Atomistry » Sodium » PDB 6chr-6ctn » 6chr
Atomistry »
  Sodium »
    PDB 6chr-6ctn »
      6chr »

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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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

Go back to Sodium Binding Sites List in 6chr
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: Tue Oct 8 06:35:41 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy