Atomistry » Calcium » PDB 6kzo-6ljf » 6lab
Atomistry »
  Calcium »
    PDB 6kzo-6ljf »
      6lab »

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

Protein crystallography data

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

Other elements in 6lab:

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

Calcium Binding Sites:

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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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 6lab

Go back to Calcium Binding Sites List in 6lab
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

Reference:

D.Sharma, C.A.Davey, Z.Adhireksan. Nucleosome 169 Bp with Linker Histone H1.0 To Be Published.
Page generated: Wed Jul 9 15:45:46 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy