Calcium in PDB 4rne: Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions

The structure of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions, PDB code: 4rne was solved by A.C.Fyfe, P.W.Dunten, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 1.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.656, 54.197, 95.677, 90.00, 90.00, 90.00
R / Rfree (%)	10.2 / 11.9

The structure of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions also contains other interesting chemical elements:

Strontium	(Sr)	7 atoms
Sodium	(Na)	6 atoms

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

Binding sites:

The binding sites of Calcium atom in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions (pdb code 4rne). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions, PDB code: 4rne:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:13.2 occ:0.74 CA B:CA304 0.0 13.2 0.7 CA B:CA304 1.4 7.5 0.3 O A:HOH1011 2.4 21.4 1.0 O B:HOH410 2.5 28.9 1.0 O A:HOH1028 2.5 30.0 1.0 O A:HOH1030 2.6 23.4 0.6 O2' B:U206 2.6 16.2 1.0 O B:HOH412 2.7 28.3 1.0 O3' B:U206 2.8 22.7 1.0 O B:HOH407 2.9 15.7 0.4 O B:HOH407 2.9 12.6 0.6 H1' B:U206 3.5 11.8 1.0 C2' B:U206 3.6 14.0 1.0 C3' B:U206 3.7 15.6 1.0 O2' A:G105 4.0 9.3 0.4 OP2 B:G205 4.0 8.5 1.0 C1' B:U206 4.1 12.6 1.0 H3' B:U206 4.3 16.8 1.0 O B:HOH419 4.4 36.0 1.0 O A:HOH1006 4.4 20.1 1.0 O2 B:U206 4.5 14.2 1.0 O2' A:G105 4.5 10.9 0.6 H2' B:U206 4.5 12.1 1.0 O B:HOH436 4.6 15.9 0.2 OP2 B:G204 4.8 10.6 1.0 C2' A:G105 4.9 7.7 0.4 N3 A:G105 4.9 9.3 1.0 N2 A:G105 4.9 9.2 1.0 C4' B:U206 4.9 14.8 1.0 O B:HOH421 4.9 20.4 0.7

Calcium binding site 2 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:7.5 occ:0.26 CA B:CA304 0.0 7.5 0.3 CA B:CA304 1.4 13.2 0.7 O3' B:U206 2.0 22.7 1.0 O A:HOH1030 2.4 23.4 0.6 O B:HOH412 2.4 28.3 1.0 O B:HOH410 2.7 28.9 1.0 O2' B:U206 3.2 16.2 1.0 C3' B:U206 3.3 15.6 1.0 O B:HOH436 3.3 15.9 0.2 O A:HOH1028 3.4 30.0 1.0 O A:HOH1011 3.5 21.4 1.0 H1' B:U206 3.6 11.8 1.0 C2' B:U206 3.7 14.0 1.0 H3' B:U206 3.8 16.8 1.0 O B:HOH407 4.1 12.6 0.6 C1' B:U206 4.2 12.6 1.0 H4' B:U206 4.2 15.7 1.0 O B:HOH407 4.2 15.7 0.4 C4' B:U206 4.3 14.8 1.0 OP2 B:G205 4.5 8.5 1.0 H2' B:U206 4.7 12.1 1.0 O A:HOH1006 4.8 20.1 1.0 O4' B:U206 4.8 12.4 1.0 O2' A:G105 4.9 9.3 0.4

Calcium binding site 3 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:10.7 occ:0.64 O C:HOH518 2.4 17.5 0.7 O C:HOH503 2.5 18.7 1.0 O3' C:U306 2.5 14.7 1.0 O B:HOH435 2.5 15.2 0.4 O C:HOH508 2.7 9.7 0.5 O2' C:U306 2.8 12.8 1.0 O C:HOH508 2.8 16.2 0.5 H1' C:U306 3.5 12.1 1.0 C3' C:U306 3.6 12.8 1.0 C2' C:U306 3.6 11.9 1.0 OP2 C:G305 3.9 11.2 1.0 H22 B:G205 4.0 9.7 1.0 H3' C:U306 4.1 12.7 1.0 C1' C:U306 4.1 12.7 1.0 O2' B:G205 4.3 11.0 1.0 OP2 C:G304 4.5 9.2 1.0 H2' C:U306 4.6 9.9 1.0 O C:HOH519 4.6 61.9 1.0 O B:HOH416 4.7 33.4 1.0 O2 C:U306 4.7 12.6 1.0 C4' C:U306 4.8 12.9 1.0 H4' C:U306 4.8 12.5 1.0 H1' B:G205 4.8 9.4 1.0 N2 B:G205 4.9 8.3 1.0 N3 B:G205 4.9 7.5 1.0

Calcium binding site 4 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:12.0 occ:0.45 O C:HOH501 1.5 26.1 0.6 O4 C:U301 2.4 13.1 1.0 C4 C:U301 3.5 10.9 1.0 H5 C:U301 3.8 10.4 1.0 C5 C:U301 4.2 11.1 1.0 N3 C:U301 4.6 9.5 1.0 H3 C:U301 4.7 9.9 1.0

Calcium binding site 5 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca9001 b:8.2 occ:1.00 OP2 D:G402 2.3 8.6 1.0 O E:HOH712 2.3 12.8 1.0 O E:HOH720 2.3 10.7 1.0 OP1 E:G503 2.4 8.9 1.0 O E:HOH702 2.4 10.2 1.0 P D:G402 3.6 8.2 1.0 P E:G503 3.6 8.5 1.0 O3' E:G502 3.6 8.8 1.0 O5' D:G402 3.8 8.0 1.0 O D:HOH9504 4.0 20.7 1.0 H5'' E:G503 4.2 13.8 1.0 H3' D:U401 4.2 11.0 1.0 H5' E:G502 4.3 13.4 1.0 O E:HOH732 4.3 24.1 0.6 OP1 D:G402 4.4 9.2 1.0 O D:HOH9511 4.4 24.9 0.9 OP2 E:G503 4.6 9.0 1.0 OP1 E:G502 4.6 11.3 1.0 O5' E:G503 4.7 8.2 1.0 H5' E:G503 4.7 13.8 1.0 C5' E:G503 4.7 8.5 1.0 O3' D:U401 4.8 8.3 1.0 O E:HOH729 4.8 20.1 0.7 H4' E:G502 4.8 14.0 1.0 H2' D:U401 4.9 9.5 1.0 H5' D:G402 4.9 10.2 1.0 C3' D:U401 4.9 8.0 1.0 C5' D:G402 4.9 7.7 1.0 C3' E:G502 5.0 8.3 1.0

Calcium binding site 6 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca9002 b:16.9 occ:0.73 O D:HOH9506 2.5 22.2 1.0 O C:HOH517 2.5 30.2 1.0 O3' D:U406 2.6 25.4 1.0 O2' D:U406 2.7 19.4 1.0 O D:HOH9515 2.8 31.5 1.0 H1' D:U406 3.4 15.8 1.0 C2' D:U406 3.6 19.4 1.0 C3' D:U406 3.6 23.6 1.0 H22 C:G305 3.9 11.4 1.0 OP2 D:G405 4.0 15.6 1.0 C1' D:U406 4.1 17.6 1.0 H3' D:U406 4.2 20.1 1.0 O2' C:G305 4.4 12.1 1.0 O2 D:U406 4.5 15.8 1.0 H2' D:U406 4.5 11.8 1.0 O D:HOH9530 4.6 22.6 0.6 O D:HOH9530 4.6 15.8 0.4 C4' D:U406 4.8 21.8 1.0 OP2 D:G404 4.8 12.1 1.0 N2 C:G305 4.8 9.8 1.0 H4' D:U406 4.8 18.6 1.0 O C:HOH511 4.9 30.1 1.0 N3 C:G305 4.9 8.8 1.0 H1' C:G305 4.9 11.0 1.0 O4' D:U406 5.0 19.6 1.0

Calcium binding site 7 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca604 b:11.8 occ:0.66 CA E:CA604 0.0 11.8 0.7 CA E:CA604 1.2 27.8 0.3 O E:HOH724 2.4 27.3 1.0 O E:HOH717 2.5 20.9 0.8 O C:HOH507 2.5 30.2 1.0 O E:HOH733 2.6 32.5 1.0 O2' E:U506 2.7 13.6 0.7 O3' E:U506 2.7 19.6 0.7 O E:HOH722 3.0 11.4 0.5 H1' E:U506 3.5 13.9 0.7 C2' E:U506 3.6 12.9 0.7 C3' E:U506 3.7 16.4 0.7 C1' E:U506 4.1 12.7 0.7 OP2 E:G505 4.1 14.7 1.0 H3' E:U506 4.2 17.1 0.7 O E:HOH719 4.5 31.4 1.0 OP1 C:G304 4.5 9.2 1.0 O2 E:U506 4.5 13.9 0.7 O E:HOH705 4.6 9.7 1.0 H2' E:U506 4.6 15.7 0.7 O E:HOH734 4.6 20.2 0.6 OP2 E:G504 4.7 10.2 1.0 O E:HOH715 4.8 15.1 1.0 C4' E:U506 4.9 16.6 0.7 H4' E:U506 5.0 17.9 0.7

