Calcium in PDB 6lab: 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0

The structure of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0, PDB code: 6lab was solved by Z.Adhireksan, D.Sharma, P.L.Lee, Q.Bao, S.Padavattan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	216.23 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.799, 102.76, 218.05, 90, 97.4, 90
R / Rfree (%)	20.9 / 26.3

The structure of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 also contains other interesting chemical elements:

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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 (pdb code 6lab). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0, PDB code: 6lab:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:121.2 occ:1.00 O D:VAL48 2.6 116.5 1.0 OE1 C:GLU64 3.3 115.2 1.0 C D:VAL48 3.8 116.9 1.0 CD C:GLU64 4.3 114.1 1.0 CA D:VAL48 4.3 120.7 1.0 OE2 C:GLU64 4.4 124.8 1.0 ND1 D:HIS49 4.5 112.0 1.0 CE1 D:HIS49 4.6 112.1 1.0 CG1 D:VAL48 4.7 140.4 1.0 O D:GLN47 4.7 115.0 1.0 N D:HIS49 4.9 116.1 1.0

Calcium binding site 2 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca101 b:102.4 occ:1.00 O6 J:DG51 2.4 150.0 1.0 O6 I:DG-52 3.0 115.0 1.0 N4 I:DC-51 3.6 141.8 1.0 C6 J:DG51 3.6 143.8 1.0 C6 I:DG-52 3.9 121.4 1.0 O6 J:DG50 4.0 129.7 1.0 N7 J:DG50 4.1 140.7 1.0 N7 I:DG-52 4.2 130.5 1.0 N7 J:DG51 4.3 143.1 1.0 C5 I:DG-52 4.3 122.7 1.0 C5 J:DG51 4.4 139.7 1.0 C6 J:DG50 4.5 140.8 1.0 C5 J:DG50 4.5 140.5 1.0 N1 J:DG51 4.7 143.6 1.0 N4 J:DC52 4.8 165.1 1.0 C4 I:DC-51 4.9 140.7 1.0 N1 I:DG-52 4.9 129.3 1.0

Calcium binding site 3 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca102 b:119.7 occ:1.00 O6 I:DG-40 3.2 160.2 1.0 O6 I:DG-41 3.4 170.7 1.0 N7 I:DG-41 3.6 202.3 1.0 C6 I:DG-41 4.0 182.2 1.0 C5 I:DG-41 4.1 196.4 1.0 C6 I:DG-40 4.2 165.9 1.0 N4 J:DC40 4.3 172.6 1.0 N7 I:DG-40 4.5 169.6 1.0 C7 I:DT-42 4.7 166.8 1.0 C8 I:DG-41 4.7 200.7 1.0 C5 I:DG-40 4.7 169.4 1.0 N6 J:DA39 4.9 137.9 1.0

Calcium binding site 4 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca103 b:121.2 occ:1.00 O6 I:DG29 3.3 112.9 1.0 O6 J:DG-30 3.6 173.2 1.0 C6 I:DG29 4.4 122.5 1.0 C6 J:DG-30 4.7 171.8 1.0 N4 J:DC-29 4.8 160.2 1.0 N4 I:DC30 4.9 146.4 1.0

Calcium binding site 5 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca104 b:134.6 occ:1.00 O4' I:DA36 3.4 185.2 1.0 C4' I:DA36 3.8 182.8 1.0 O4' J:DA-33 3.9 159.3 1.0 C1' I:DA36 4.2 181.8 1.0 C4' J:DA-33 4.3 163.7 1.0 O2 I:DT35 4.4 203.7 1.0 C5' J:DA-33 4.5 163.0 1.0 N3 I:DA36 4.5 183.0 1.0 O3' I:DA36 4.6 187.9 1.0 N2 J:DG-34 4.8 156.6 1.0 C3' I:DA36 4.8 187.3 1.0 C5' I:DA36 4.8 177.4 1.0

Calcium binding site 6 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca105 b:128.3 occ:1.00 O6 I:DG51 2.5 191.0 1.0 O6 J:DG-52 3.3 174.0 1.0 C6 I:DG51 3.5 178.7 1.0 N7 I:DG50 3.7 168.9 1.0 N4 J:DC-51 4.0 195.6 1.0 N7 I:DG51 4.0 160.8 1.0 C5 I:DG51 4.1 168.8 1.0 C6 J:DG-52 4.2 162.2 1.0 O6 I:DG50 4.2 162.7 1.0 N4 I:DC52 4.4 189.6 1.0 C5 I:DG50 4.4 169.6 1.0 C8 I:DG50 4.6 168.4 1.0 C6 I:DG50 4.6 172.0 1.0 N1 I:DG51 4.7 178.6 1.0 N7 J:DG-52 4.7 158.7 1.0 C5 J:DG-52 4.8 159.5 1.0

Calcium binding site 7 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca106 b:125.0 occ:1.00 N7 I:DG62 2.7 177.4 1.0 C8 I:DG62 3.4 183.5 1.0 C5 I:DC61 3.7 181.5 1.0 C6 I:DC61 3.9 181.4 1.0 C5 I:DG62 3.9 179.3 1.0 O6 I:DG62 4.3 185.6 1.0 C4 I:DC61 4.4 185.1 1.0 C6 I:DG62 4.5 178.4 1.0 N1 I:DC61 4.6 180.7 1.0 N9 I:DG62 4.7 191.9 1.0 C2' I:DC61 4.8 191.2 1.0 O6 I:DG63 4.8 190.8 1.0 N4 I:DC61 4.9 183.7 1.0 OP2 I:DG62 5.0 203.2 1.0 C4 I:DG62 5.0 183.3 1.0

Calcium binding site 8 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca101 b:129.0 occ:1.00 OP1 J:DT67 4.5 142.2 1.0

Calcium binding site 9 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca102 b:125.7 occ:1.00 O4' J:DG56 3.4 143.5 1.0 C4' J:DG56 3.8 140.8 1.0 O2 J:DC55 4.0 139.1 1.0 O4' J:DC55 4.2 143.8 1.0 C5' J:DG56 4.2 147.8 1.0 C4' J:DC55 4.5 146.5 1.0 C1' J:DG56 4.7 139.7 1.0 N2 I:DG-55 4.8 131.4 1.0 C1' J:DC55 5.0 141.0 1.0

Calcium binding site 10 out of 20 in the 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of 169 Bp Nucleosome, Harboring Cohesive Dna Termini, Assembled with Linker Histone H1.0 within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca201 b:114.0 occ:1.00 O N:VAL48 2.7 93.4 1.0 OE1 M:GLU64 3.5 87.7 1.0 C N:VAL48 3.8 85.9 1.0 CA N:VAL48 4.3 84.5 1.0 CG1 N:VAL48 4.4 86.0 1.0 CD M:GLU64 4.5 87.6 1.0 OE2 M:GLU64 4.7 98.3 1.0 N N:HIS49 4.9 87.5 1.0 O N:GLN47 4.9 88.0 1.0

D.Sharma, C.A.Davey, Z.Adhireksan. Nucleosome 169 Bp with Linker Histone H1.0 To Be Published.