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Manganese in PDB 5ay8: Crystal Structure of Human Nucleosome Containing H3.Y

Protein crystallography data

The structure of Crystal Structure of Human Nucleosome Containing H3.Y, PDB code: 5ay8 was solved by T.Kujirai, N.Horikoshi, K.Sato, K.Maehara, S.Machida, A.Osakabe, H.Kimura, Y.Ohkawa, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.95 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.522, 101.922, 175.736, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.9

Other elements in 5ay8:

The structure of Crystal Structure of Human Nucleosome Containing H3.Y also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Nucleosome Containing H3.Y (pdb code 5ay8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Human Nucleosome Containing H3.Y, PDB code: 5ay8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5ay8

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Manganese binding site 1 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:77.3
occ:1.00
 NE A:ARG63 3.2 56.5 1.0
N A:ARG63 3.3 43.7 1.0
OG1 B:THR30 3.4 45.5 1.0
O B:GLY28 3.4 44.8 1.0
CG A:ARG63 3.5 48.2 1.0
CB B:ALA33 3.6 43.2 1.0
CB A:ARG63 3.6 41.5 1.0
N B:THR30 3.7 50.4 1.0
CD A:ARG63 3.8 58.0 1.0
CG2 B:THR30 3.9 49.8 1.0
CA A:ARG63 4.0 42.4 1.0
CZ A:ARG63 4.1 60.5 1.0
CB B:THR30 4.1 47.8 1.0
C A:LEU62 4.2 43.3 1.0
NH2 A:ARG63 4.2 55.0 1.0
CA A:LEU62 4.2 39.2 1.0
CA B:ILE29 4.4 51.0 1.0
C B:GLY28 4.5 52.0 1.0
CA B:THR30 4.6 48.8 1.0
CB A:LEU62 4.6 36.6 1.0
C B:ILE29 4.6 51.6 1.0
CD2 A:LEU62 4.6 32.6 1.0
O A:ARG63 4.6 47.3 1.0
OP1 I:DC60 4.7 56.1 1.0
CG A:PRO66 4.7 52.0 1.0
C A:ARG63 4.9 44.1 1.0
N B:ILE29 4.9 54.9 1.0
CA B:ALA33 5.0 43.8 1.0
CB A:PRO66 5.0 43.6 1.0

Manganese binding site 2 out of 8 in 5ay8

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Manganese binding site 2 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn201

b:78.7
occ:1.00
 N H:SER91 3.2 43.4 1.0
N G:GLY46 3.2 52.6 1.0
N G:ALA45 3.6 65.5 1.0
N G:ALA47 3.6 44.0 1.0
CA G:GLY46 3.6 48.2 1.0
CA H:THR90 3.6 46.0 1.0
CB H:THR90 3.7 50.2 1.0
CA G:GLY44 3.7 46.9 1.0
C G:GLY44 3.7 57.1 1.0
C H:THR90 3.8 45.3 1.0
C G:GLY46 4.0 43.2 1.0
CB H:SER91 4.0 47.3 1.0
OP1 I:DA111 4.1 76.5 1.0
CA H:SER91 4.2 42.3 1.0
C G:ALA45 4.3 51.5 1.0
CG2 H:THR90 4.4 42.2 1.0
OG H:SER91 4.4 49.6 1.0
O G:GLY44 4.5 58.6 1.0
CA G:ALA45 4.5 52.9 1.0
CA G:ALA47 4.6 46.3 1.0
CB G:ALA47 4.7 42.3 1.0
OG1 H:THR90 4.8 48.7 1.0
N G:GLY44 4.9 51.8 1.0
O G:GLY46 5.0 43.6 1.0
O H:THR90 5.0 46.9 1.0

Manganese binding site 3 out of 8 in 5ay8

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Manganese binding site 3 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn201

b:89.9
occ:1.00
 O4' I:DT64 4.2 79.2 1.0
C4' I:DT64 4.4 83.2 1.0
C5' I:DT64 4.4 85.8 1.0
N3 J:DA231 4.6 88.0 1.0
N3 I:DG63 4.7 82.1 1.0
N2 I:DG63 4.8 80.7 1.0
C2 J:DA231 4.8 85.5 1.0

Manganese binding site 4 out of 8 in 5ay8

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Manganese binding site 4 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn202

b:0.7
occ:1.00
 N2 I:DG15 3.0 84.9 1.0
O4' I:DC16 3.7 96.5 1.0
C2 I:DG15 4.0 86.0 1.0
N3 I:DG15 4.1 93.9 1.0
C4' I:DC16 4.2 92.6 1.0
N3 J:DA279 4.3 69.0 1.0
C2 J:DA279 4.8 72.3 1.0
O2 I:DC16 4.8 86.2 1.0
O4' J:DA279 4.8 79.5 1.0
C1' I:DC16 4.9 92.8 1.0
O3' I:DC16 5.0 81.9 1.0

Manganese binding site 5 out of 8 in 5ay8

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Manganese binding site 5 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn301

b:78.4
occ:1.00
 OP1 J:DG283 2.4 84.0 1.0
P J:DG283 3.7 76.8 1.0
O5' J:DG283 4.0 78.9 1.0
OP2 J:DG283 4.3 73.3 1.0
C5' J:DG283 4.7 77.8 1.0
O3' J:DT282 4.9 75.4 1.0

Manganese binding site 6 out of 8 in 5ay8

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Manganese binding site 6 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn302

b:95.5
occ:1.00
 N7 J:DG283 3.0 76.0 1.0
C8 J:DG283 3.7 79.2 1.0
C5 J:DG283 3.8 72.7 1.0
O6 J:DG284 4.0 56.7 1.0
O6 J:DG283 4.1 69.2 1.0
C6 J:DG283 4.2 70.4 1.0
N9 J:DG283 4.7 78.3 1.0
C4 J:DG283 4.8 73.7 1.0
OP2 J:DG283 4.9 73.3 1.0
C6 J:DG284 4.9 63.3 1.0
N7 J:DG284 4.9 62.2 1.0

Manganese binding site 7 out of 8 in 5ay8

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Manganese binding site 7 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn303

b:71.7
occ:1.00
 N7 J:DG280 2.5 74.5 1.0
O6 J:DG280 3.0 73.2 1.0
C5 J:DG280 3.3 71.0 1.0
C6 J:DG280 3.5 71.2 1.0
C8 J:DG280 3.6 77.8 1.0
C8 J:DA279 4.0 68.4 1.0
N7 J:DA279 4.2 68.9 1.0
O6 J:DG281 4.6 69.4 1.0
C4 J:DG280 4.6 73.1 1.0
N9 J:DG280 4.7 78.7 1.0
OP2 J:DA279 4.8 73.7 1.0
N1 J:DG280 4.9 69.9 1.0
N7 J:DG281 4.9 70.9 1.0
C2' J:DA279 5.0 79.1 1.0

Manganese binding site 8 out of 8 in 5ay8

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Manganese binding site 8 out of 8 in the Crystal Structure of Human Nucleosome Containing H3.Y


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Human Nucleosome Containing H3.Y within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn304

b:93.8
occ:1.00
 O6 J:DG246 2.4 89.7 1.0
C6 J:DG246 3.6 85.2 1.0
O6 I:DG46 4.0 88.6 1.0
N7 J:DA245 4.3 73.5 1.0
C5 J:DG246 4.5 85.7 1.0
C8 J:DA245 4.5 76.4 1.0
N7 J:DG246 4.6 85.9 1.0
N1 J:DG246 4.6 81.0 1.0
C6 I:DG46 4.9 89.0 1.0
N7 I:DG46 5.0 85.2 1.0

Reference:

T.Kujirai, N.Horikoshi, K.Sato, K.Maehara, S.Machida, A.Osakabe, H.Kimura, Y.Ohkawa, H.Kurumizaka. Structure and Function of Human Histone H3.Y Nucleosome Nucleic Acids Res. V. 44 6127 2016.
ISSN: ESSN 1362-4962
PubMed: 27016736
DOI: 10.1093/NAR/GKW202
Page generated: Sat Oct 5 23:32:21 2024

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