Manganese in PDB 1m19: Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna

The structure of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna, PDB code: 1m19 was solved by R.K.Suto, R.S.Edayathumangalam, C.L.White, C.Melander, J.M.Gottesfeld, P.B.Dervan, K.Luger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.045, 109.662, 183.018, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.3

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna (pdb code 1m19). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna, PDB code: 1m19:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn703 b:83.4 occ:1.00 O I:HOH2093 2.3 88.6 1.0 N7 I:DG134 2.5 68.5 1.0 C5 I:DG134 3.5 68.4 1.0 C8 I:DG134 3.5 74.6 1.0 O6 I:DG134 3.5 58.9 1.0 O I:HOH2072 3.7 80.7 1.0 C6 I:DG134 3.9 64.7 1.0 N7 I:DA133 4.1 69.8 1.0 C8 I:DA133 4.1 72.2 1.0 O6 I:DG135 4.2 78.2 1.0 C4 I:DG134 4.7 71.5 1.0 N9 I:DG134 4.7 75.2 1.0 C5 I:DA133 4.9 71.1 1.0 N9 I:DA133 5.0 73.9 1.0 N7 I:DG135 5.0 86.1 1.0

Manganese binding site 2 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn705 b:95.0 occ:1.00 N7 I:DG70 2.6 54.5 1.0 O I:HOH2098 3.1 65.0 1.0 C8 I:DG70 3.5 56.8 1.0 C5 I:DG70 3.6 54.0 1.0 O6 I:DG70 3.8 53.0 1.0 O6 I:DG71 4.0 65.0 1.0 C6 I:DG70 4.1 54.3 1.0 C6 I:DC69 4.4 48.6 1.0 C2' I:DC69 4.5 45.1 1.0 C5 I:DC69 4.7 50.0 1.0 N9 I:DG70 4.7 57.1 1.0 N4 J:DC222 4.8 66.0 1.0 C4 I:DG70 4.8 55.6 1.0 C6 I:DG71 4.9 64.4 1.0

Manganese binding site 3 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn707 b:0.9 occ:1.00 O J:HOH2064 2.2 63.0 1.0 O I:HOH2095 3.3 66.5 1.0 O4' I:DC88 3.8 60.8 1.0 C4' I:DC88 4.0 62.2 1.0 O4' I:DG87 4.0 68.7 1.0 C5' I:DC88 4.1 62.2 1.0 O2 I:DT86 4.2 72.8 1.0 C4' I:DG87 4.4 71.2 1.0 O4' J:DT208 4.5 47.8 1.0 C1' I:DG87 4.9 73.5 1.0 C2 J:DA207 4.9 55.7 1.0 N3 I:DG87 4.9 79.6 1.0 O2 J:DT208 4.9 58.3 1.0 N3 J:DA207 4.9 50.1 1.0

Manganese binding site 4 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn709 b:0.2 occ:1.00 N7 I:DG138 2.2 72.3 1.0 O I:HOH2034 2.6 70.0 1.0 C8 I:DG138 3.2 76.1 1.0 C5 I:DG138 3.2 70.3 1.0 O6 I:DG138 3.4 67.0 1.0 C6 I:DG138 3.7 67.4 1.0 N7 I:DG137 4.1 87.8 1.0 C8 I:DG137 4.1 88.9 1.0 N9 I:DG138 4.4 77.1 1.0 C4 I:DG138 4.4 72.4 1.0 C5 I:DG137 4.8 85.8 1.0 N6 I:DA139 4.8 59.1 1.0 O I:HOH2102 4.8 61.1 1.0 N9 I:DG137 4.8 90.1 1.0

Manganese binding site 5 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn710 b:0.6 occ:1.00 N7 I:DG39 2.5 78.5 1.0 O6 I:DG39 3.2 77.1 1.0 C7 I:DT38 3.3 79.7 1.0 C5 I:DG39 3.4 79.6 1.0 C6 I:DG39 3.6 79.6 1.0 C8 I:DG39 3.6 78.0 1.0 C5 I:DT38 3.8 82.9 1.0 C6 I:DT38 4.0 80.1 1.0 OP2 I:DT38 4.6 90.8 1.0 C4 I:DG39 4.6 78.1 1.0 N9 I:DG39 4.8 77.3 1.0 O I:HOH2043 4.9 63.0 1.0 C4 I:DT38 4.9 83.4 1.0 N1 I:DG39 5.0 78.0 1.0

