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Magnesium in PDB 3ggk: 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: 3ggk 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) 30.60 / 0.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 32.135, 25.156, 34.113, 90.00, 116.24, 90.00
R / Rfree (%) 11.9 / 13.4

Other elements in 3ggk:

The structure of Locating Monovalent Cations in One Turn of G/C Rich B-Dna also contains other interesting chemical elements:

Rubidium (Rb) 2 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 3ggk). 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: 3ggk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ggk

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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:7.8
occ:0.90
 O A:HOH295 2.1 7.9 0.9
O A:HOH293 2.1 7.8 0.9
O A:HOH294 2.1 10.1 0.9
O A:HOH296 2.2 9.8 0.9
O A:HOH297 2.2 9.2 0.9
O A:HOH292 2.2 11.8 0.9
O A:HOH202 4.0 9.1 1.0
O A:HOH208 4.0 11.1 1.0
O A:HOH287 4.2 10.9 0.2
OP2 A:DA3 4.3 4.8 0.6
O6 A:DG4 4.3 5.6 1.0
N7 A:DA3 4.3 5.0 1.0
N7 A:DG4 4.4 5.9 1.0
O A:HOH213 4.4 15.3 1.0
C8 A:DA3 4.8 5.2 1.0
OP2 A:DA3 4.8 9.5 0.4
O A:HOH251 5.0 17.0 0.8

Magnesium binding site 2 out of 8 in 3ggk

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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:5.7
occ:0.50
 MG A:MG22 0.0 5.7 0.5
O A:HOH270 1.9 8.2 0.3
O A:HOH269 1.9 6.7 0.3
O A:HOH303 2.2 6.7 0.5
O A:HOH302 2.2 7.0 0.5
O A:HOH300 2.2 7.8 0.5
O A:HOH299 2.2 7.0 0.5
O A:HOH301 2.2 6.4 0.5
O A:HOH298 2.2 7.8 0.5
RB A:RB102 2.4 11.2 0.2
O A:HOH299 3.0 10.2 0.3
O A:HOH302 3.1 9.4 0.3
O A:HOH238 3.4 7.2 0.2
O A:HOH211 3.9 7.4 1.0
O A:HOH205 4.0 6.8 1.0
O A:HOH282 4.1 11.1 0.2
O A:HOH201 4.1 9.2 1.0
O A:HOH238 4.1 12.5 0.5
MG A:MG22 4.2 8.6 0.3
O A:HOH248 4.4 10.9 0.2
O A:HOH219 4.4 9.0 0.5
O A:HOH301 4.4 9.1 0.3
N7 A:DG9 4.5 6.0 1.0
O6 A:DG9 4.5 5.6 1.0
C2' A:DT8 4.6 6.2 1.0
RB A:RB101 4.6 8.7 0.1
O A:HOH260 4.7 10.5 0.6
O A:HOH300 5.0 10.7 0.3

Magnesium binding site 3 out of 8 in 3ggk

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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:8.6
occ:0.30
 MG A:MG22 0.0 8.6 0.3
O A:HOH260 1.7 10.5 0.6
O A:HOH277 2.0 11.9 0.3
O A:HOH303 2.2 10.2 0.3
O A:HOH301 2.2 9.1 0.3
O A:HOH302 2.2 9.4 0.3
O A:HOH300 2.2 10.7 0.3
O A:HOH299 2.2 10.2 0.3
O A:HOH298 2.2 9.0 0.3
O A:HOH299 2.7 7.0 0.5
O A:HOH282 2.8 11.1 0.2
O A:HOH283 2.9 11.6 0.2
O A:HOH300 3.5 7.8 0.5
RB A:RB101 4.0 8.7 0.1
MG A:MG22 4.2 5.7 0.5
O A:HOH205 4.4 6.8 1.0
O A:HOH303 4.5 6.7 0.5
RB A:RB102 4.5 11.2 0.2
O A:HOH302 4.9 7.0 0.5

