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Caesium in PDB 4e8r: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+, PDB code: 4e8r 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) 48.50 / 3.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.200, 94.915, 225.710, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.8

Other elements in 4e8r:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 23 atoms

Caesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Caesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ (pdb code 4e8r). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 35 binding sites of Caesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+, PDB code: 4e8r:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Caesium binding site 1 out of 35 in 4e8r

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Caesium binding site 1 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs424

b:0.4
occ:1.00
O6 A:G15 3.0 0.6 1.0
O A:HOH918 3.1 0.5 1.0
O6 A:G16 3.2 0.9 1.0
O4 A:U255 3.4 0.3 1.0
O4 A:U256 3.5 0.0 1.0
C6 A:G15 4.0 0.3 1.0
N3 A:U256 4.1 0.0 1.0
C6 A:G16 4.1 0.8 1.0
C4 A:U256 4.2 0.4 1.0
N7 A:G15 4.2 0.7 1.0
N7 A:G16 4.3 0.8 1.0
C4 A:U255 4.3 0.5 1.0
N3 A:U255 4.4 0.8 1.0
C5 A:G15 4.4 0.9 1.0
N6 A:A254 4.4 0.7 1.0
C5 A:G16 4.6 0.3 1.0
O6 A:G14 4.9 1.0 1.0

Caesium binding site 2 out of 35 in 4e8r

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Caesium binding site 2 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs425

b:0.3
occ:0.61
O6 A:G385 2.9 0.2 1.0
O A:HOH919 3.1 90.0 1.0
O4 A:U384 3.7 0.3 1.0
N7 A:G385 3.8 1.0 1.0
C6 A:G385 3.8 0.9 1.0
O6 A:G359 3.9 0.8 1.0
O6 A:G386 4.1 0.6 1.0
C5 A:G385 4.1 0.9 1.0
N4 A:C358 4.2 0.6 1.0
N3 A:U384 4.2 0.0 1.0
N2 A:G288 4.3 0.4 1.0
C4 A:U384 4.3 0.2 1.0
C6 A:G359 4.6 0.1 1.0
N1 A:G288 4.7 0.2 1.0
C2 A:G288 4.7 0.9 1.0
C6 A:G386 4.8 0.4 1.0

Caesium binding site 3 out of 35 in 4e8r

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Caesium binding site 3 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs426

b:0.5
occ:0.59
O2' A:A134 3.3 0.4 1.0
OP1 A:G133 3.3 0.1 1.0
OP1 A:G135 3.6 0.2 1.0
OP1 A:C361 3.8 0.1 1.0
O3' A:A134 3.8 0.1 1.0
O3' A:C360 4.3 0.7 1.0
P A:G133 4.3 0.3 1.0
OP2 A:G133 4.4 0.6 1.0
P A:G135 4.5 0.5 1.0
C2' A:A134 4.5 0.8 1.0
C3' A:A134 4.6 0.1 1.0
P A:C361 4.7 0.4 1.0
C4' A:A134 4.7 0.2 1.0
O3' A:U132 4.9 0.4 1.0

Caesium binding site 4 out of 35 in 4e8r

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Caesium binding site 4 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs427

b:0.6
occ:0.87
O2' A:G58 3.3 76.1 1.0
O6 A:G48 3.9 92.1 1.0
MG A:MG407 4.0 63.9 1.0
C2' A:G58 4.1 73.6 1.0
OP2 A:G46 4.7 0.1 1.0
OP2 A:U59 4.8 71.7 1.0
C3' A:G58 4.9 75.6 1.0

Caesium binding site 5 out of 35 in 4e8r

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Caesium binding site 5 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs428

b:0.1
occ:0.60
O6 A:G29 3.2 82.1 1.0
O6 A:G30 3.5 98.0 1.0
N7 A:G29 3.7 89.7 1.0
C6 A:G29 3.9 80.0 1.0
N7 A:G30 4.0 89.6 1.0
C5 A:G29 4.1 82.7 1.0
C6 A:G30 4.3 90.5 1.0
C5 A:G30 4.5 91.3 1.0
O A:HOH924 4.6 43.6 1.0
N4 A:C39 4.7 0.1 1.0
C8 A:G29 4.8 83.6 1.0
N4 A:C38 4.8 97.8 1.0
O2' A:A35 4.9 1.0 1.0

Caesium binding site 6 out of 35 in 4e8r

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Caesium binding site 6 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs429

b:0.4
occ:0.52
O6 A:G275 2.9 0.9 1.0
O6 A:G274 3.1 97.1 1.0
O A:HOH902 3.2 69.1 1.0
O4 A:U273 3.2 88.6 1.0
C6 A:G275 3.7 0.3 1.0
N1 A:G275 4.0 0.5 1.0
C4 A:U273 4.1 88.7 1.0
N4 A:C279 4.2 98.9 1.0
C6 A:G274 4.2 92.0 1.0
N7 A:G274 4.5 87.8 1.0
N6 A:A280 4.5 85.3 1.0
C5 A:U273 4.7 91.4 1.0
C5 A:G274 4.7 88.4 1.0
C5 A:G275 4.8 0.1 1.0
N3 A:U273 5.0 89.3 1.0

Caesium binding site 7 out of 35 in 4e8r

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Caesium binding site 7 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs430

b:0.9
occ:0.45
OP1 A:C112 2.6 0.2 1.0
O3' A:G111 3.2 0.3 1.0
O2 A:U13 3.4 0.8 1.0
P A:C112 3.5 0.5 1.0
OP1 A:A110 3.6 99.2 1.0
O8 A:EPE462 3.6 91.8 0.5
O5' A:A110 3.9 0.1 1.0
P A:A110 4.0 0.8 1.0
OP2 A:A110 4.0 0.8 1.0
C2 A:U13 4.1 0.5 1.0
C5' A:C112 4.2 0.6 1.0
O5' A:C112 4.4 0.4 1.0
O5' A:G111 4.4 0.4 1.0
N3 A:U13 4.4 0.8 1.0
C3' A:G111 4.5 0.3 1.0
O2' A:G111 4.6 0.7 1.0
OP1 A:G111 4.7 0.5 1.0
C4' A:G111 4.7 0.4 1.0
OP2 A:C112 4.8 0.7 1.0
C8 A:EPE462 5.0 0.9 0.5

Caesium binding site 8 out of 35 in 4e8r

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Caesium binding site 8 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs431

b:0.6
occ:0.65
O6 A:G266 2.7 92.2 1.0
O A:HOH906 3.0 71.0 1.0
O A:HOH907 3.3 74.9 1.0
C6 A:G266 3.3 91.1 1.0
N7 A:G267 3.4 98.0 1.0
N7 A:G266 3.7 96.9 1.0
C5 A:G266 3.7 94.4 1.0
O6 A:G267 3.8 95.9 1.0
C5 A:G267 4.3 93.0 1.0
N1 A:G266 4.4 88.0 1.0
C6 A:G267 4.4 94.2 1.0
C8 A:G267 4.5 0.8 1.0
C8 A:G266 4.8 97.3 1.0
C4 A:G266 4.9 92.5 1.0

Caesium binding site 9 out of 35 in 4e8r

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Caesium binding site 9 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs432

b:0.9
occ:0.36
N7 A:G320 3.0 0.5 1.0
OP2 A:G320 3.4 0.4 1.0
O6 A:G321 3.6 0.3 1.0
N1 A:A297 3.8 0.7 1.0
C8 A:G320 3.9 97.6 1.0
C5 A:G320 4.0 0.3 1.0
N7 A:G321 4.0 0.1 1.0
O6 A:G320 4.1 0.6 1.0
C6 A:G321 4.3 0.8 1.0
C6 A:G320 4.4 0.1 1.0
N6 A:A297 4.5 0.6 1.0
C5 A:G321 4.5 0.9 1.0
C2 A:A297 4.5 0.1 1.0
C6 A:A297 4.6 0.5 1.0
P A:G320 4.8 0.2 1.0

Caesium binding site 10 out of 35 in 4e8r

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Caesium binding site 10 out of 35 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Cs+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs433

b:0.6
occ:0.81
O2' A:A333 2.9 0.5 1.0
O6 A:G336 3.2 0.6 1.0
O6 A:G335 3.4 0.4 1.0
C2' A:A333 3.8 0.3 1.0
O A:HOH910 3.9 94.6 1.0
N4 A:C346 4.0 0.6 1.0
C6 A:G336 4.1 0.9 1.0
N4 A:C345 4.2 0.1 1.0
C6 A:G335 4.3 0.4 1.0
N7 A:G336 4.4 0.6 1.0
C3' A:A333 4.5 0.8 1.0
N7 A:G335 4.5 0.3 1.0
C5 A:G336 4.6 0.3 1.0
O3' A:A333 4.7 0.0 1.0
C5 A:G335 4.7 0.8 1.0

Reference:

M.Marcia, A.M.Pyle. Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033
Page generated: Sun Dec 13 10:56:17 2020

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