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Calcium in PDB 6mc4: Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex

Protein crystallography data

The structure of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex, PDB code: 6mc4 was solved by B.Chu, P.J.Paukstelis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.99 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.743, 53.743, 99.389, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 26.8

Other elements in 6mc4:

The structure of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex also contains other interesting chemical elements:

Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex (pdb code 6mc4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex, PDB code: 6mc4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6mc4

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Calcium binding site 1 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:23.7
occ:1.00
 OP1 A:DA5 2.3 27.5 1.0
OP2 C:DT3 2.3 22.2 1.0
OP1 A:DT3 2.4 26.3 1.0
P C:DT3 3.7 28.0 1.0
P A:DA5 3.7 26.2 1.0
P A:DT3 3.7 26.5 1.0
O5' A:DT3 4.2 22.3 1.0
OP1 C:DT3 4.2 23.8 1.0
C5' A:DT3 4.3 24.1 1.0
OP2 A:DA5 4.4 24.9 1.0
OP2 A:DT3 4.4 25.1 1.0
O C:HOH205 4.5 20.3 1.0
O5' A:DA5 4.5 29.3 1.0
O5' C:DT3 4.5 23.2 1.0
O3' C:DG2 4.6 27.1 1.0
O3' A:DC4 4.7 24.7 1.0
O C:HOH210 4.8 14.3 1.0
O A:HOH212 4.8 35.9 1.0
C3' A:DC4 4.8 27.0 1.0
O3' A:DG2 4.9 23.5 1.0
C3' A:DG2 4.9 27.8 1.0
C2' A:DC4 5.0 27.1 1.0

Calcium binding site 2 out of 10 in 6mc4

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Calcium binding site 2 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:24.6
occ:1.00
 OP1 C:DA5 2.2 21.9 1.0
OP1 C:DT3 2.2 23.8 1.0
OP2 A:DT3 2.3 25.1 1.0
O C:HOH206 2.3 33.8 1.0
O C:HOH205 2.6 20.3 1.0
P C:DT3 3.6 28.0 1.0
P C:DA5 3.7 24.0 1.0
P A:DT3 3.7 26.5 1.0
O5' C:DT3 4.2 23.2 1.0
C5' C:DT3 4.2 24.4 1.0
O C:HOH210 4.3 14.3 1.0
OP1 A:DT3 4.3 26.3 1.0
O5' C:DA5 4.4 29.8 1.0
OP2 C:DT3 4.4 22.2 1.0
OP2 C:DA5 4.4 23.7 1.0
O5' A:DT3 4.5 22.3 1.0
O3' C:DC4 4.6 22.9 1.0
O3' A:DG2 4.7 23.5 1.0
O3' C:DG2 4.7 27.1 1.0
C3' C:DC4 4.7 24.9 1.0
C2' C:DC4 4.8 24.8 1.0
C3' C:DG2 4.8 28.2 1.0

Calcium binding site 3 out of 10 in 6mc4

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Calcium binding site 3 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:46.4
occ:1.00
 OP2 C:DA5 2.2 23.7 1.0
OP1 C:DG2 2.5 31.9 1.0
P C:DA5 3.6 24.0 1.0
P C:DG2 4.0 36.3 1.0
O5' C:DA5 4.2 29.8 1.0
C5' C:DA5 4.3 28.3 1.0
C4' C:DA5 4.3 31.3 1.0
O3' C:DC4 4.5 22.9 1.0
OP1 C:DA5 4.5 21.9 1.0
O3' C:DC1 4.6 41.1 1.0
O3' C:DA5 4.8 33.4 1.0
C3' C:DA5 4.9 33.0 1.0
O5' C:DG2 4.9 34.3 1.0

Calcium binding site 4 out of 10 in 6mc4

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Calcium binding site 4 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca103

b:45.2
occ:1.00
 O D:HOH207 1.9 29.4 1.0
O H:HOH210 2.1 32.4 1.0
O G:HOH109 2.3 52.0 1.0
O C:HOH203 2.4 30.3 1.0
O D:HOH208 2.5 46.0 1.0
N7 C:DG7 4.0 72.6 1.0
O6 G:DG7 4.5 85.6 1.0
N7 H:DG7 4.5 28.5 1.0
N7 D:DG7 4.5 25.4 1.0
O6 C:DG7 4.6 62.7 1.0
O6 D:DG7 4.6 19.5 1.0
O6 H:DG7 4.7 21.1 1.0
C2' H:DG6 4.7 47.8 1.0
C8 C:DG7 4.8 71.4 1.0
C5 C:DG7 4.9 71.0 1.0

Calcium binding site 5 out of 10 in 6mc4

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Calcium binding site 5 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca104

b:47.6
occ:1.00
 O2 C:DT3 2.5 24.6 1.0
O D:HOH203 3.4 27.5 1.0
C2 C:DT3 3.8 24.0 1.0
N6 C:DA5 4.5 25.2 1.0
C1' C:DT3 4.6 24.4 1.0
N3 C:DT3 4.6 25.6 1.0
N1 C:DT3 4.7 24.0 1.0
C2' C:DT3 4.9 23.9 1.0

