Sodium in PDB 4r0d: Crystal Structure of A Eukaryotic Group II Intron Lariat

The structure of Crystal Structure of A Eukaryotic Group II Intron Lariat, PDB code: 4r0d was solved by A.R.Robart, R.T.Chan, J.K.Peters, 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 (%)	23.9 / 27.4

The structure of Crystal Structure of A Eukaryotic Group II Intron Lariat also contains other interesting chemical elements:

Magnesium	(Mg)	83 atoms
Iridium	(Ir)	38 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of A Eukaryotic Group II Intron Lariat (pdb code 4r0d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Crystal Structure of A Eukaryotic Group II Intron Lariat, PDB code: 4r0d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na822 b:68.5 occ:1.00 C2' A:G550 2.7 0.7 1.0 O6 A:G421 2.7 1.0 1.0 O2' A:G550 2.8 0.3 1.0 C3' A:G550 3.2 0.7 1.0 OP2 A:A551 3.8 0.1 1.0 OP1 A:A574 3.8 0.6 1.0 MG A:MG741 3.8 0.4 1.0 C6 A:G421 3.9 0.4 1.0 C1' A:G550 4.0 0.6 1.0 C5' A:G550 4.1 0.4 1.0 C4' A:G550 4.1 0.9 1.0 O3' A:A573 4.2 0.2 1.0 O3' A:G550 4.3 0.1 1.0 O5' A:A574 4.3 94.0 1.0 P A:A574 4.4 0.8 1.0 N9 A:G550 4.4 0.0 1.0 OP2 A:G552 4.4 0.3 1.0 C8 A:G550 4.5 0.5 1.0 O4' A:G550 4.6 0.1 1.0 P A:A551 4.6 0.7 1.0 C5 A:G421 4.7 0.7 1.0 O5' A:A551 4.8 0.2 1.0 N7 A:G421 4.8 0.9 1.0 N1 A:G421 4.9 0.1 1.0 O2' A:A573 4.9 0.2 1.0

Sodium binding site 2 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na823 b:0.9 occ:1.00 N7 A:G103 4.3 0.1 1.0 O6 A:G103 4.3 0.7 1.0 N6 A:A75 4.5 0.4 1.0

Sodium binding site 3 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na824 b:0.3 occ:1.00 OP2 A:U183 2.9 0.4 1.0 O6 A:G172 3.8 0.5 1.0 MG A:MG800 4.0 43.5 1.0 P A:U183 4.2 99.7 1.0 O5' A:U183 4.4 95.7 1.0 N2 A:G180 4.4 0.5 1.0 N1 A:G180 4.4 0.7 1.0 OP1 A:A184 4.5 0.8 1.0 OP1 A:A171 4.6 92.7 1.0 OP2 A:A184 4.6 95.5 1.0 C2 A:G180 4.7 0.8 1.0 P A:A184 4.9 99.6 1.0 C6 A:G172 5.0 0.5 1.0 N4 A:C179 5.0 0.8 1.0

Sodium binding site 4 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na825 b:0.7 occ:1.00 MG A:MG790 2.6 86.5 1.0 OP1 A:C351 2.6 0.3 1.0 P A:C351 3.7 0.7 1.0 OP1 A:G350 3.7 0.0 1.0 OP2 A:C351 3.9 0.6 1.0 O3' A:G350 4.3 1.0 1.0 OP1 A:U409 4.4 0.9 1.0 OP2 A:A410 4.7 0.4 1.0 OP1 A:A410 4.8 0.8 1.0 P A:G350 5.0 1.0 1.0

Sodium binding site 5 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na826 b:0.6 occ:1.00 OP2 A:C47 3.6 0.4 1.0 C8 A:G48 3.8 0.6 1.0 N7 A:G48 4.0 0.5 1.0 C5 A:C47 4.6 0.2 1.0 OP2 A:C46 4.9 0.6 1.0 P A:C47 4.9 0.4 1.0

