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Rubidium 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:

Magnesium (Mg) 8 atoms

Rubidium Binding Sites:

The binding sites of Rubidium 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 Rubidium atom.
In total 2 binding sites of Rubidium where determined in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna, PDB code: 3ggk:
Jump to Rubidium binding site number: 1; 2;

Rubidium binding site 1 out of 2 in 3ggk

Go back to Rubidium Binding Sites List in 3ggk
Rubidium binding site 1 out of 2 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb 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:Rb101

b:8.7
occ:0.15
O A:HOH301 2.3 9.1 0.3
RB A:RB102 2.8 11.2 0.2
O6 A:DG10 2.9 5.5 1.0
O A:HOH260 3.1 10.5 0.6
O A:HOH282 3.1 11.1 0.2
O A:HOH299 3.5 7.0 0.5
O A:HOH302 3.5 7.0 0.5
O A:HOH299 3.6 10.2 0.3
C6 A:DG10 3.8 4.7 1.0
MG A:MG22 4.0 8.6 0.3
N7 A:DG10 4.1 5.2 1.0
O A:HOH303 4.3 10.2 0.3
C5 A:DG10 4.3 4.7 1.0
MG A:MG22 4.6 5.7 0.5
O A:HOH238 4.8 12.5 0.5
O A:HOH300 4.8 7.8 0.5
O A:HOH302 4.8 9.4 0.3
O A:HOH238 4.9 7.2 0.2
N7 A:DG9 4.9 6.0 1.0

Rubidium binding site 2 out of 2 in 3ggk

Go back to Rubidium Binding Sites List in 3ggk
Rubidium binding site 2 out of 2 in the Locating Monovalent Cations in One Turn of G/C Rich B-Dna


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb 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:Rb102

b:11.2
occ:0.18
O A:HOH302 0.9 7.0 0.5
MG A:MG22 2.4 5.7 0.5
O A:HOH238 2.7 7.2 0.2
O A:HOH299 2.7 7.0 0.5
RB A:RB101 2.8 8.7 0.1
O A:HOH269 2.8 6.7 0.3
N7 A:DG9 3.0 6.0 1.0
O6 A:DG10 3.1 5.5 1.0
O A:HOH301 3.1 6.4 0.5
O A:HOH238 3.1 12.5 0.5
O A:HOH299 3.2 10.2 0.3
O A:HOH300 3.3 7.8 0.5
O A:HOH282 3.4 11.1 0.2
O A:HOH270 3.7 8.2 0.3
O A:HOH301 3.7 9.1 0.3
O A:HOH298 3.8 7.8 0.5
C8 A:DG9 3.8 6.3 1.0
C5 A:DG9 3.9 5.1 1.0
O6 A:DG9 4.0 5.6 1.0
C6 A:DG10 4.1 4.7 1.0
C6 A:DG9 4.3 5.2 1.0
O A:HOH302 4.3 9.4 0.3
O A:HOH260 4.3 10.5 0.6
N7 A:DG10 4.5 5.2 1.0
MG A:MG22 4.5 8.6 0.3
O A:HOH303 4.5 6.7 0.5
C5 A:DG10 4.7 4.7 1.0
O A:HOH205 4.8 6.8 1.0
C2' A:DT8 4.9 6.2 1.0
O A:HOH219 5.0 9.0 0.5
N9 A:DG9 5.0 5.8 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 Dec 16 02:06:46 2020

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