Calcium in PDB 7xvm: Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)

The structure of Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xvm was solved by Z.Adhireksan, B.Qiuye, P.L.Lee, D.Sharma, S.Padavattan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 2.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.16, 103.758, 212.955, 90, 100.97, 90
R / Rfree (%)	20 / 25.9

The structure of Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) (pdb code 7xvm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xvm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:123.2 occ:1.00 O D:VAL48 2.7 91.7 1.0 OE1 C:GLU64 3.2 86.8 1.0 C D:VAL48 3.9 81.8 1.0 OE2 C:GLU64 4.0 107.5 1.0 CD C:GLU64 4.1 93.1 1.0 CE1 D:HIS49 4.3 96.0 1.0 ND1 D:HIS49 4.4 93.3 1.0 CA D:VAL48 4.6 78.7 1.0 NE2 D:HIS49 4.6 82.7 1.0 CG1 D:VAL48 4.7 87.7 1.0 CG D:HIS49 4.8 80.4 1.0 N D:HIS49 4.9 76.5 1.0 CD2 D:HIS49 5.0 82.4 1.0

Calcium binding site 2 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca101 b:88.8 occ:1.00 O6 J:DG-52 2.8 90.1 1.0 O6 I:DG51 2.8 111.1 1.0 C6 J:DG-52 3.8 92.6 1.0 C6 I:DG51 3.9 102.2 1.0 N4 I:DC52 4.2 111.7 1.0 N4 J:DC-51 4.3 99.4 1.0 N7 I:DG51 4.4 101.8 1.0 N7 J:DG-52 4.4 101.0 1.0 N7 I:DG50 4.4 90.1 1.0 C5 J:DG-52 4.5 93.1 1.0 C5 I:DG51 4.5 104.8 1.0 O6 I:DG50 4.6 84.9 1.0 C5 I:DG50 4.9 89.6 1.0 N1 J:DG-52 4.9 86.7 1.0 C6 I:DG50 5.0 89.7 1.0 N1 I:DG51 5.0 100.3 1.0

Calcium binding site 3 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca102 b:89.4 occ:1.00 O6 J:DG51 2.6 114.6 1.0 O6 I:DG-52 2.8 96.6 1.0 C6 J:DG51 3.8 111.9 1.0 C6 I:DG-52 3.8 99.2 1.0 N4 I:DC-51 4.1 111.8 1.0 N4 J:DC52 4.3 108.4 1.0 N7 J:DG51 4.3 115.3 1.0 N7 J:DG50 4.4 124.7 1.0 C5 J:DG51 4.4 109.1 1.0 N7 I:DG-52 4.4 91.6 1.0 C5 I:DG-52 4.5 100.9 1.0 O6 J:DG50 4.7 108.8 1.0 N1 I:DG-52 4.8 91.2 1.0 C5 J:DG50 4.9 110.0 1.0 N1 J:DG51 4.9 116.6 1.0

Calcium binding site 4 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca103 b:146.4 occ:1.00 N7 I:DG-3 3.4 96.7 1.0 N7 I:DG-2 3.8 106.5 1.0 O6 I:DG-2 3.9 102.1 1.0 C8 I:DG-3 4.0 101.3 1.0 C5 I:DG-3 4.5 101.4 1.0 C5 I:DG-2 4.6 110.5 1.0 C6 I:DG-2 4.6 105.6 1.0 O6 I:DG-3 4.9 99.8 1.0 C8 I:DG-2 4.9 102.7 1.0 O4 J:DT1 5.0 125.0 1.0

Calcium binding site 5 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca104 b:136.1 occ:1.00 O6 I:DG29 3.2 112.9 1.0 O6 J:DG-30 4.1 127.5 1.0 C6 I:DG29 4.3 123.2 1.0 N7 I:DA28 4.7 110.2 1.0 N7 I:DG29 4.7 117.5 1.0 N4 J:DC-29 4.7 134.2 1.0 C5 I:DG29 4.9 127.1 1.0

Calcium binding site 6 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca105 b:122.0 occ:1.00 O4' J:DA-33 4.3 126.7 1.0 O4' I:DA36 4.3 134.3 1.0 C5' J:DA-33 4.4 139.7 1.0 C4' J:DA-33 4.5 133.2 1.0 C5' I:DC37 4.7 119.8 1.0 C4' I:DA36 4.8 143.2 1.0 C1' I:DA36 4.9 127.9 1.0 O4' J:DG-34 4.9 119.6 1.0

Calcium binding site 7 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca106 b:112.1 occ:1.00 C4' I:DG-53 4.3 87.4 1.0 C5' I:DG-53 4.5 81.6 1.0 O4' I:DG-53 4.5 87.2 1.0 O4' J:DG56 4.6 107.0 1.0 N3 I:DA-54 4.6 88.8 1.0 C2 I:DA-54 4.8 86.3 1.0 C4' J:DG56 4.8 110.5 1.0 O2 J:DC55 5.0 107.1 1.0

Calcium binding site 8 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca107 b:124.5 occ:1.00 O2 I:DC-57 3.8 122.9 1.0 C5' I:DC-56 4.0 109.3 1.0 N2 I:DG-58 4.2 116.7 1.0 O4' I:DC-57 4.3 129.8 1.0 O4' I:DC-56 4.4 108.7 1.0 C4' I:DC-56 4.5 107.6 1.0 C1' I:DC-57 4.5 117.7 1.0 O3' I:DC-57 4.6 125.4 1.0 C4' I:DC-57 4.7 127.6 1.0 O4' J:DA59 4.7 92.9 1.0 C2 I:DC-57 4.8 113.9 1.0 N2 J:DG57 5.0 91.8 1.0

Calcium binding site 9 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca108 b:129.7 occ:1.00 N2 I:DG-3 3.9 115.7 1.0 N3 I:DG-3 4.4 112.4 1.0 N2 J:DG4 4.4 106.0 1.0 C2 I:DG-3 4.7 106.8 1.0 O4' I:DG-2 4.7 100.2 1.0 N3 J:DG4 4.7 108.0 1.0 C5' I:DG-2 4.7 107.3 1.0 C4' I:DG-2 4.9 102.0 1.0 C2 J:DG4 5.0 109.5 1.0

Calcium binding site 10 out of 18 in the Crystal Structure of Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment)


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 Nucleosome-H5 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca101 b:121.0 occ:1.00 O6 J:DG29 3.5 101.1 1.0 O6 I:DG-30 4.1 127.8 1.0 C6 J:DG29 4.5 101.7 1.0 N7 J:DG29 4.8 104.8 1.0 N4 J:DC30 4.9 116.3 1.0

Z.Adhireksan, B.Qiuye, P.L.Lee, D.Sharma, S.Padavattan, C.A.Davey. Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (Sticky-169A Dna Fragment) To Be Published.