Calcium binding site 8 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca604 b:27.8 occ:0.34 CA E:CA604 0.0 27.8 0.3 CA E:CA604 1.2 11.8 0.7 O3' E:U506 1.9 19.6 0.7 O E:HOH733 2.3 32.5 1.0 O C:HOH507 2.3 30.2 1.0 O E:HOH717 2.7 20.9 0.8 O E:HOH724 3.1 27.3 1.0 O2' E:U506 3.1 13.6 0.7 C3' E:U506 3.1 16.4 0.7 H1' E:U506 3.4 13.9 0.7 O E:HOH734 3.5 20.2 0.6 C2' E:U506 3.6 12.9 0.7 H3' E:U506 3.6 17.1 0.7 O E:HOH722 4.0 11.4 0.5 C1' E:U506 4.0 12.7 0.7 H4' E:U506 4.2 17.9 0.7 C4' E:U506 4.3 16.6 0.7 O E:HOH719 4.4 31.4 1.0 OP2 E:G505 4.5 14.7 1.0 H2' E:U506 4.6 15.7 0.7 OP1 C:G304 4.6 9.2 1.0 O4' E:U506 4.7 15.6 0.7 O C:HOH518 4.7 17.5 0.7

Calcium binding site 9 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca702 b:9.9 occ:0.50 CA F:CA702 0.0 9.9 0.5 CA F:CA702 0.7 25.5 0.5 O F:HOH815 2.5 36.7 1.0 O F:HOH802 2.5 26.3 1.0 O3' F:U606 2.6 18.6 0.7 O F:HOH810 2.7 17.9 0.6 O2' F:U606 2.7 14.5 0.7 O F:HOH810 3.2 11.5 0.4 O2' F:U606 3.5 17.4 0.3 C2' F:U606 3.6 12.8 0.7 C3' F:U606 3.6 16.5 0.7 O3' F:U606 3.7 29.6 0.3 H22 E:G505 4.1 19.6 1.0 C1' F:U606 4.1 13.3 0.7 OP2 F:G605 4.2 13.4 1.0 O2' E:G505 4.2 21.2 1.0 O F:HOH819 4.3 37.9 1.0 C2' F:U606 4.5 17.3 0.3 O2 F:U606 4.6 14.0 0.7 O E:HOH725 4.6 41.7 1.0 C3' F:U606 4.7 23.7 0.3 OP2 F:G604 4.7 12.7 1.0 H1' E:G505 4.7 24.5 1.0 O F:HOH824 4.8 19.2 0.5 C4' F:U606 4.9 15.7 0.7 C1' F:U606 4.9 20.0 0.3 N3 E:G505 4.9 11.6 1.0 O2 F:U606 5.0 23.6 0.3

Calcium binding site 10 out of 11 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca702 b:25.5 occ:0.50 CA F:CA702 0.0 25.5 0.5 CA F:CA702 0.7 9.9 0.5 O3' F:U606 2.0 18.6 0.7 O2' F:U606 2.1 14.5 0.7 O F:HOH802 2.5 26.3 1.0 O F:HOH815 2.6 36.7 1.0 O F:HOH810 2.8 17.9 0.6 O2' F:U606 2.9 17.4 0.3 C2' F:U606 2.9 12.8 0.7 C3' F:U606 3.0 16.5 0.7 O3' F:U606 3.1 29.6 0.3 O F:HOH810 3.2 11.5 0.4 C1' F:U606 3.5 13.3 0.7 OP2 F:G605 3.8 13.4 1.0 C2' F:U606 3.9 17.3 0.3 H22 E:G505 3.9 19.6 1.0 C3' F:U606 4.0 23.7 0.3 C4' F:U606 4.2 15.7 0.7 O2 F:U606 4.2 14.0 0.7 C1' F:U606 4.2 20.0 0.3 O4' F:U606 4.4 14.1 0.7 O2 F:U606 4.5 23.6 0.3 O F:HOH824 4.5 19.2 0.5 O E:HOH725 4.5 41.7 1.0 N1 F:U606 4.5 12.8 0.7 O2' E:G505 4.6 21.2 1.0 N2 E:G505 4.7 11.3 1.0 C2 F:U606 4.8 11.9 0.7 N3 E:G505 4.9 11.6 1.0 C4' F:U606 4.9 22.7 0.3 O F:HOH819 4.9 37.9 1.0

A.C.Fyfe, P.W.Dunten, W.G.Scott. Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions To Be Published.