Magnesium binding site 4 out of 8 in 3ggk

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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:6.2
occ:0.50
 O A:HOH307 2.2 7.5 0.5
O A:HOH304 2.2 6.3 0.5
O A:HOH308 2.2 7.6 0.5
O A:HOH306 2.2 7.0 0.5
O A:HOH305 2.2 8.3 0.5
O A:HOH309 2.2 8.1 0.5
O A:HOH266 2.7 17.4 0.5
O A:HOH267 3.1 14.2 0.5
OP1 A:DT8 4.0 9.7 0.7
O A:HOH262 4.1 14.4 0.5
O A:HOH272 4.2 6.3 0.3
OP2 A:DT8 4.3 6.1 0.3
O A:HOH219 4.3 9.0 0.5
O A:HOH217 4.3 8.6 0.8
O A:HOH249 4.4 9.8 0.8
O A:HOH284 4.4 8.4 0.2
OP2 A:DT8 4.7 9.1 0.7
P A:DT8 4.8 7.8 0.7
O A:HOH248 4.8 10.9 0.2
O A:HOH224 4.9 10.5 0.5

Magnesium binding site 5 out of 8 in 3ggk

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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:8.4
occ:0.30
 MG A:MG24 0.0 8.4 0.3
O A:HOH310 1.9 6.3 0.2
O A:HOH315 2.1 8.5 0.3
O A:HOH275 2.2 6.4 0.3
O A:HOH314 2.2 9.3 0.3
O A:HOH310 2.2 9.0 0.3
O A:HOH311 2.2 10.0 0.3
O A:HOH315 2.2 8.9 0.3
O A:HOH312 2.2 9.7 0.3
O A:HOH313 2.2 9.2 0.3
O A:HOH276 2.2 13.7 0.3
O A:HOH314 2.3 6.7 0.2
O A:HOH261 2.5 12.4 0.5
MG A:MG24 2.7 6.5 0.2
O A:HOH312 2.7 6.4 0.2
O A:HOH274 3.1 14.7 0.3
O A:HOH312 3.2 9.3 0.3
O A:HOH291 3.4 5.3 0.1
O A:HOH280 3.6 11.3 0.2
MG A:MG24 3.7 7.9 0.3
O A:HOH241 4.0 11.1 0.2
O A:HOH273 4.0 9.4 0.3
O A:HOH268 4.1 6.4 0.4
O A:HOH313 4.1 6.7 0.2
O A:HOH310 4.1 9.1 0.3
O4' A:DC6 4.2 6.8 0.7
N2 A:DG5 4.2 6.3 0.7
C4' A:DC6 4.3 7.2 0.7
O A:HOH244 4.3 8.8 0.2
O A:HOH245 4.3 8.8 0.2
O A:HOH315 4.3 7.0 0.2
O A:HOH241 4.5 10.6 0.2
O A:HOH311 4.5 7.3 0.3
N2 A:DG4 4.5 6.4 1.0
O A:HOH311 4.5 6.5 0.2
N3 A:DG5 4.7 5.8 0.7
C5' A:DC6 4.7 7.5 0.7
N2 A:DG5 4.8 7.2 0.3
C2 A:DG5 4.9 5.3 0.7

