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Magnesium in PDB 3u89: Crystal Structure of One Turn of G/C Rich B-Dna Revisited

Protein crystallography data

The structure of Crystal Structure of One Turn of G/C Rich B-Dna Revisited, PDB code: 3u89 was solved by T.Maehigashi, K.K.Woods, T.Moulaei, S.Komeda, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.06 / 0.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 32.136, 25.172, 34.094, 90.00, 116.25, 90.00
R / Rfree (%) 10.3 / 12.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited (pdb code 3u89). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited, PDB code: 3u89:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3u89

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Magnesium binding site 1 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg21

b:9.2
occ:0.90
 O A:HOH284 2.1 9.3 0.9
O A:HOH287 2.1 11.4 0.9
O A:HOH286 2.1 9.1 0.9
O A:HOH283 2.1 14.0 0.9
O A:HOH288 2.1 11.0 0.9
O A:HOH285 2.1 12.7 0.9
O A:HOH202 4.0 10.3 1.0
O A:HOH224 4.0 11.8 0.8
O A:HOH244 4.2 17.9 0.2
O6 A:DG4 4.3 6.6 1.0
N7 A:DA3 4.3 5.8 1.0
OP2 A:DA3 4.4 7.0 0.8
N7 A:DG4 4.4 6.9 1.0
O A:HOH223 4.4 20.7 1.0
O A:HOH249 4.7 12.8 0.2
C8 A:DA3 4.8 5.9 1.0
O A:HOH217 4.9 25.5 1.0

Magnesium binding site 2 out of 8 in 3u89

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Magnesium binding site 2 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg22

b:8.8
occ:0.60
 MG A:MG22 0.0 8.8 0.6
O A:HOH289 2.1 9.6 0.6
O A:HOH291 2.1 10.9 0.6
O A:HOH272 2.1 7.1 0.3
O A:HOH292 2.1 8.9 0.6
O A:HOH290 2.1 10.1 0.6
O A:HOH294 2.1 9.9 0.6
O A:HOH293 2.1 9.5 0.6
O A:HOH281 2.5 12.1 0.2
O A:HOH293 3.0 5.3 0.1
O A:HOH290 3.2 8.8 0.1
O A:HOH273 3.3 10.0 0.2
O A:HOH207 3.9 8.2 1.0
O A:HOH201 4.1 10.8 1.0
O A:HOH247 4.2 14.2 0.2
MG A:MG22 4.2 6.8 0.1
O A:HOH232 4.3 11.0 0.5
O A:HOH278 4.5 18.5 0.2
N7 A:DG9 4.5 7.6 1.0
O6 A:DG9 4.5 6.5 1.0
C2' A:DT8 4.6 7.4 1.0
O A:HOH292 4.6 7.8 0.1
O A:HOH291 4.8 8.7 0.1
O A:HOH262 4.9 14.2 0.5

Magnesium binding site 3 out of 8 in 3u89

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Magnesium binding site 3 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg22

b:6.8
occ:0.15
 MG A:MG22 0.0 6.8 0.1
O A:HOH267 1.8 14.9 0.5
O A:HOH278 1.8 18.5 0.2
O A:HOH291 2.1 8.7 0.1
O A:HOH292 2.1 7.8 0.1
O A:HOH294 2.1 7.9 0.1
O A:HOH293 2.1 5.3 0.1
O A:HOH289 2.1 6.4 0.1
O A:HOH290 2.1 8.8 0.1
O A:HOH290 2.8 10.1 0.6
O A:HOH291 3.5 10.9 0.6
O A:HOH247 3.8 14.2 0.2
O A:HOH281 4.1 12.1 0.2
MG A:MG22 4.2 8.8 0.6
O A:HOH262 4.3 14.2 0.5
O A:HOH207 4.5 8.2 1.0
O A:HOH294 4.5 9.9 0.6
O A:HOH293 4.9 9.5 0.6

Magnesium binding site 4 out of 8 in 3u89

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Magnesium binding site 4 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg23

b:7.8
occ:0.40
 O A:HOH256 1.9 83.8 0.5
O A:HOH299 2.1 9.2 0.4
O A:HOH296 2.1 9.4 0.4
O A:HOH298 2.1 8.1 0.4
O A:HOH295 2.1 7.4 0.4
O A:HOH300 2.1 10.1 0.4
O A:HOH297 2.1 8.4 0.4
O A:HOH264 2.4 23.3 0.5
O A:HOH241 3.4 14.3 0.3
OP1 A:DT8 3.9 11.5 0.8
O A:HOH279 4.0 18.3 0.2
O A:HOH225 4.2 12.7 0.8
OP2 A:DT8 4.3 7.5 0.2
O A:HOH238 4.3 9.4 0.5
O A:HOH241 4.4 23.1 0.3
O A:HOH232 4.4 11.0 0.5
O A:HOH251 4.5 13.4 0.8
OP2 A:DT8 4.7 10.6 0.8
O A:HOH238 4.7 19.9 0.5
P A:DT8 4.7 8.5 0.8
O A:HOH250 4.9 10.0 0.2

Magnesium binding site 5 out of 8 in 3u89

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Magnesium binding site 5 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg24

b:10.8
occ:0.35
 MG A:MG24 0.0 10.8 0.3
O A:HOH301 1.7 6.8 0.1
O A:HOH303 2.1 11.4 0.3
O A:HOH306 2.1 12.4 0.3
O A:HOH305 2.1 10.7 0.3
O A:HOH304 2.1 11.4 0.3
O A:HOH301 2.1 12.9 0.3
O A:HOH302 2.1 10.7 0.3
O A:HOH305 2.2 3.9 0.1
O A:HOH269 2.2 8.4 0.4
O A:HOH306 2.3 11.7 0.3
O A:HOH271 2.3 16.1 0.3
O A:HOH257 2.5 13.9 0.5
MG A:MG24 2.6 6.2 0.1
O A:HOH303 2.7 6.1 0.1
O A:HOH303 3.2 13.2 0.3
O A:HOH282 3.4 8.4 0.1
MG A:MG24 3.7 11.6 0.3
O A:HOH304 3.9 6.5 0.1
O A:HOH259 3.9 18.0 0.5
O A:HOH276 4.0 19.3 0.2
O A:HOH268 4.0 11.9 0.4
O A:HOH301 4.1 14.2 0.3
O A:HOH306 4.1 6.4 0.1
O A:HOH270 4.2 8.2 0.5
O4' A:DC6 4.2 7.6 0.8
O A:HOH243 4.2 19.0 0.2
N2 A:DG5 4.3 7.3 0.8
C4' A:DC6 4.3 8.2 0.8
O A:HOH246 4.3 11.7 0.2
O A:HOH302 4.4 6.1 0.1
O A:HOH302 4.5 12.2 0.3
N2 A:DG4 4.5 7.3 1.0
O A:HOH243 4.5 14.2 0.2
N3 A:DG5 4.6 7.0 0.8
N2 A:DG5 4.7 10.2 0.2
C5' A:DC6 4.7 8.6 0.8
C2 A:DG5 4.9 5.9 0.8
N3 A:DG5 4.9 7.3 0.2

Magnesium binding site 6 out of 8 in 3u89

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Magnesium binding site 6 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg24

b:6.2
occ:0.15
 MG A:MG24 0.0 6.2 0.1
O A:HOH306 0.8 12.4 0.3
O A:HOH303 1.4 13.2 0.3
MG A:MG24 1.4 11.6 0.3
O A:HOH306 1.7 11.7 0.3
O A:HOH270 2.0 8.2 0.5
O A:HOH305 2.0 3.9 0.1
O A:HOH306 2.1 6.4 0.1
O A:HOH304 2.1 6.5 0.1
O A:HOH303 2.1 6.1 0.1
O A:HOH301 2.1 6.8 0.1
O A:HOH302 2.1 6.1 0.1
O A:HOH282 2.1 8.4 0.1
O A:HOH302 2.2 12.2 0.3
O A:HOH268 2.2 11.9 0.4
MG A:MG24 2.6 10.8 0.3
O A:HOH301 2.8 14.2 0.3
O A:HOH302 3.0 10.7 0.3
O A:HOH269 3.1 8.4 0.4
O A:HOH305 3.1 12.9 0.3
O A:HOH304 3.2 11.4 0.3
O A:HOH304 3.3 13.2 0.3
O A:HOH303 3.4 11.4 0.3
O A:HOH276 3.6 19.3 0.2
O A:HOH301 3.7 12.9 0.3
O A:HOH257 3.7 13.9 0.5
O A:HOH255 3.8 19.2 0.6
O A:HOH271 4.0 16.1 0.3
O A:HOH233 4.5 11.6 0.3
N2 A:DG4 4.6 7.3 1.0
O A:HOH305 4.6 10.7 0.3
O A:HOH233 4.8 11.0 0.7
O A:HOH243 4.9 14.2 0.2

Magnesium binding site 7 out of 8 in 3u89

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Magnesium binding site 7 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg24

b:11.6
occ:0.35
 MG A:MG24 0.0 11.6 0.3
O A:HOH304 1.2 6.5 0.1
MG A:MG24 1.4 6.2 0.1
O A:HOH282 1.6 8.4 0.1
O A:HOH302 1.7 6.1 0.1
O A:HOH268 2.0 11.9 0.4
O A:HOH304 2.1 13.2 0.3
O A:HOH306 2.1 11.7 0.3
O A:HOH305 2.1 12.9 0.3
O A:HOH301 2.1 14.2 0.3
O A:HOH302 2.1 12.2 0.3
O A:HOH303 2.1 13.2 0.3
O A:HOH270 2.2 8.2 0.5
O A:HOH306 2.2 12.4 0.3
O A:HOH305 2.4 3.9 0.1
O A:HOH255 2.6 19.2 0.6
O A:HOH306 2.6 6.4 0.1
O A:HOH301 3.1 6.8 0.1
O A:HOH276 3.3 19.3 0.2
O A:HOH302 3.3 10.7 0.3
O A:HOH303 3.3 6.1 0.1
O A:HOH233 3.5 11.6 0.3
MG A:MG24 3.7 10.8 0.3
O A:HOH233 3.9 11.0 0.7
O A:HOH257 4.1 13.9 0.5
O A:HOH303 4.2 11.4 0.3
O A:HOH269 4.2 8.4 0.4
O A:HOH304 4.3 11.4 0.3
N2 A:DG4 4.6 7.3 1.0
O A:HOH221 4.7 14.8 1.0
O A:HOH245 4.9 12.4 0.2

Magnesium binding site 8 out of 8 in 3u89

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Magnesium binding site 8 out of 8 in the Crystal Structure of One Turn of G/C Rich B-Dna Revisited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of One Turn of G/C Rich B-Dna Revisited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg25

b:6.4
occ:0.40
 O A:HOH310 2.1 9.1 0.4
O A:HOH312 2.1 7.6 0.4
O A:HOH309 2.1 8.7 0.4
O A:HOH307 2.1 8.7 0.4
O A:HOH311 2.1 6.2 0.4
O A:HOH308 2.1 5.9 0.4
O A:HOH219 4.2 17.3 1.0
O A:HOH209 4.2 13.0 1.0
O2 A:DC1 4.3 7.0 1.0
C5' A:DC2 4.3 7.2 0.6
O4' A:DC2 4.5 6.1 1.0
C5' A:DC2 4.6 6.6 0.4
C4' A:DC2 4.6 6.4 1.0

Reference:

T.Maehigashi, C.Hsiao, K.K.Woods, T.Moulaei, N.V.Hud, L.D.Williams. B-Dna Structure Is Intrinsically Polymorphic: Even at the Level of Base Pair Positions. Nucleic Acids Res. V. 40 3714 2012.
ISSN: ISSN 0305-1048
PubMed: 22180536
DOI: 10.1093/NAR/GKR1168
Page generated: Thu Aug 15 12:25:37 2024

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