Sodium in PDB 8k0y: Crystal Structure of A Medaka Mascrna U23G

The structure of Crystal Structure of A Medaka Mascrna U23G, PDB code: 8k0y was solved by Y.He, J.Deng, X.Lin, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.08 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.36, 29.25, 98.08, 90, 118.56, 90
R / Rfree (%)	24.9 / 28.5

The structure of Crystal Structure of A Medaka Mascrna U23G also contains other interesting chemical elements:

Iridium

(Ir)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of A Medaka Mascrna U23G (pdb code 8k0y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Crystal Structure of A Medaka Mascrna U23G, PDB code: 8k0y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:57.7 occ:1.00 OP1 A:G8 2.3 80.8 1.0 O2 A:U43 2.7 99.7 1.0 OP1 A:C33 3.2 92.4 1.0 C2 A:U43 3.6 98.9 1.0 P A:G8 3.8 86.6 1.0 P A:C33 4.1 94.4 1.0 OP2 A:C33 4.2 88.1 1.0 O2' A:U43 4.3 103.9 1.0 N3 A:U43 4.4 98.6 1.0 C1' A:U43 4.4 89.6 1.0 N1 A:U43 4.4 97.5 1.0 O3' A:A32 4.4 92.8 1.0 O3' A:G7 4.5 81.1 1.0 C3' A:G7 4.5 60.4 1.0 C2' A:U43 4.6 87.2 1.0 C3' A:A32 4.7 88.6 1.0 OP2 A:G8 4.7 84.6 1.0 O5' A:G8 4.7 76.8 1.0 O2' A:G7 4.8 71.0 1.0 N7 A:G8 4.8 81.5 1.0

Sodium binding site 2 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:85.2 occ:1.00 OP2 A:C33 3.1 88.1 1.0 O5' A:C33 3.2 95.0 1.0 O3' A:A32 3.3 92.8 1.0 P A:C33 3.4 94.4 1.0 OP2 A:G8 3.6 84.6 1.0 O4' A:C33 3.6 86.7 1.0 O3' A:G7 4.4 81.1 1.0 C5' A:C33 4.4 88.3 1.0 O2' A:A32 4.4 88.8 1.0 C3' A:A32 4.5 88.6 1.0 C4' A:C33 4.5 90.4 1.0 P A:G8 4.6 86.6 1.0 C6 A:C33 4.6 61.8 1.0 C1' A:C33 4.7 78.6 1.0 C4' A:A32 4.7 93.8 1.0 O2' A:G7 4.8 71.0 1.0 OP1 A:C33 4.9 92.4 1.0

Sodium binding site 3 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:58.0 occ:1.00 O4 A:U39 2.5 72.2 1.0 C4 A:U39 3.4 62.2 1.0 C5 A:U39 3.6 59.3 1.0 OP2 A:U38 4.1 68.9 1.0 C5 A:U38 4.2 61.0 1.0 N3 A:U39 4.7 56.6 1.0 OP1 A:A41 4.8 74.0 1.0 O4 A:U38 4.9 61.1 1.0 C4 A:U38 4.9 59.1 1.0 C6 A:U39 4.9 62.1 1.0 C6 A:U38 5.0 66.5 1.0

Sodium binding site 4 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:65.8 occ:1.00 C5 A:U55 4.5 59.1 1.0 OP2 A:U55 4.5 57.4 1.0 OP1 B:G1 4.6 90.3 1.0 OP2 A:G54 4.7 68.1 1.0 O4 A:U55 4.9 45.8 1.0 N4 A:C56 4.9 51.8 1.0

Sodium binding site 5 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:85.2 occ:1.00 OP1 A:G7 3.8 76.4 1.0 O6 A:G11 4.1 107.2 1.0 N7 A:G11 4.2 108.4 1.0 OP2 A:G10 4.7 108.9 1.0 OP1 A:C45 4.7 86.6 1.0 C6 A:G11 4.9 106.5 1.0 C5 A:G11 4.9 110.4 1.0

Sodium binding site 6 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:76.0 occ:1.00 O2' B:C45 4.0 75.0 1.0 O2 B:C45 4.8 67.1 1.0

Sodium binding site 7 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:85.0 occ:1.00 OP2 B:G22 3.9 163.0 1.0 N7 B:G23 4.5 146.8 1.0 O6 B:G23 4.9 128.0 1.0

Sodium binding site 8 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:73.1 occ:1.00 N7 B:G34 4.0 62.2 1.0 NA B:NA108 4.1 69.6 1.0 OP1 B:U44 4.2 95.9 1.0 O3' B:U43 4.4 93.3 1.0 O6 B:G35 4.4 57.5 1.0 OP2 B:G34 4.6 102.3 1.0 N7 B:G35 4.6 65.5 1.0 O6 B:G34 4.7 58.9 1.0 C8 B:G34 4.8 55.4 1.0 C5 B:G34 4.9 51.6 1.0 N4 B:C33 4.9 55.1 1.0 P B:U44 4.9 87.1 1.0 C4 B:C33 5.0 65.0 1.0

Sodium binding site 9 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:83.0 occ:1.00 O6 B:G31 4.7 107.8 1.0 O6 B:G30 4.9 115.7 1.0

Sodium binding site 10 out of 13 in the Crystal Structure of A Medaka Mascrna U23G


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 Medaka Mascrna U23G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na108 b:69.6 occ:1.00 O6 B:G36 2.6 59.2 1.0 N7 B:G36 2.7 57.3 1.0 O6 B:G35 3.2 57.5 1.0 C6 B:G36 3.2 58.7 1.0 C5 B:G36 3.3 55.3 1.0 C6 B:G35 3.7 57.7 1.0 N7 B:G35 3.8 65.5 1.0 C5 B:G35 3.9 62.2 1.0 C8 B:G36 4.0 57.6 1.0 NA B:NA106 4.1 73.1 1.0 N1 B:G36 4.6 54.9 1.0 C4 B:G36 4.6 54.5 1.0 N1 B:G35 4.8 56.9 1.0 O6 B:G37 4.8 61.8 1.0 C8 B:G35 4.8 53.4 1.0 N4 B:C46 4.8 59.3 1.0 N9 B:G36 4.9 58.5 1.0

Y.He, J.Deng, X.Lin, L.Huang. Crystal Structure of Mascrna and Menrna To Be Published.