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Sodium in PDB 6cih: Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State

Protein crystallography data

The structure of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State, PDB code: 6cih was solved by R.T.Chan, J.K.Peters, A.R.Robart, T.Wiryaman, K.R.Rajashankar, N.Toor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.82 / 3.68
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 163.639, 255.361, 136.786, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.5

Other elements in 6cih:

The structure of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State also contains other interesting chemical elements:

Magnesium (Mg) 86 atoms
Iridium (Ir) 41 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State (pdb code 6cih). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State, PDB code: 6cih:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6cih

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Sodium binding site 1 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na822

b:93.5
occ:1.00
 O6 A:G421 2.2 0.1 1.0
C2' A:G550 3.0 1.0 1.0
O2' A:G550 3.1 0.2 1.0
C6 A:G421 3.4 0.3 1.0
MG A:MG741 3.8 0.1 1.0
C3' A:G550 3.9 0.4 1.0
OP1 A:A574 3.9 0.3 1.0
O3' A:A573 4.1 0.9 1.0
OP2 A:G550 4.1 0.5 1.0
C8 A:G550 4.2 0.7 1.0
C1' A:G550 4.2 0.5 1.0
C5 A:G421 4.3 0.9 1.0
N9 A:G550 4.4 0.7 1.0
N7 A:G421 4.4 0.7 1.0
N1 A:G421 4.5 0.2 1.0
P A:A574 4.5 0.9 1.0
C5' A:G550 4.6 0.4 1.0
O5' A:A574 4.6 0.2 1.0
O2' A:A573 4.6 0.5 1.0
C4' A:G550 4.7 0.7 1.0
OP2 A:A551 4.8 0.2 1.0
O4' A:G550 4.9 0.2 1.0
N7 A:A551 4.9 0.0 1.0
C8 A:A551 5.0 0.6 1.0

Sodium binding site 2 out of 9 in 6cih

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Sodium binding site 2 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na827

b:96.5
occ:1.00
 N7 A:A152 2.5 0.5 1.0
N6 A:A152 2.7 0.6 1.0
O4' A:A115 2.7 0.5 1.0
C5 A:A152 2.8 0.6 1.0
C6 A:A152 3.0 0.7 1.0
O6 A:G153 3.1 0.6 1.0
C4' A:A115 3.3 0.7 1.0
C5' A:A115 3.3 0.5 1.0
C8 A:A152 3.5 0.7 1.0
O4 A:U68 3.6 0.1 1.0
OP2 A:A115 3.6 0.8 1.0
C6 A:G153 3.9 0.0 1.0
N7 A:G153 4.0 0.0 1.0
C4 A:A152 4.0 0.6 1.0
C1' A:A115 4.0 0.8 1.0
N1 A:A152 4.1 0.1 1.0
C8 A:A115 4.2 0.3 1.0
C5 A:G153 4.3 0.4 1.0
N9 A:A152 4.3 0.4 1.0
O5' A:A115 4.3 0.4 1.0
O2' A:G114 4.4 0.2 1.0
O A:HOH1104 4.4 0.7 1.0
P A:A115 4.4 0.5 1.0
N9 A:A115 4.5 0.7 1.0
O3' A:G114 4.5 0.8 1.0
C4 A:U68 4.5 0.0 1.0
OP1 A:C116 4.6 0.3 1.0
C3' A:A115 4.7 0.3 1.0
C2 A:A152 4.9 0.5 1.0
N4 A:C67 4.9 0.6 1.0
N3 A:A152 4.9 0.6 1.0

Sodium binding site 3 out of 9 in 6cih

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Sodium binding site 3 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na828

b:0.1
occ:1.00
 O2' A:U447 2.6 1.0 1.0
C1' A:U447 3.5 0.7 1.0
C2' A:U447 3.6 0.7 1.0
O4' A:G448 4.0 0.2 1.0
O4' A:U447 4.1 0.3 1.0
O2 A:U447 4.1 0.1 1.0
C4' A:U447 4.6 0.5 1.0
N2 A:G453 4.7 0.3 1.0
C1' A:G448 4.7 0.5 1.0
N1 A:U447 4.8 0.1 1.0
C3' A:U447 4.8 0.3 1.0
C2 A:U447 4.9 0.8 1.0

