Sodium in PDB 6ldm: Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1

The structure of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1, PDB code: 6ldm was solved by A.Traczyk, D.J.Gill, W.L.Chong, D.Rhodes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.09 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.680, 70.200, 64.850, 90.00, 97.72, 90.00
R / Rfree (%)	20.3 / 23.3

The structure of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 also contains other interesting chemical elements:

Potassium

(K)

5 atoms

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 (pdb code 6ldm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1, PDB code: 6ldm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:92.1 occ:1.00 CG1 A:VAL409 2.4 66.9 1.0 NA B:NA109 2.5 73.2 1.0 ND1 A:HIS405 3.0 48.5 1.0 O4 B:DT18 3.4 80.1 1.0 O6 B:DG13 3.4 52.9 1.0 CD A:ARG408 3.6 76.3 1.0 C6 B:DG13 3.6 52.8 1.0 CG A:ARG408 3.7 70.3 1.0 CB A:VAL409 3.8 65.0 1.0 CG A:HIS405 3.9 47.8 1.0 CE1 A:HIS405 3.9 48.7 1.0 CB A:HIS405 4.0 49.0 1.0 O A:HIS405 4.1 52.2 1.0 N1 B:DG13 4.1 53.0 1.0 NE A:ARG408 4.1 81.2 1.0 C5 B:DG13 4.1 53.0 1.0 C4 B:DT18 4.2 80.0 1.0 CG2 A:VAL409 4.2 65.3 1.0 N3 B:DT18 4.2 80.2 1.0 CA A:HIS405 4.3 49.9 1.0 C A:HIS405 4.6 51.6 1.0 N1 B:DG9 4.6 64.1 1.0 N7 B:DG13 4.6 52.0 1.0 N A:VAL409 4.7 61.6 1.0 O6 B:DG17 4.7 66.3 1.0 O6 B:DG9 4.7 62.9 1.0 CA A:VAL409 4.8 63.0 1.0 C2 B:DG13 4.8 53.4 1.0 C4 B:DG13 4.8 53.0 1.0 C6 B:DG9 4.9 63.7 1.0 CZ A:ARG408 5.0 83.5 1.0

Sodium binding site 2 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:64.0 occ:1.00 OD1 A:ASN401 2.5 61.4 1.0 NH1 A:ARG404 3.0 59.3 1.0 NE2 A:HIS405 3.3 48.3 1.0 CG A:ASN401 3.5 59.5 1.0 CD A:ARG404 3.5 52.2 1.0 CD2 A:HIS405 3.5 47.9 1.0 CG A:ARG404 3.5 52.5 1.0 O A:HOH706 3.7 54.8 1.0 CB A:ARG404 3.8 50.5 1.0 ND2 A:ASN401 3.9 58.7 1.0 CE1 A:HIS405 4.0 48.7 1.0 CZ A:ARG404 4.1 58.0 1.0 NE A:ARG404 4.2 54.8 1.0 CG A:HIS405 4.3 47.8 1.0 O A:ASN401 4.4 51.2 1.0 ND1 A:HIS405 4.5 48.5 1.0 CB A:ASN401 4.7 54.8 1.0 N A:HIS405 4.7 50.0 1.0 CA A:ASN401 4.8 53.1 1.0 C A:ARG404 4.8 50.4 1.0 CD2 A:HIS385 4.8 51.9 1.0 NE2 A:HIS385 4.9 53.5 1.0 CA A:ARG404 4.9 49.1 1.0

Sodium binding site 3 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:79.4 occ:1.00 O B:HOH213 2.6 45.3 1.0 O A:ALA361 3.0 68.5 1.0 CE1 A:PHE363 3.2 64.6 1.0 CD1 A:PHE363 3.4 64.7 1.0 OP2 B:DG13 3.5 64.5 1.0 C2' B:DG12 3.6 62.2 1.0 C3' B:DG12 3.7 63.2 1.0 CA A:SER362 4.1 70.8 1.0 C A:ALA361 4.1 69.4 1.0 O B:HOH205 4.1 46.2 1.0 O5' B:DG12 4.2 67.6 1.0 OP2 B:DG12 4.3 67.7 1.0 CZ A:PHE363 4.4 64.4 1.0 NA B:NA106 4.5 66.4 1.0 O A:HOH701 4.5 48.1 1.0 N A:SER362 4.5 69.7 1.0 O3' B:DG12 4.6 63.8 1.0 C A:SER362 4.6 70.6 1.0 P B:DG13 4.7 63.6 1.0 CG A:PHE363 4.7 65.4 1.0 N A:PHE363 4.7 69.7 1.0 CE1 A:HIS398 4.8 64.0 1.0 C4' B:DG12 4.8 64.1 1.0 P B:DG12 4.9 67.9 1.0 NH1 A:ARG406 4.9 63.7 1.0 C5' B:DG12 5.0 66.0 1.0

Sodium binding site 4 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:66.4 occ:1.00 O B:HOH201 2.4 56.1 1.0 N3 B:DG9 3.2 65.3 1.0 C2' B:DG11 3.6 64.2 1.0 O4' B:DG9 3.7 68.8 1.0 C8 B:DG12 3.7 59.4 1.0 N2 B:DG8 3.7 62.7 1.0 C1' B:DG9 3.8 67.7 1.0 C5' B:DT10 3.9 74.8 1.0 C2 B:DG9 3.9 64.9 1.0 C4 B:DG9 4.0 65.7 1.0 N2 B:DG9 4.0 65.1 1.0 N7 B:DG12 4.0 59.3 1.0 O A:HOH701 4.0 48.1 1.0 O B:HOH213 4.2 45.3 1.0 N9 B:DG9 4.3 66.4 1.0 NA A:NA605 4.5 79.4 1.0 C4' B:DT10 4.5 76.3 1.0 O3' B:DG9 4.6 70.4 1.0 C4' B:DG9 4.6 69.7 1.0 C3' B:DG11 4.6 65.3 1.0 OP1 B:DG11 4.7 70.1 1.0 OP2 B:DG12 4.7 67.7 1.0 C2 B:DG8 4.8 63.2 1.0 O5' B:DT10 4.8 73.5 1.0 N9 B:DG12 4.9 59.7 1.0 C1' B:DG11 4.9 63.2 1.0 C3' B:DT10 4.9 76.1 1.0 O3' B:DT10 5.0 73.8 1.0 O5' B:DG12 5.0 67.6 1.0 N9 B:DG11 5.0 61.5 1.0

Sodium binding site 5 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:82.8 occ:1.00 O B:HOH207 2.4 54.6 1.0 O B:HOH202 2.7 57.6 1.0 N2 B:DG3 3.1 63.3 1.0 O4' B:DG4 3.8 70.6 1.0 C2 B:DG3 4.1 63.5 1.0 N3 B:DG3 4.2 64.4 1.0 OP1 B:DG7 4.5 82.1 1.0 C1' B:DG4 4.7 68.4 1.0 C4' B:DG4 4.8 71.8 1.0 OP2 B:DG7 4.9 82.1 1.0 N7 B:DG7 5.0 63.5 1.0

Sodium binding site 6 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na108 b:79.8 occ:1.00 OP1 B:DG7 2.7 82.1 1.0 O4' B:DG5 2.7 72.2 1.0 N2 B:DG4 3.2 61.4 1.0 C4' B:DG5 3.5 74.3 1.0 C1' B:DG5 3.6 70.9 1.0 O3' B:DT6 3.7 84.0 1.0 C2' B:DG7 3.7 71.8 1.0 C3' B:DT6 3.7 85.9 1.0 C5' B:DT6 3.7 85.3 1.0 O B:HOH202 3.7 57.6 1.0 P B:DG7 3.8 81.9 1.0 NA B:NA110 3.8 87.1 1.0 C4' B:DT6 3.8 86.4 1.0 N3 B:DG4 4.0 62.5 1.0 C2 B:DG4 4.1 61.8 1.0 N9 B:DG5 4.1 67.5 1.0 N3 B:DG5 4.2 64.5 1.0 C4 B:DG5 4.3 65.4 1.0 C8 B:DG7 4.4 64.8 1.0 C5' B:DG5 4.4 74.9 1.0 N7 B:DG8 4.6 66.7 1.0 C3' B:DG7 4.6 74.8 1.0 C3' B:DG5 4.6 75.7 1.0 O5' B:DT6 4.7 84.5 1.0 C8 B:DG8 4.7 67.8 1.0 O3' B:DG5 4.7 79.9 1.0 N9 B:DG7 4.7 66.3 1.0 O5' B:DG7 4.7 80.0 1.0 C1' B:DG7 4.8 70.1 1.0 C2' B:DG5 4.8 72.7 1.0 C5' B:DG7 4.9 77.5 1.0 OP2 B:DG7 4.9 82.1 1.0 C8 B:DG5 4.9 66.3 1.0