Magnesium binding site 6 out of 8 in 3ggk

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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:6.5
occ:0.25
 MG A:MG24 0.0 6.5 0.2
O A:HOH311 0.8 10.0 0.3
MG A:MG24 1.3 7.9 0.3
O A:HOH312 1.5 9.3 0.3
O A:HOH315 1.8 8.5 0.3
O A:HOH268 1.8 6.4 0.4
O A:HOH291 2.1 5.3 0.1
O A:HOH311 2.2 7.3 0.3
O A:HOH273 2.2 9.4 0.3
O A:HOH314 2.2 6.7 0.2
O A:HOH315 2.2 7.0 0.2
O A:HOH311 2.2 6.5 0.2
O A:HOH312 2.2 6.4 0.2
O A:HOH313 2.2 6.7 0.2
O A:HOH310 2.2 6.3 0.2
MG A:MG24 2.7 8.4 0.3
O A:HOH310 2.9 9.1 0.3
O A:HOH313 3.0 9.2 0.3
O A:HOH314 3.1 9.3 0.3
O A:HOH275 3.1 6.4 0.3
O A:HOH313 3.3 9.8 0.3
O A:HOH315 3.4 8.9 0.3
O A:HOH241 3.5 11.1 0.2
O A:HOH314 3.5 9.3 0.3
O A:HOH239 3.7 12.7 0.4
O A:HOH261 3.8 12.4 0.5
O A:HOH312 3.9 9.7 0.3
O A:HOH276 4.0 13.7 0.3
O A:HOH241 4.2 10.6 0.2
O A:HOH239 4.3 14.8 0.3
O A:HOH229 4.5 10.4 0.3
O A:HOH285 4.5 15.0 0.2
N2 A:DG4 4.6 6.4 1.0
O A:HOH229 4.7 9.0 0.7
O A:HOH310 4.8 9.0 0.3

Magnesium binding site 7 out of 8 in 3ggk

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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:7.9
occ:0.30
 MG A:MG24 0.0 7.9 0.3
MG A:MG24 1.3 6.5 0.2
O A:HOH313 1.3 6.7 0.2
O A:HOH291 1.6 5.3 0.1
O A:HOH311 1.8 6.5 0.2
O A:HOH273 2.0 9.4 0.3
O A:HOH311 2.1 10.0 0.3
O A:HOH268 2.1 6.4 0.4
O A:HOH311 2.2 7.3 0.3
O A:HOH315 2.2 8.5 0.3
O A:HOH313 2.2 9.8 0.3
O A:HOH310 2.2 9.1 0.3
O A:HOH314 2.2 9.3 0.3
O A:HOH312 2.2 9.3 0.3
O A:HOH314 2.4 6.7 0.2
O A:HOH239 2.6 12.7 0.4
O A:HOH315 2.6 7.0 0.2
O A:HOH310 3.1 6.3 0.2
O A:HOH241 3.2 11.1 0.2
O A:HOH313 3.3 9.2 0.3
O A:HOH312 3.3 6.4 0.2
O A:HOH239 3.3 14.8 0.3
O A:HOH285 3.4 15.0 0.2
O A:HOH229 3.6 10.4 0.3
MG A:MG24 3.7 8.4 0.3
O A:HOH229 3.9 9.0 0.7
O A:HOH261 4.1 12.4 0.5
O A:HOH275 4.1 6.4 0.3
O A:HOH241 4.2 10.6 0.2
O A:HOH314 4.2 9.3 0.3
O A:HOH315 4.3 8.9 0.3
N2 A:DG4 4.6 6.4 1.0
O A:HOH228 4.7 10.0 0.7

Magnesium binding site 8 out of 8 in 3ggk

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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:6.0
occ:0.40
 O A:HOH290 1.7 10.9 0.2
O A:HOH317 2.2 5.3 0.4
O A:HOH316 2.2 7.5 0.4
O A:HOH321 2.2 6.7 0.4
O A:HOH319 2.2 7.5 0.4
O A:HOH318 2.2 8.5 0.4
O A:HOH320 2.2 5.9 0.4
O A:HOH227 4.0 7.7 0.2
O A:HOH210 4.1 14.6 1.0
O A:HOH226 4.2 9.1 0.7
O A:HOH226 4.2 7.7 0.2
O2 A:DC1 4.3 6.2 1.0
C5' A:DC2 4.4 6.8 0.7
O4' A:DC2 4.5 5.7 1.0
C5' A:DC2 4.6 6.2 0.3
C4' A:DC2 4.6 5.7 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 14:45:48 2024

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