Sodium binding site 4 out of 9 in 6cih

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Sodium binding site 4 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na829

b:0.7
occ:1.00
 O6 A:G84 3.7 0.6 1.0
N7 A:G84 4.1 0.8 1.0
N4 A:C85 4.2 0.3 1.0
N6 A:A83 4.3 0.8 1.0
C6 A:G84 4.6 0.6 1.0
C5 A:G84 4.7 0.6 1.0
C6 A:A83 4.9 0.0 1.0

Sodium binding site 5 out of 9 in 6cih

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Sodium binding site 5 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na831

b:0.6
occ:1.00
 N6 A:A594 2.3 0.1 1.0
N1 A:A595 2.8 0.7 1.0
C6 A:A595 3.3 0.5 1.0
C2 A:A595 3.3 0.0 1.0
C6 A:A594 3.5 0.6 1.0
N6 A:A595 3.6 0.3 1.0
C1' A:A611 3.8 0.0 1.0
N7 A:A594 3.8 0.8 1.0
N9 A:A611 3.8 0.2 1.0
O4' A:A611 3.9 0.2 1.0
O2 A:U610 3.9 0.4 1.0
C5 A:A594 3.9 0.8 1.0
C5 A:A595 4.1 0.5 1.0
N3 A:A595 4.2 0.4 1.0
C8 A:A611 4.2 0.7 1.0
C4 A:A611 4.2 0.1 1.0
C4 A:A595 4.4 0.8 1.0
N3 A:A611 4.6 0.2 1.0
N1 A:A594 4.6 0.7 1.0
C5 A:A611 4.7 0.3 1.0
N7 A:A611 4.7 0.2 1.0
O2' A:U610 4.8 0.1 1.0
C2' A:U610 4.8 0.7 1.0
C2 A:U610 4.9 0.3 1.0

Sodium binding site 6 out of 9 in 6cih

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Sodium binding site 6 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na832

b:0.9
occ:1.00
 O5' A:A64 2.1 0.8 1.0
O3' A:G63 2.2 1.0 1.0
P A:A64 2.5 0.7 1.0
OP2 A:A64 2.7 0.6 1.0
C5' A:A64 3.3 0.4 1.0
C8 A:A64 3.5 0.0 1.0
C3' A:G63 3.5 0.8 1.0
OP2 A:G65 3.7 0.4 1.0
OP1 A:A64 3.9 0.9 1.0
C4' A:A64 4.0 0.0 1.0
N7 A:A64 4.0 0.8 1.0
C3' A:A64 4.1 0.7 1.0
C4' A:G63 4.1 0.8 1.0
O4' A:A64 4.2 0.4 1.0
C5' A:G63 4.2 0.5 1.0
N9 A:A64 4.4 0.5 1.0
C2' A:G63 4.7 0.3 1.0
O2' A:G63 4.7 0.7 1.0
C1' A:A64 4.8 0.4 1.0
O3' A:A64 4.9 0.6 1.0
P A:G65 5.0 0.9 1.0

Sodium binding site 7 out of 9 in 6cih

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Sodium binding site 7 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na834

b:0.1
occ:1.00
 OP1 A:U294 4.6 0.4 1.0
OP2 A:A295 4.8 0.3 1.0

Sodium binding site 8 out of 9 in 6cih

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Sodium binding site 8 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na835

b:0.3
occ:1.00
 N6 A:A543 3.9 0.0 1.0
O4 A:U511 4.3 0.8 1.0
O4 A:U510 4.6 0.9 1.0

Sodium binding site 9 out of 9 in 6cih

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Sodium binding site 9 out of 9 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na837

b:0.9
occ:1.00
 OP1 A:C374 3.3 0.1 1.0
P A:C374 4.4 0.6 1.0
O3' A:A373 4.7 0.1 1.0
OP2 A:C374 4.8 0.9 1.0

Reference:

R.T.Chan, J.K.Peters, A.R.Robart, T.Wiryaman, K.R.Rajashankar, N.Toor. Structural Basis For the Second Step of Group II Intron Splicing. Nat Commun V. 9 4676 2018.
ISSN: ESSN 2041-1723
PubMed: 30410046
DOI: 10.1038/S41467-018-06678-0
Page generated: Tue Dec 15 12:02:33 2020

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