Sodium binding site 7 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na109 b:73.2 occ:1.00 NA A:NA603 2.5 92.1 1.0 N3 B:DT18 2.9 80.2 1.0 O6 B:DG17 3.0 66.3 1.0 O B:HOH209 3.1 74.2 1.0 O6 B:DG5 3.2 63.8 1.0 CG1 A:VAL409 3.2 66.9 1.0 O4 B:DT18 3.3 80.1 1.0 O6 B:DG13 3.4 52.9 1.0 C6 B:DG17 3.5 66.1 1.0 C4 B:DT18 3.6 80.0 1.0 O6 B:DG9 3.7 62.9 1.0 N1 B:DG17 3.8 65.5 1.0 K B:K101 3.8 51.5 1.0 C2 B:DT18 3.9 80.4 1.0 C6 B:DG5 3.9 63.8 1.0 O2 B:DT18 3.9 80.7 1.0 C6 B:DG13 4.1 52.8 1.0 N1 B:DG13 4.2 53.0 1.0 N1 B:DG5 4.2 63.5 1.0 C6 B:DG9 4.5 63.7 1.0 CB A:VAL409 4.5 65.0 1.0 NE A:ARG408 4.5 81.2 1.0 C5 B:DG17 4.6 66.7 1.0 N1 B:DG9 4.8 64.1 1.0 CD A:ARG408 4.8 76.3 1.0 C2 B:DG17 4.8 65.5 1.0 CZ A:ARG408 4.9 83.5 1.0 C5 B:DG5 4.9 65.0 1.0 C5 B:DT18 5.0 79.8 1.0

Sodium binding site 8 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na110 b:87.1 occ:1.00 OP2 B:DG8 2.2 78.1 1.0 C4' B:DT6 2.6 86.4 1.0 C5' B:DT6 3.1 85.3 1.0 O4' B:DT6 3.3 88.0 1.0 P B:DG8 3.5 77.9 1.0 O3' B:DT6 3.7 84.0 1.0 C3' B:DG7 3.7 74.8 1.0 C2' B:DG7 3.7 71.8 1.0 C3' B:DT6 3.7 85.9 1.0 NA B:NA108 3.8 79.8 1.0 O5' B:DG8 3.8 76.7 1.0 O3' B:DG7 4.1 76.7 1.0 C1' B:DT6 4.4 89.1 1.0 O5' B:DT6 4.5 84.5 1.0 OP1 B:DG8 4.8 78.6 1.0 C2' B:DT6 4.8 87.4 1.0 OP1 B:DG7 4.9 82.1 1.0 P B:DG7 4.9 81.9 1.0

Sodium binding site 9 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na111 b:85.6 occ:1.00 OP1 B:DG11 2.7 70.1 1.0 N3 B:DG8 3.1 64.8 1.0 O B:HOH210 3.1 64.5 1.0 N2 B:DG7 3.2 61.0 1.0 O B:HOH201 3.3 56.1 1.0 O4' B:DG8 3.6 72.2 1.0 C1' B:DG8 3.6 70.6 1.0 C2 B:DG8 3.8 63.2 1.0 C4 B:DG8 3.8 66.4 1.0 C8 B:DG11 3.8 60.5 1.0 N7 B:DG11 3.9 60.5 1.0 N2 B:DG8 3.9 62.7 1.0 P B:DG11 3.9 71.0 1.0 N9 B:DG8 4.1 68.5 1.0 O4' B:DG9 4.2 68.8 1.0 C2 B:DG7 4.3 61.0 1.0 O5' B:DG11 4.3 68.2 1.0 C4' B:DG8 4.3 73.3 1.0 C5' B:DG9 4.5 70.9 1.0 N3 B:DG7 4.6 62.3 1.0 OP2 B:DG11 4.7 72.1 1.0 C4' B:DG9 4.8 69.7 1.0 N1 B:DG8 4.9 63.1 1.0 C2' B:DG8 5.0 71.4 1.0

Sodium binding site 10 out of 11 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na112 b:92.5 occ:1.00 N3 B:DG16 3.0 62.9 1.0 N2 B:DG15 3.2 54.5 1.0 O B:HOH206 3.3 51.8 1.0 O4' B:DG16 3.6 62.8 1.0 C1' B:DG16 3.7 62.9 1.0 C4 B:DG16 3.8 63.0 1.0 C8 B:DG3 3.8 66.0 1.0 C2 B:DG16 3.8 62.0 1.0 N2 B:DG16 4.0 61.4 1.0 N9 B:DG16 4.0 62.9 1.0 N7 B:DG3 4.0 65.0 1.0 K B:K104 4.3 97.5 1.0 C2 B:DG15 4.3 55.1 1.0 C4' B:DG16 4.5 63.5 1.0 N3 B:DG15 4.7 56.0 1.0 O4' B:DG17 4.9 69.9 1.0 N1 B:DG16 4.9 62.2 1.0 C5 B:DG16 4.9 62.8 1.0 O3' B:DG16 5.0 66.9 1.0 C5' B:DG17 5.0 70.8 1.0

A.Traczyk, D.J.Gill, W.L.Chong, D.Rhodes. Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962