Sodium in PDB 8k2z: Crystal Structure of A Human Mascrna A2G

The structure of Crystal Structure of A Human Mascrna A2G, PDB code: 8k2z 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)	28.67 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.365, 30.111, 89.353, 90, 105.73, 90
R / Rfree (%)	27.7 / 29.2

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of A Human Mascrna A2G (pdb code 8k2z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of A Human Mascrna A2G, PDB code: 8k2z:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:51.6 occ:1.00 O4 A:U40 3.6 67.8 1.0 C4 A:U40 4.6 68.3 1.0

Sodium binding site 2 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:46.6 occ:1.00 O A:HOH203 3.0 69.0 1.0 OP2 A:A44 3.3 95.7 1.0 NA A:NA107 3.9 68.8 1.0 O2' A:A43 4.0 68.1 1.0 O6 A:G38 4.5 67.3 1.0 N7 A:G37 4.5 65.8 1.0 P A:A44 4.6 93.2 1.0 O6 A:G37 4.8 70.5 1.0 O A:HOH207 4.9 54.7 1.0 N7 A:G38 4.9 66.5 1.0 C2' A:A43 5.0 85.5 1.0

Sodium binding site 3 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:67.4 occ:1.00 O A:HOH208 3.5 70.7 1.0 OP2 A:G10 3.8 83.0 1.0 N7 A:G11 3.9 85.2 1.0 OP1 A:G7 4.0 93.3 1.0 O3' A:U6 4.0 80.6 1.0 O6 A:G11 4.2 84.8 1.0 C5' A:U6 4.3 80.5 1.0 N7 A:G10 4.4 85.2 1.0 NA A:NA104 4.5 50.2 1.0 P A:G7 4.6 88.1 1.0 C8 A:G10 4.6 85.2 1.0 C4' A:U6 4.7 92.4 1.0 C5 A:G11 4.8 85.8 1.0 C6 A:G11 4.8 87.8 1.0 OP2 A:G11 4.9 92.0 1.0 C8 A:G11 4.9 87.4 1.0 P A:G10 4.9 99.5 1.0 O5' A:G10 5.0 98.5 1.0 C3' A:U6 5.0 86.5 1.0

Sodium binding site 4 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:50.2 occ:1.00 OP1 A:G7 2.3 93.3 1.0 O A:HOH208 2.5 70.7 1.0 P A:G7 3.6 88.1 1.0 OP2 A:G7 4.2 81.2 1.0 O6 A:G11 4.2 84.8 1.0 NA A:NA103 4.5 67.4 1.0 O5' A:G7 4.5 87.3 1.0 O4 A:U9 4.6 85.7 1.0 C5 A:U9 4.6 84.5 1.0 O3' A:U6 4.7 80.6 1.0 N3 A:A44 4.8 91.2 1.0 C5' A:G7 4.8 83.2 1.0 C4 A:U9 4.9 85.4 1.0 O2' A:A44 4.9 69.8 1.0 OP2 A:U9 5.0 88.5 1.0

Sodium binding site 5 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:68.8 occ:1.00 OP1 A:G14 3.2 111.3 1.0 N7 A:G14 3.2 92.0 1.0 C8 A:G14 3.7 90.1 1.0 O2' A:U13 4.0 93.5 1.0 C5 A:G14 4.5 90.3 1.0 P A:G14 4.6 125.9 1.0 N6 A:A42 4.6 81.3 1.0 O3' A:U13 4.9 90.8 1.0

Sodium binding site 6 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:55.5 occ:1.00 O4 A:U3 2.1 75.1 1.0 O6 A:G55 2.3 69.0 1.0 O6 A:G2 2.7 73.9 1.0 C4 A:U3 3.2 75.8 1.0 C6 A:G2 3.5 75.6 1.0 C6 A:G55 3.5 69.6 1.0 N7 A:G2 3.6 74.8 1.0 O A:HOH209 3.7 58.8 1.0 C5 A:G2 3.8 76.6 1.0 C5 A:U3 4.0 75.7 1.0 N1 A:G55 4.1 70.1 1.0 N3 A:U3 4.1 75.2 1.0 O6 A:G4 4.2 75.8 1.0 N4 A:C54 4.3 68.6 1.0 O4 A:U56 4.3 69.3 1.0 O6 A:G1 4.4 73.5 1.0 N1 A:G2 4.6 74.5 1.0 N3 A:U56 4.6 70.1 1.0 C6 A:G1 4.7 73.7 1.0 C5 A:G55 4.7 70.0 1.0 C8 A:G2 4.8 75.2 1.0 C4 A:U56 4.9 69.9 1.0

Sodium binding site 7 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:68.8 occ:1.00 O6 A:G37 2.6 70.5 1.0 O A:HOH203 2.8 69.0 1.0 O6 A:G36 3.2 65.8 1.0 C6 A:G37 3.6 66.2 1.0 N4 A:C47 3.7 67.2 1.0 NA A:NA102 3.9 46.6 1.0 N7 A:G37 4.0 65.8 1.0 OP1 A:U45 4.0 78.1 1.0 N4 A:C48 4.1 66.3 1.0 C5 A:G37 4.1 65.9 1.0 O6 A:G38 4.2 67.3 1.0 C6 A:G36 4.3 65.6 1.0 N4 A:C46 4.6 68.2 1.0 OP2 A:U45 4.7 80.4 1.0 N1 A:G37 4.7 66.3 1.0 P A:U45 4.8 83.3 1.0 O2' A:A43 4.9 68.1 1.0 C6 A:G38 4.9 67.2 1.0 N7 A:G36 4.9 65.6 1.0 C5 A:G36 5.0 65.5 1.0 C4 A:C47 5.0 67.4 1.0 OP2 A:A44 5.0 95.7 1.0

Sodium binding site 8 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:33.7 occ:1.00 O B:HOH208 1.9 39.3 1.0 O4 B:U40 2.6 57.2 1.0 O B:HOH207 2.6 36.4 1.0 C4 B:U40 3.6 56.2 1.0 C5 B:U40 3.9 55.8 1.0 OP2 B:U39 4.3 69.0 1.0 C5 B:U39 4.7 52.4 1.0 N3 B:U40 4.9 56.5 1.0

Sodium binding site 9 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:56.1 occ:1.00 N7 B:G14 3.1 55.5 1.0 C8 B:G14 3.8 56.1 1.0 C5 B:G14 4.3 56.3 1.0 N6 B:A42 4.6 58.8 1.0 O6 B:G14 4.6 55.7 1.0 O2' B:U13 4.7 107.4 1.0 OP2 B:G14 4.8 82.2 1.0 C6 B:G14 4.9 56.4 1.0

Sodium binding site 10 out of 12 in the Crystal Structure of A Human Mascrna A2G


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 Human Mascrna A2G within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:46.9 occ:1.00 OP2 B:A44 4.2 89.3 1.0 O6 B:G38 4.2 60.4 1.0 N7 B:G38 4.6 51.6 1.0 O2' B:A43 4.6 65.4 1.0 O6 B:G37 4.7 53.3 1.0 N7 B:G37 4.9 58.9 1.0

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