Sodium in PDB 6t3n: Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon, PDB code: 6t3n was solved by M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.15 / 3.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.895, 95.271, 217.844, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 24.2

Other elements in 6t3n:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon also contains other interesting chemical elements:

Magnesium (Mg) 19 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon (pdb code 6t3n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon, PDB code: 6t3n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6t3n

Go back to Sodium Binding Sites List in 6t3n
Sodium binding site 1 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na420

b:0.8
occ:1.00
O6 A:G320 3.4 0.6 1.0
O6 A:G321 3.5 0.3 1.0
N7 A:G320 3.6 0.2 1.0
N1 A:A297 3.8 0.1 1.0
OP2 A:G320 3.9 0.4 1.0
C6 A:G320 4.1 0.7 1.0
C5 A:G320 4.2 0.3 1.0
OP2 A:A319 4.2 0.4 1.0
C6 A:G321 4.4 0.1 1.0
OP1 A:A319 4.5 98.3 1.0
C2 A:A297 4.5 0.0 1.0
N6 A:A297 4.6 0.4 1.0
N7 A:G321 4.6 0.7 1.0
P A:A319 4.7 99.7 1.0
O5' A:A319 4.7 0.6 1.0
C6 A:A297 4.7 0.2 1.0
C8 A:G320 4.7 0.2 1.0
C5 A:G321 4.8 0.8 1.0

Sodium binding site 2 out of 7 in 6t3n

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Sodium binding site 2 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na421

b:0.3
occ:1.00
OP2 A:G14 2.9 0.1 1.0
OP2 A:G15 3.4 83.8 1.0
O5' A:G14 3.5 87.2 1.0
P A:G14 3.8 0.7 1.0
O A:HOH521 3.9 0.2 1.0
N7 A:G14 4.2 0.8 1.0
C8 A:G14 4.4 0.7 1.0
N7 A:G15 4.5 0.7 1.0
O2' A:A12 4.5 0.2 1.0
C3' A:G14 4.7 85.0 1.0
C5' A:G14 4.7 93.3 1.0
C5 A:G14 4.8 0.8 1.0
P A:G15 4.8 94.2 1.0
O3' A:U13 4.9 0.1 1.0
OP1 A:G14 4.9 0.1 1.0

Sodium binding site 3 out of 7 in 6t3n

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Sodium binding site 3 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na422

b:98.6
occ:1.00
O6 A:G28 2.9 65.3 1.0
N7 A:G28 3.2 72.6 1.0
C6 A:G28 3.7 67.0 1.0
C5 A:G28 3.8 70.0 1.0
OP2 A:A27 3.9 0.7 1.0
N2 A:G41 4.1 88.8 1.0
C8 A:G28 4.4 76.1 1.0
OP1 A:U26 4.5 89.2 1.0
O5' A:A25 4.8 77.7 1.0
C3' A:A25 4.8 93.6 1.0
C5' A:A25 4.8 0.5 1.0
OP1 A:A25 5.0 80.4 1.0
C2 A:G41 5.0 85.5 1.0

Sodium binding site 4 out of 7 in 6t3n

Go back to Sodium Binding Sites List in 6t3n
Sodium binding site 4 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na423

b:0.8
occ:1.00
N7 A:G264 3.0 0.5 1.0
C5 A:C263 3.6 0.8 1.0
OP2 A:G264 3.9 0.6 1.0
C8 A:G264 3.9 0.6 1.0
C4 A:C263 4.0 0.1 1.0
C6 A:C263 4.1 98.2 1.0
C5 A:G264 4.1 91.0 1.0
O6 A:G264 4.1 0.9 1.0
N4 A:C263 4.2 0.8 1.0
C6 A:G264 4.5 94.7 1.0
OP2 A:C263 4.6 74.3 1.0
N3 A:C263 4.6 92.6 1.0
N1 A:C263 4.7 94.7 1.0
N7 A:G265 4.8 0.4 1.0
O6 A:G265 5.0 1.0 1.0
C2 A:C263 5.0 99.8 1.0

Sodium binding site 5 out of 7 in 6t3n

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Sodium binding site 5 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na424

b:0.8
occ:1.00
O4 A:U195 3.2 93.8 1.0
C4 A:U195 4.2 89.9 1.0
O6 A:G194 4.3 0.9 1.0
N6 A:A171 4.5 73.1 1.0
C5 A:U195 4.6 84.9 1.0

Sodium binding site 6 out of 7 in 6t3n

Go back to Sodium Binding Sites List in 6t3n
Sodium binding site 6 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na425

b:1.0
occ:1.00
OP2 A:G269 2.5 0.4 1.0
O A:HOH525 2.9 0.4 1.0
P A:G269 3.6 0.4 1.0
OP1 A:G269 4.0 0.7 1.0
O5' A:A268 4.1 0.0 1.0
C5' A:A268 4.2 0.7 1.0
O3' A:A268 4.3 0.3 1.0
C3' A:A268 4.9 0.6 1.0
O5' A:G269 5.0 96.8 1.0

Sodium binding site 7 out of 7 in 6t3n

Go back to Sodium Binding Sites List in 6t3n
Sodium binding site 7 out of 7 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na427

b:0.3
occ:1.00
O6 A:G266 2.3 0.9 1.0
C6 A:G266 3.4 0.5 1.0
O6 A:G265 4.0 1.0 1.0
C5 A:G266 4.1 0.3 1.0
N7 A:G266 4.1 0.1 1.0
O6 A:G267 4.2 0.6 1.0
N1 A:G266 4.5 0.6 1.0
N7 A:G267 4.6 0.5 1.0
N4 A:C6 4.6 0.7 1.0
C6 A:G265 4.8 0.5 1.0

Reference:

J.Manigrasso, I.Chillon, V.Genna, S.Somarowthu, A.M.Pyle, M.De Vivo, M.Marcia. Visualizing Group II Intron Dynamics Between the First and Second Steps of Splicing To Be Published.
Page generated: Tue Dec 15 13:02:14 2020

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