Calcium binding site 6 out of 10 in 6mc4

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Calcium binding site 6 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:62.3
occ:1.00
 OP1 D:DA5 2.3 66.0 1.0
OP1 D:DT3 2.7 38.7 1.0
P D:DA5 3.7 65.7 1.0
P D:DT3 4.0 49.9 1.0
OP2 D:DA5 4.3 53.5 1.0
O5' D:DT3 4.4 49.1 1.0
O5' D:DA5 4.5 49.2 1.0
C5' D:DT3 4.6 54.9 1.0
O3' D:DC4 4.6 60.3 1.0
OP2 D:DT3 4.9 50.2 1.0
C3' D:DC4 5.0 59.3 1.0

Calcium binding site 7 out of 10 in 6mc4

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Calcium binding site 7 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:38.1
occ:1.00
 OP1 E:DA5 2.0 30.1 1.0
O E:HOH206 2.5 38.0 1.0
O E:HOH203 2.6 33.4 1.0
P E:DA5 3.4 26.5 1.0
O5' E:DA5 4.1 27.9 1.0
OP1 E:DT3 4.2 37.2 1.0
OP2 E:DA5 4.3 39.9 1.0
C3' E:DC4 4.4 28.6 1.0
O3' E:DC4 4.4 28.0 1.0
C2' E:DC4 4.5 28.9 1.0
C5' E:DA5 4.5 24.9 1.0
OP1 E:DG2 4.9 33.9 1.0

Calcium binding site 8 out of 10 in 6mc4

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Calcium binding site 8 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:32.6
occ:1.00
 O E:HOH207 2.3 39.6 1.0
O F:HOH206 2.4 31.6 1.0
O B:HOH206 2.4 24.4 1.0
O A:HOH208 2.5 35.9 1.0
O F:HOH201 2.6 24.2 1.0
O6 A:DG7 4.1 45.2 1.0
O6 F:DG7 4.1 19.1 1.0
O6 B:DG7 4.3 20.8 1.0
N7 F:DG7 4.3 21.3 1.0
N7 B:DG7 4.5 22.3 1.0
O6 E:DG7 4.5 39.2 1.0
N7 A:DG7 4.5 42.2 1.0
N7 E:DG7 4.7 38.1 1.0
C6 F:DG7 4.8 18.0 1.0
C2' F:DG6 4.9 31.4 1.0
C6 A:DG7 4.9 44.0 1.0
C5 F:DG7 4.9 20.1 1.0
C6 B:DG7 5.0 22.0 1.0

Calcium binding site 9 out of 10 in 6mc4

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Calcium binding site 9 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:54.1
occ:1.00
 O A:HOH218 2.1 37.4 1.0
O A:HOH203 2.4 37.0 1.0
OP2 F:DG6 2.5 40.2 1.0
P F:DG6 3.7 42.4 1.0
O5' F:DG6 4.0 35.0 1.0
C2' F:DA5 4.0 46.6 1.0
C3' F:DA5 4.0 50.0 1.0
O6 A:DG9 4.2 51.0 1.0
C5 A:DC8 4.3 48.2 1.0
OP1 A:DG7 4.4 26.7 1.0
OP2 A:DG7 4.4 27.9 1.0
O3' F:DA5 4.4 43.0 1.0
O A:HOH216 4.6 39.4 1.0
P A:DG7 4.8 30.2 1.0
OP1 F:DG6 5.0 32.8 1.0

Calcium binding site 10 out of 10 in 6mc4

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Calcium binding site 10 out of 10 in the Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca101

b:58.5
occ:1.00
 OP2 H:DG6 2.1 37.8 1.0
O H:HOH211 2.6 33.9 1.0
O C:HOH207 2.8 29.1 1.0
P H:DG6 3.5 46.6 1.0
O5' H:DG6 3.8 46.9 1.0
OP1 C:DG7 4.1 42.8 1.0
C2' H:DA5 4.3 54.1 1.0
OP1 H:DG6 4.5 33.0 1.0
O3' H:DA5 4.5 51.4 1.0
C3' H:DA5 4.5 54.6 1.0
O6 C:DG9 4.6 69.8 1.0
P C:DG7 4.8 60.0 1.0
OP2 C:DG7 4.9 56.1 1.0

Reference:

B.Chu, D.Zhang, W.Hwang, P.J.Paukstelis. Crystal Structure of A Tetrameric Dna Fold-Back Quadruplex. J. Am. Chem. Soc. V. 140 16291 2018.
ISSN: ESSN 1520-5126
PubMed: 30384604
DOI: 10.1021/JACS.8B10153
Page generated: Tue Jul 16 11:17:25 2024

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