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Chlorine in PDB 5oy7: Structure of the 4_601_157 Tetranucleosome (P1 Form)

Protein crystallography data

The structure of Structure of the 4_601_157 Tetranucleosome (P1 Form), PDB code: 5oy7 was solved by B.Ekundayo, T.J.Richmond, T.Schalch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.41 / 5.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.624, 161.465, 227.915, 78.94, 83.86, 83.74
R / Rfree (%) 21.9 / 23.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the 4_601_157 Tetranucleosome (P1 Form) (pdb code 5oy7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of the 4_601_157 Tetranucleosome (P1 Form), PDB code: 5oy7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5oy7

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Chlorine binding site 1 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl201

b:0.1
occ:0.00
 N O:GLY46 2.8 0.3 1.0
N O:ALA45 3.2 0.9 1.0
CA O:GLY46 3.4 0.3 1.0
N P:SER88 3.4 0.2 1.0
N O:ALA47 3.4 0.8 1.0
CA O:GLY44 3.4 0.9 1.0
OG P:SER88 3.5 0.2 1.0
C O:GLY44 3.6 0.9 1.0
CA P:THR87 3.6 0.3 1.0
CB P:THR87 3.7 0.3 1.0
C O:GLY46 3.9 0.3 1.0
C O:ALA45 3.9 0.9 1.0
C P:THR87 4.0 0.3 1.0
CA O:ALA45 4.1 0.9 1.0
CG2 P:THR87 4.2 0.3 1.0
OP1 g:DT585 4.3 0.2 1.0
CB P:SER88 4.4 0.2 1.0
CB O:ALA47 4.5 0.8 1.0
CA P:SER88 4.5 0.2 1.0
CA O:ALA47 4.5 0.8 1.0
N O:GLY44 4.6 0.9 1.0
O O:GLY44 4.6 0.9 1.0
OG1 P:THR87 4.9 0.3 1.0
N P:THR87 4.9 0.3 1.0

Chlorine binding site 2 out of 8 in 5oy7

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Chlorine binding site 2 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1101

b:0.2
occ:0.00
 N C:GLY46 3.1 0.2 1.0
N C:ALA45 3.4 0.7 1.0
CA C:GLY44 3.4 0.9 1.0
N D:SER88 3.5 0.9 1.0
C C:GLY44 3.6 0.9 1.0
CA C:GLY46 3.7 0.2 1.0
CA D:THR87 3.7 0.3 1.0
CB D:THR87 3.7 0.3 1.0
OP1 h:DG-353 3.8 0.5 1.0
N C:ALA47 3.9 0.4 1.0
C C:ALA45 4.1 0.7 1.0
C D:THR87 4.1 0.3 1.0
CA C:ALA45 4.3 0.7 1.0
C C:GLY46 4.3 0.2 1.0
O C:GLY44 4.4 0.9 1.0
CB D:SER88 4.5 0.9 1.0
OG D:SER88 4.5 0.9 1.0
N C:GLY44 4.6 0.9 1.0
CA D:SER88 4.6 0.9 1.0
CG2 D:THR87 4.6 0.3 1.0
OG1 D:THR87 4.7 0.3 1.0
CB C:ALA47 4.8 0.4 1.0
CA C:ALA47 4.9 0.4 1.0
N D:THR87 5.0 0.3 1.0
O D:ILE86 5.0 0.1 1.0

Chlorine binding site 3 out of 8 in 5oy7

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Chlorine binding site 3 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:0.7
occ:0.00
 N G:GLY46 2.8 0.2 1.0
N G:ALA45 3.2 0.6 1.0
CA G:GLY46 3.4 0.2 1.0
N H:SER88 3.4 0.9 1.0
N G:ALA47 3.4 0.4 1.0
CA G:GLY44 3.4 0.8 1.0
OG H:SER88 3.5 0.9 1.0
C G:GLY44 3.6 0.8 1.0
CA H:THR87 3.6 0.8 1.0
CB H:THR87 3.7 0.8 1.0
C G:GLY46 3.9 0.2 1.0
C G:ALA45 3.9 0.6 1.0
C H:THR87 4.0 0.8 1.0
CA G:ALA45 4.1 0.6 1.0
CG2 H:THR87 4.2 0.8 1.0
OP1 g:DT429 4.3 0.8 1.0
CB H:SER88 4.4 0.9 1.0
CB G:ALA47 4.5 0.4 1.0
CA H:SER88 4.5 0.9 1.0
CA G:ALA47 4.5 0.4 1.0
N G:GLY44 4.6 0.8 1.0
O G:GLY44 4.6 0.8 1.0
OG1 H:THR87 4.9 0.8 1.0
N H:THR87 4.9 0.8 1.0

Chlorine binding site 4 out of 8 in 5oy7

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Chlorine binding site 4 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl1101

b:0.8
occ:0.00
 N K:GLY46 3.1 1.0 1.0
N K:ALA45 3.4 0.1 1.0
CA K:GLY44 3.4 0.2 1.0
N L:SER88 3.5 0.5 1.0
C K:GLY44 3.6 0.2 1.0
CA K:GLY46 3.7 1.0 1.0
CA L:THR87 3.7 0.8 1.0
CB L:THR87 3.7 0.8 1.0
OP1 h:DG-509 3.8 0.6 1.0
N K:ALA47 3.9 0.2 1.0
C K:ALA45 4.1 0.1 1.0
C L:THR87 4.1 0.8 1.0
CA K:ALA45 4.3 0.1 1.0
C K:GLY46 4.3 1.0 1.0
O K:GLY44 4.4 0.2 1.0
OG L:SER88 4.5 0.5 1.0
CB L:SER88 4.5 0.5 1.0
CA L:SER88 4.6 0.5 1.0
N K:GLY44 4.6 0.2 1.0
CG2 L:THR87 4.6 0.8 1.0
OG1 L:THR87 4.7 0.8 1.0
CB K:ALA47 4.8 0.2 1.0
CA K:ALA47 4.9 0.2 1.0
N L:THR87 5.0 0.8 1.0
O L:ILE86 5.0 0.2 1.0

Chlorine binding site 5 out of 8 in 5oy7

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Chlorine binding site 5 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl1101

b:0.8
occ:0.00
 N S:GLY46 3.1 0.3 1.0
N S:ALA45 3.4 0.9 1.0
CA S:GLY44 3.4 0.8 1.0
N T:SER88 3.5 0.7 1.0
C S:GLY44 3.6 0.8 1.0
CA S:GLY46 3.7 0.3 1.0
CA T:THR87 3.7 0.4 1.0
CB T:THR87 3.7 0.4 1.0
OP1 h:DG-197 3.8 0.7 1.0
N S:ALA47 3.9 0.5 1.0
C S:ALA45 4.1 0.9 1.0
C T:THR87 4.1 0.4 1.0
CA S:ALA45 4.3 0.9 1.0
C S:GLY46 4.3 0.3 1.0
O S:GLY44 4.4 0.8 1.0
CB T:SER88 4.5 0.7 1.0
OG T:SER88 4.5 0.7 1.0
N S:GLY44 4.6 0.8 1.0
CA T:SER88 4.6 0.7 1.0
CG2 T:THR87 4.6 0.4 1.0
OG1 T:THR87 4.7 0.4 1.0
CB S:ALA47 4.8 0.5 1.0
CA S:ALA47 4.9 0.5 1.0
N T:THR87 5.0 0.4 1.0
O T:ILE86 5.0 0.0 1.0

Chlorine binding site 6 out of 8 in 5oy7

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Chlorine binding site 6 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Cl201

b:0.8
occ:0.00
 N W:GLY46 2.8 0.9 1.0
N W:ALA45 3.2 0.5 1.0
CA W:GLY46 3.4 0.9 1.0
N X:SER88 3.4 0.5 1.0
N W:ALA47 3.4 0.4 1.0
CA W:GLY44 3.4 0.2 1.0
OG X:SER88 3.5 0.5 1.0
C W:GLY44 3.6 0.2 1.0
CA X:THR87 3.6 0.2 1.0
CB X:THR87 3.7 0.2 1.0
C W:GLY46 3.9 0.9 1.0
C W:ALA45 3.9 0.5 1.0
C X:THR87 4.0 0.2 1.0
CA W:ALA45 4.1 0.5 1.0
CG2 X:THR87 4.2 0.2 1.0
OP1 g:DT273 4.3 0.3 1.0
CB X:SER88 4.4 0.5 1.0
CB W:ALA47 4.5 0.4 1.0
CA X:SER88 4.5 0.5 1.0
CA W:ALA47 4.5 0.4 1.0
N W:GLY44 4.6 0.2 1.0
O W:GLY44 4.6 0.2 1.0
OG1 X:THR87 4.9 0.2 1.0
N X:THR87 4.9 0.2 1.0

Chlorine binding site 7 out of 8 in 5oy7

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Chlorine binding site 7 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl1101

b:0.2
occ:0.00
 N a:GLY46 3.1 0.1 1.0
N a:ALA45 3.4 0.7 1.0
CA a:GLY44 3.4 0.3 1.0
N b:SER88 3.5 0.8 1.0
C a:GLY44 3.6 0.3 1.0
CA a:GLY46 3.7 0.1 1.0
CA b:THR87 3.7 0.8 1.0
CB b:THR87 3.7 0.8 1.0
OP1 h:DG-41 3.8 0.7 1.0
N a:ALA47 3.9 0.3 1.0
C a:ALA45 4.1 0.7 1.0
C b:THR87 4.1 0.8 1.0
CA a:ALA45 4.3 0.7 1.0
C a:GLY46 4.3 0.1 1.0
O a:GLY44 4.4 0.3 1.0
CB b:SER88 4.5 0.8 1.0
OG b:SER88 4.5 0.8 1.0
N a:GLY44 4.6 0.3 1.0
CA b:SER88 4.6 0.8 1.0
CG2 b:THR87 4.6 0.8 1.0
OG1 b:THR87 4.7 0.8 1.0
CB a:ALA47 4.8 0.3 1.0
CA a:ALA47 4.9 0.3 1.0
N b:THR87 5.0 0.8 1.0
O b:ILE86 5.0 0.5 1.0

Chlorine binding site 8 out of 8 in 5oy7

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Chlorine binding site 8 out of 8 in the Structure of the 4_601_157 Tetranucleosome (P1 Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the 4_601_157 Tetranucleosome (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Cl201

b:0.8
occ:0.00
 N e:GLY46 2.8 0.0 1.0
N e:ALA45 3.2 0.8 1.0
CA e:GLY46 3.4 0.0 1.0
N f:SER88 3.4 0.4 1.0
N e:ALA47 3.4 0.1 1.0
CA e:GLY44 3.4 0.7 1.0
OG f:SER88 3.5 0.4 1.0
C e:GLY44 3.6 0.7 1.0
CA f:THR87 3.6 0.8 1.0
CB f:THR87 3.7 0.8 1.0
C e:GLY46 3.9 0.0 1.0
C e:ALA45 3.9 0.8 1.0
C f:THR87 4.0 0.8 1.0
CA e:ALA45 4.1 0.8 1.0
CG2 f:THR87 4.2 0.8 1.0
OP1 g:DT117 4.3 0.3 1.0
CB f:SER88 4.4 0.4 1.0
CB e:ALA47 4.5 0.1 1.0
CA f:SER88 4.5 0.4 1.0
CA e:ALA47 4.5 0.1 1.0
N e:GLY44 4.6 0.7 1.0
O e:GLY44 4.6 0.7 1.0
OG1 f:THR87 4.9 0.8 1.0
N f:THR87 4.9 0.8 1.0

Reference:

B.Ekundayo, T.J.Richmond, T.Schalch. Capturing Structural Heterogeneity in Chromatin Fibers. J. Mol. Biol. V. 429 3031 2017.
ISSN: ESSN 1089-8638
PubMed: 28893533
DOI: 10.1016/J.JMB.2017.09.002
Page generated: Fri Jul 26 14:59:12 2024

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