Sodium binding site 6 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na827 b:0.5 occ:1.00 O4' A:A115 2.2 0.2 1.0 N7 A:A152 2.4 0.7 1.0 C5 A:A152 2.6 0.2 1.0 O6 A:G153 2.7 0.6 1.0 N6 A:A152 2.9 0.1 1.0 C6 A:A152 2.9 0.7 1.0 C4' A:A115 3.0 0.3 1.0 C8 A:A152 3.2 0.7 1.0 C5' A:A115 3.2 0.3 1.0 C1' A:A115 3.4 0.7 1.0 C6 A:G153 3.5 0.1 1.0 C4 A:A152 3.6 0.5 1.0 N7 A:G153 3.7 0.2 1.0 C8 A:A115 3.7 0.9 1.0 N9 A:A115 3.8 0.3 1.0 N9 A:A152 3.9 0.7 1.0 OP2 A:A115 3.9 0.0 1.0 C5 A:G153 3.9 0.7 1.0 N1 A:A152 4.0 0.8 1.0 O4 A:U68 4.1 0.4 1.0 O5' A:A115 4.4 0.5 1.0 C3' A:A115 4.4 0.7 1.0 N3 A:A152 4.5 0.5 1.0 C2' A:A115 4.5 0.3 1.0 C2 A:A152 4.6 0.4 1.0 P A:A115 4.7 0.6 1.0 N1 A:G153 4.7 0.4 1.0 N4 A:C67 4.8 0.9 1.0 OP1 A:C116 4.8 1.0 1.0 N7 A:A115 4.9 0.6 1.0 O3' A:G114 4.9 0.1 1.0 C8 A:G153 4.9 0.4 1.0 O2' A:G114 4.9 0.3 1.0 C4 A:U68 4.9 0.8 1.0

Sodium binding site 7 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na828 b:0.7 occ:1.00 O2' A:U447 2.9 0.7 1.0 N2 A:G453 3.3 0.9 1.0 C1' A:U447 3.4 0.5 1.0 O2 A:U447 3.5 0.4 1.0 C2' A:U447 3.7 0.6 1.0 O4' A:G448 4.0 0.4 1.0 C1' A:G448 4.1 0.5 1.0 O4' A:U447 4.2 0.8 1.0 C2 A:U447 4.3 0.2 1.0 N1 A:U447 4.4 0.6 1.0 N3 A:A454 4.5 0.2 1.0 C2 A:G453 4.6 0.7 1.0 N9 A:G448 4.7 0.3 1.0 C2 A:A454 4.8 0.3 1.0 C4' A:U447 4.8 0.9 1.0 C3' A:U447 5.0 0.4 1.0

Sodium binding site 8 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na829 b:0.0 occ:1.00 O6 A:G84 4.4 0.7 1.0 N4 A:C85 4.5 1.0 1.0 N7 A:G84 4.7 0.5 1.0

Sodium binding site 9 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


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 Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na830 b:0.7 occ:1.00 N1 A:G469 3.6 0.1 1.0 O4 A:U471 3.8 0.7 1.0 N3 A:U471 4.2 0.3 1.0 N2 A:G469 4.2 0.7 1.0 O6 A:G469 4.2 0.1 1.0 C2 A:G469 4.3 0.5 1.0 C6 A:G469 4.3 0.6 1.0 N1 A:A436 4.5 0.1 1.0 C4 A:U471 4.5 0.7 1.0

Sodium binding site 10 out of 16 in the Crystal Structure of A Eukaryotic Group II Intron Lariat


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range: probe atom residue distance (Å) B Occ A:Na831 b:0.2 occ:1.00 N6 A:A594 2.9 0.1 1.0 N1 A:A595 2.9 0.9 1.0 C6 A:A595 3.2 0.3 1.0 C2 A:A595 3.3 0.3 1.0 N6 A:A595 3.6 0.3 1.0 O2 A:U610 3.6 0.1 1.0 C6 A:A594 3.9 0.7 1.0 C5 A:A595 3.9 0.2 1.0 N3 A:A595 4.0 0.2 1.0 O2' A:U610 4.2 0.3 1.0 C4 A:A595 4.2 0.2 1.0 N7 A:A594 4.4 0.3 1.0 C5 A:A594 4.4 0.9 1.0 C1' A:A611 4.6 1.0 1.0 N9 A:A611 4.6 0.6 1.0 O4' A:A611 4.6 1.0 1.0 C2' A:U610 4.7 0.6 1.0 C2 A:U610 4.7 0.3 1.0 N1 A:A594 4.8 0.8 1.0 N7 A:A595 4.9 0.4 1.0 C8 A:A611 4.9 0.7 1.0 C4 A:A611 5.0 0.9 1.0

A.R.Robart, R.T.Chan, J.K.Peters, K.R.Rajashankar, N.Toor. Crystal Structure of A Eukaryotic Group II Intron Lariat. Nature V. 514 193 2014.
ISSN: ISSN 0028-0836
PubMed: 25252982
DOI: 10.1038/NATURE13790