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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:

Thallium (Tl) 6 atoms

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

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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

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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

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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

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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

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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

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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

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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

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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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