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Sodium in PDB 6chr: Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State)

Protein crystallography data

The structure of Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State), PDB code: 6chr 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) 50.08 / 3.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.015, 256.893, 137.232, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.3

Other elements in 6chr:

The structure of Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State) also contains other interesting chemical elements:

Magnesium (Mg) 82 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State) (pdb code 6chr). 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 with An Intact 3' Splice Site (Pre-2S State), PDB code: 6chr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6chr

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Sodium binding site 1 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na742

b:0.6
occ:1.00
 OP2 A:G174 2.5 0.7 1.0
P A:G174 3.8 0.2 1.0
O5' A:G174 3.9 0.8 1.0
C8 A:G174 4.2 0.5 1.0
N7 A:G174 4.2 1.0 1.0
OP2 A:C173 4.4 0.8 1.0
O5' A:C173 4.5 0.1 1.0
OP2 A:A175 4.6 0.2 1.0
OP1 A:G174 4.7 0.2 1.0
O3' A:C173 4.9 0.9 1.0
P A:C173 4.9 1.0 1.0
C3' A:C173 4.9 0.1 1.0

Sodium binding site 2 out of 9 in 6chr

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Sodium binding site 2 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na743

b:0.5
occ:1.00
 OP2 A:A551 2.4 0.1 1.0
O6 A:G421 3.1 0.1 1.0
OP1 A:A574 3.5 0.3 1.0
O2 A:U549 3.8 0.6 1.0
MG A:MG701 3.8 0.5 1.0
P A:A551 3.8 0.1 1.0
C6 A:G421 4.1 0.4 1.0
O3' A:A573 4.2 0.7 1.0
N7 A:G421 4.2 1.0 1.0
C2 A:U549 4.4 0.7 1.0
P A:A574 4.5 0.2 1.0
O5' A:A551 4.5 0.2 1.0
O2' A:U549 4.5 0.9 1.0
C5 A:G421 4.5 0.7 1.0
C1' A:U549 4.7 0.1 1.0
C3' A:G550 4.7 0.7 1.0
O3' A:G550 4.7 0.0 1.0
OP1 A:A551 4.7 0.9 1.0
N1 A:U549 4.9 0.5 1.0
C5' A:G550 5.0 0.5 1.0
O5' A:A574 5.0 1.0 1.0

Sodium binding site 3 out of 9 in 6chr

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Sodium binding site 3 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na744

b:0.4
occ:1.00
 OP2 A:G18 2.5 0.1 1.0
O A:HOH1013 3.0 0.8 1.0
P A:G18 3.8 0.5 1.0
O A:HOH864 4.3 0.2 1.0
OP1 A:G18 4.4 0.9 1.0
O5' A:G18 4.4 1.0 1.0
MG A:MG767 4.7 0.6 1.0
O A:HOH960 4.7 0.6 1.0
O5' A:A17 4.8 0.9 1.0
N7 A:G18 5.0 1.0 1.0
OP2 A:A17 5.0 0.5 1.0

Sodium binding site 4 out of 9 in 6chr

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Sodium binding site 4 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na745

b:0.1
occ:1.00
 OP2 A:G453 3.0 0.2 1.0
P A:G453 4.1 0.1 1.0
OP1 A:G453 4.3 0.8 1.0
N7 A:G453 4.3 0.1 1.0
OP1 A:C452 4.4 0.7 1.0
C8 A:G453 4.8 0.1 1.0
O5' A:G453 4.8 0.1 1.0

Sodium binding site 5 out of 9 in 6chr

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Sodium binding site 5 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na746

b:0.7
occ:1.00
 O4 A:U563 3.1 0.1 1.0
O6 A:G564 3.5 0.8 1.0
N7 A:A562 3.8 0.8 1.0
O A:HOH968 4.0 0.3 1.0
O A:HOH895 4.0 0.5 1.0
O A:HOH979 4.1 0.3 1.0
N6 A:A562 4.1 0.8 1.0
C4 A:U563 4.2 0.2 1.0
C5 A:A562 4.5 0.8 1.0
C6 A:G564 4.6 0.7 1.0
C8 A:A562 4.7 0.4 1.0
C6 A:A562 4.7 0.9 1.0
C5 A:U563 4.7 0.6 1.0
N7 A:G561 4.8 0.7 1.0
MG A:MG787 4.9 0.7 1.0

Sodium binding site 6 out of 9 in 6chr

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Sodium binding site 6 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na747

b:0.2
occ:1.00
 O5' A:A348 3.1 0.6 1.0
OP2 A:A348 3.3 0.2 1.0
P A:A348 3.4 0.0 1.0
OP1 A:A348 3.5 1.0 1.0
C5' A:A348 4.0 0.8 1.0
OP1 A:G431 4.2 0.2 1.0
OP1 A:C488 4.9 0.9 1.0
C4' A:A348 4.9 0.1 1.0
O3' A:U347 5.0 0.3 1.0

Sodium binding site 7 out of 9 in 6chr

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Sodium binding site 7 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na748

b:0.5
occ:1.00
 OP1 A:U581 3.1 0.7 1.0
OP2 A:U581 3.6 0.5 1.0
P A:U581 3.7 0.8 1.0
O3' A:G580 4.2 0.7 1.0
OP1 A:G580 4.6 0.4 1.0
C5' A:G580 4.9 0.7 1.0

Sodium binding site 8 out of 9 in 6chr

Go back to Sodium Binding Sites List in 6chr
Sodium binding site 8 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na749

b:0.1
occ:1.00
 OP2 A:C583 3.0 0.0 1.0
OP1 A:C583 3.1 0.9 1.0
P A:C583 3.3 0.2 1.0
O3' A:U582 3.5 0.2 1.0
C5' A:U582 3.7 0.1 1.0
O2' A:C179 4.2 0.2 1.0
C3' A:U582 4.3 0.6 1.0
C4' A:U582 4.3 0.3 1.0
OP1 A:U582 4.5 0.0 1.0
O5' A:C583 4.8 0.6 1.0
O5' A:U582 4.9 0.9 1.0

Sodium binding site 9 out of 9 in 6chr

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Sodium binding site 9 out of 9 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na750

b:0.8
occ:1.00
 C5' A:G463 2.9 0.8 1.0
C5' A:A462 3.1 0.9 1.0
O5' A:A462 3.4 0.9 1.0
O5' A:G463 3.5 0.8 1.0
C3' A:A462 3.8 0.7 1.0
C4' A:G463 3.9 0.1 1.0
C4' A:A462 3.9 0.9 1.0
OP1 A:A462 4.3 0.5 1.0
P A:A462 4.4 0.4 1.0
O3' A:A462 4.7 0.8 1.0
P A:G463 4.7 1.0 1.0
C2' A:A462 4.8 0.7 1.0
O3' A:G463 4.8 0.7 1.0
C3' A:G463 4.8 0.8 1.0
OP2 A:A462 4.9 0.8 1.0
O4' A:G463 4.9 0.0 1.0
OP2 A:G463 5.0 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: Mon Aug 18 04:02:17 2025

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