
|
5.2
|
0.1
|
O
|
A:HOH276
|
1.9
|
7.0
|
0.2
|
TL
|
A:TL106
|
1.9
|
14.7
|
0.1
|
O
|
A:HOH300
|
2.2
|
9.9
|
0.3
|
O
|
A:HOH298
|
2.2
|
11.0
|
0.3
|
O
|
A:HOH297
|
2.2
|
10.7
|
0.3
|
O
|
A:HOH299
|
2.2
|
10.0
|
0.3
|
O
|
A:HOH295
|
2.2
|
11.1
|
0.3
|
O
|
A:HOH296
|
2.2
|
11.1
|
0.3
|
O
|
A:HOH300
|
2.2
|
11.2
|
0.3
|
O
|
A:HOH265
|
2.5
|
11.1
|
0.4
|
O
|
A:HOH300
|
2.5
|
5.4
|
0.1
|
O
|
A:HOH299
|
2.6
|
5.5
|
0.1
|
O
|
A:HOH239
|
3.1
|
15.0
|
0.4
|
O
|
A:HOH295
|
3.2
|
5.7
|
0.1
|
O
|
A:HOH296
|
3.2
|
10.6
|
0.3
|
O
|
A:HOH297
|
3.4
|
5.1
|
0.1
|
O
|
A:HOH234
|
3.7
|
9.2
|
0.3
|
O
|
A:HOH240
|
3.7
|
11.6
|
0.3
|
MG
|
A:MG24
|
3.7
|
10.0
|
0.3
|
O
|
A:HOH241
|
3.9
|
7.3
|
0.3
|
O
|
A:HOH234
|
3.9
|
10.1
|
0.7
|
O
|
A:HOH240
|
4.1
|
8.8
|
0.3
|
O
|
A:HOH297
|
4.3
|
9.9
|
0.3
|
O
|
A:HOH298
|
4.4
|
9.4
|
0.3
|
O
|
A:HOH241
|
4.5
|
7.5
|
0.1
|
N2
|
A:DG4
|
4.6
|
6.5
|
1.0
|
O
|
A:HOH248
|
5.0
|
9.6
|
0.2
|
|
Magnesium binding site 8 out
of 8 in 3ggi
Go back to
Magnesium Binding Sites List in 3ggi
Magnesium binding site 8 out
of 8 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Locating Monovalent Cations in One Turn of G/C Rich B-Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg25
b:6.4
occ:0.45
|
O
|
A:HOH302
|
2.2
|
5.9
|
0.5
|
O
|
A:HOH301
|
2.2
|
7.4
|
0.5
|
O
|
A:HOH306
|
2.2
|
6.3
|
0.5
|
O
|
A:HOH304
|
2.2
|
8.1
|
0.5
|
O
|
A:HOH303
|
2.2
|
7.9
|
0.5
|
O
|
A:HOH305
|
2.2
|
5.2
|
0.5
|
O
|
A:HOH207
|
4.1
|
10.1
|
1.0
|
O
|
A:HOH210
|
4.2
|
10.6
|
1.0
|
O
|
A:HOH217
|
4.2
|
13.5
|
1.0
|
O2
|
A:DC1
|
4.3
|
5.9
|
1.0
|
C5'
|
A:DC2
|
4.4
|
6.2
|
0.7
|
O4'
|
A:DC2
|
4.6
|
5.5
|
1.0
|
C5'
|
A:DC2
|
4.6
|
5.9
|
0.3
|
C4'
|
A:DC2
|
4.7
|
5.5
|
1.0
|
|
Reference:
T.Maehigashi,
T.Moulaei,
D.Watkins,
S.Komeda,
L.D.Williams.
Locating Monovalent Cations in One Turn of G/C Rich B-Dna To Be Published.
Page generated: Wed Aug 14 14:45:34 2024
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