Manganese binding site 6 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn711 b:0.6 occ:1.00 N7 I:DG121 2.6 87.7 1.0 C6 I:DT120 3.1 89.2 1.0 C5 I:DT120 3.3 90.6 1.0 C7 I:DT120 3.4 86.7 1.0 O6 I:DG121 3.6 83.6 1.0 C5 I:DG121 3.6 86.5 1.0 C8 I:DG121 3.6 85.2 1.0 N1 I:DT120 3.8 88.2 1.0 C2' I:DT120 3.9 87.1 1.0 C6 I:DG121 4.0 86.1 1.0 C4 I:DT120 4.2 89.7 1.0 C1' I:DT120 4.4 87.7 1.0 C2 I:DT120 4.6 87.3 1.0 O I:HOH2035 4.6 59.4 1.0 N3 I:DT120 4.7 87.9 1.0 OP2 I:DT120 4.8 98.1 1.0 C4 I:DG121 4.8 83.9 1.0 N9 I:DG121 4.8 83.0 1.0

Manganese binding site 7 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn702 b:75.0 occ:1.00 N7 J:DG280 2.5 94.3 1.0 C8 J:DG280 3.4 96.3 1.0 C5 J:DG280 3.6 95.3 1.0 O6 J:DG280 3.8 91.2 1.0 C6 J:DG280 4.1 95.4 1.0 C8 J:DA279 4.3 75.9 1.0 O6 J:DG281 4.4 0.9 1.0 N7 J:DA279 4.4 75.5 1.0 N9 J:DG280 4.7 96.7 1.0 C4 J:DG280 4.7 96.3 1.0

Manganese binding site 8 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn704 b:89.7 occ:1.00 N7 J:DG217 2.2 49.8 1.0 C5 J:DG217 3.1 48.6 1.0 O6 J:DG217 3.2 51.0 1.0 C8 J:DG217 3.3 49.1 1.0 C6 J:DG217 3.5 52.8 1.0 N6 J:DA218 3.8 53.9 1.0 O J:HOH2029 3.9 74.3 1.0 C8 J:DG216 4.1 51.3 1.0 C2' J:DG216 4.3 45.5 1.0 C4 J:DG217 4.3 49.8 1.0 N9 J:DG217 4.4 49.2 1.0 N7 J:DG216 4.4 55.8 1.0 O J:HOH2032 4.5 54.6 1.0 N9 J:DG216 4.6 48.6 1.0 O J:HOH2041 4.7 65.2 1.0 C6 J:DA218 4.7 57.7 1.0 N1 J:DG217 4.9 45.6 1.0 O4 I:DT75 5.0 68.2 1.0 N7 J:DA218 5.0 57.5 1.0

Manganese binding site 9 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn706 b:98.5 occ:1.00 N7 J:DG267 2.4 98.0 1.0 O J:HOH2051 2.4 74.8 1.0 C8 J:DG267 3.1 97.0 1.0 C5 J:DG267 3.6 97.3 1.0 O J:HOH2024 3.8 77.3 1.0 OP2 J:DG267 4.0 0.8 1.0 O6 J:DG267 4.2 95.8 1.0 C6 J:DG267 4.3 96.8 1.0 N9 J:DG267 4.4 96.6 1.0 C2' J:DT266 4.4 99.8 1.0 O3' J:DT266 4.6 0.2 1.0 O6 J:DG268 4.6 87.7 1.0 C4 J:DG267 4.6 96.3 1.0 C3' J:DT266 4.9 1.0 1.0 O J:HOH2063 5.0 71.7 1.0 P J:DG267 5.0 0.2 1.0

Manganese binding site 10 out of 11 in the Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Ligand Binding Alters the Structure and Dynamics of Nucleosomal Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn708 b:80.9 occ:1.00 OP1 J:DG246 3.3 79.5 1.0 P J:DG246 4.7 80.8 1.0

R.K.Suto, R.S.Edayathumangalam, C.L.White, C.Melander, J.M.Gottesfeld, P.B.Dervan, K.Luger. Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove Dna-Binding Ligands J.Mol.Biol. V. 326 371 2003.
ISSN: ISSN 0022-2836
PubMed: 12559907
DOI: 10.1016/S0022-2836(02)01407-9