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Manganese in PDB 3lz0: Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)

Protein crystallography data

The structure of Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1), PDB code: 3lz0 was solved by D.Vasudevan, E.Y.D.Chua, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.04 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.370, 109.660, 175.750, 90.00, 90.00, 90.00
R / Rfree (%) 26.8 / 31.8

Other elements in 3lz0:

The structure of Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) (pdb code 3lz0). 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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1), PDB code: 3lz0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3lz0

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Manganese binding site 1 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:70.9
occ:1.00
 OD1 A:ASP77 2.1 76.2 1.0
CG A:ASP77 2.8 72.5 1.0
OD2 A:ASP77 3.0 71.9 1.0
OE1 A:GLN76 4.1 70.9 1.0
CB A:ASP77 4.1 70.7 1.0
O B:LEU22 4.3 72.8 1.0
N A:ASP77 4.5 70.2 1.0
CA A:ASP77 4.6 70.8 1.0
CG A:GLU73 4.7 60.2 1.0
CB A:GLN76 4.8 70.0 1.0
CD A:GLN76 4.9 71.5 1.0

Manganese binding site 2 out of 8 in 3lz0

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Manganese binding site 2 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1002

b:0.2
occ:1.00
 N7 I:DA-72 2.2 0.8 1.0
C8 I:DA-72 2.5 0.9 1.0
C5 I:DA-72 3.6 0.9 1.0
N9 I:DA-72 3.8 0.2 1.0
C4 I:DA-72 4.4 0.1 1.0
C6 I:DA-72 4.6 0.0 1.0
N6 I:DA-72 4.6 0.1 1.0
O4' I:DA-72 4.7 0.0 1.0
C1' I:DA-72 4.9 0.5 1.0

Manganese binding site 3 out of 8 in 3lz0

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Manganese binding site 3 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1003

b:0.1
occ:1.00
 N7 I:DG-61 2.2 0.7 1.0
O6 I:DG-61 3.0 0.5 1.0
C5 I:DG-61 3.0 0.6 1.0
C8 I:DG-61 3.3 0.6 1.0
C6 I:DG-61 3.4 0.6 1.0
C6 I:DC-62 3.5 0.4 1.0
C5 I:DC-62 3.7 0.2 1.0
C2' I:DC-62 4.0 0.2 1.0
N1 I:DC-62 4.1 0.5 1.0
C4 I:DG-61 4.3 0.5 1.0
N9 I:DG-61 4.4 0.5 1.0
C4 I:DC-62 4.5 0.3 1.0
C1' I:DC-62 4.6 0.7 1.0
N1 I:DG-61 4.7 0.6 1.0
OP2 I:DC-62 4.8 0.9 1.0
C2 I:DC-62 4.8 0.5 1.0
N3 I:DC-62 5.0 0.4 1.0

Manganese binding site 4 out of 8 in 3lz0

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Manganese binding site 4 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1004

b:0.5
occ:1.00
 N7 J:DG38 2.4 0.1 1.0
C8 J:DG38 3.0 0.8 1.0
C5 J:DG38 3.3 0.1 1.0
N6 J:DA39 3.4 0.2 1.0
O6 J:DG38 3.9 0.1 1.0
C6 J:DG38 3.9 0.2 1.0
N9 J:DG38 4.1 0.4 1.0
C4 J:DG38 4.2 0.8 1.0
C6 J:DA39 4.4 0.2 1.0
N7 J:DA39 4.5 0.1 1.0
C6 J:DC37 4.7 0.2 1.0
O4 I:DT-39 4.7 0.2 1.0
C2' J:DC37 4.8 0.5 1.0
N1 J:DC37 4.8 0.6 1.0
C5 J:DA39 4.8 0.3 1.0
C5 J:DC37 4.8 0.2 1.0
C2 J:DC37 5.0 0.7 1.0

Manganese binding site 5 out of 8 in 3lz0

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Manganese binding site 5 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1005

b:0.4
occ:1.00
 N7 I:DG-34 2.4 0.2 1.0
C8 I:DG-34 3.1 0.1 1.0
C5 I:DG-34 3.6 0.2 1.0
O6 I:DG-34 4.1 0.8 1.0
C8 I:DA-35 4.2 0.1 1.0
N7 I:DA-35 4.3 0.2 1.0
C6 I:DG-34 4.3 0.8 1.0
N6 I:DA-33 4.3 0.4 1.0
N9 I:DG-34 4.4 0.8 1.0
C4 I:DG-34 4.7 0.1 1.0

Manganese binding site 6 out of 8 in 3lz0

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Manganese binding site 6 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1006

b:0.0
occ:1.00
 N7 J:DG27 2.7 0.2 1.0
C8 J:DA26 3.5 0.9 1.0
C8 J:DG27 3.5 0.8 1.0
N7 J:DA26 3.6 0.1 1.0
C5 J:DG27 3.8 1.0 1.0
O6 J:DG27 3.9 0.6 1.0
C6 J:DG27 4.2 0.7 1.0
N9 J:DA26 4.5 0.5 1.0
C5 J:DA26 4.7 0.8 1.0
C2' J:DA26 4.8 0.9 1.0
N9 J:DG27 4.8 0.4 1.0
C4 J:DG27 4.9 0.9 1.0
O4 I:DT-28 4.9 0.9 1.0
OP2 J:DA26 5.0 0.3 1.0

Manganese binding site 7 out of 8 in 3lz0

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Manganese binding site 7 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1007

b:0.2
occ:1.00
 N7 I:DG27 2.2 0.1 1.0
C8 I:DG26 2.9 0.1 1.0
C8 I:DG27 3.1 0.1 1.0
C5 I:DG27 3.1 0.1 1.0
N7 I:DG26 3.2 0.2 1.0
O6 I:DG27 3.5 0.2 1.0
C6 I:DG27 3.6 0.1 1.0
N9 I:DG26 3.9 1.0 1.0
C2' I:DG26 4.0 0.6 1.0
N9 I:DG27 4.2 0.0 1.0
C4 I:DG27 4.2 0.1 1.0
C5 I:DG26 4.2 0.1 1.0
OP2 I:DG26 4.4 0.3 1.0
C1' I:DG26 4.5 0.8 1.0
C4 I:DG26 4.6 0.1 1.0
N1 I:DG27 5.0 0.9 1.0

Manganese binding site 8 out of 8 in 3lz0

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Manganese binding site 8 out of 8 in the Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1)


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 Nucleosome Core Particle Composed of the Widom 601 Dna Sequence (Orientation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1008

b:0.7
occ:1.00
 N7 J:DA-72 2.4 0.7 1.0
C8 J:DA-72 2.9 0.8 1.0
C5 J:DA-72 3.6 0.7 1.0
N9 J:DA-72 4.1 0.9 1.0
N6 J:DA-72 4.3 0.8 1.0
C6 J:DA-72 4.4 0.8 1.0
C4 J:DA-72 4.5 0.7 1.0
O4 J:DT-71 5.0 0.4 1.0

Reference:

D.Vasudevan, E.Y.Chua, C.A.Davey. Crystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence J.Mol.Biol. V. 403 1 2010.
ISSN: ISSN 0022-2836
PubMed: 20800598
DOI: 10.1016/J.JMB.2010.08.039
Page generated: Sat Oct 5 16:53:24 2024

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