Manganese in PDB 1s32: Molecular Recognition of the Nucleosomal 'Supergroove'

The structure of Molecular Recognition of the Nucleosomal 'Supergroove', PDB code: 1s32 was solved by R.S.Edayathumangalam, P.Weyermann, 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)	100.00 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.352, 109.717, 181.827, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.3

The structure of Molecular Recognition of the Nucleosomal 'Supergroove' also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Molecular Recognition of the Nucleosomal 'Supergroove' (pdb code 1s32). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Molecular Recognition of the Nucleosomal 'Supergroove', PDB code: 1s32:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2003 b:83.4 occ:0.98 N7 I:DG70 2.1 56.2 1.0 O I:HOH3400 2.3 61.9 1.0 C8 I:DG70 3.1 56.1 1.0 C5 I:DG70 3.2 54.5 1.0 O6 I:DG71 3.2 66.2 1.0 O6 I:DG70 3.5 51.6 1.0 C6 I:DG70 3.7 53.0 1.0 C6 I:DG71 4.1 66.5 1.0 O I:HOH3276 4.2 58.0 1.0 N9 I:DG70 4.3 55.8 1.0 C4 I:DG70 4.3 54.9 1.0 C2' I:DC69 4.4 56.7 1.0 C6 I:DC69 4.4 57.1 1.0 N7 I:DG71 4.5 65.9 1.0 N4 J:DC222 4.5 89.3 1.0 C5 I:DG71 4.6 66.6 1.0 C5 I:DC69 4.7 57.6 1.0 N1 I:DC69 4.8 57.3 1.0

Manganese binding site 2 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2004 b:77.7 occ:0.82 O I:HOH3402 2.3 68.7 1.0 O I:HOH3403 2.3 66.9 1.0 O I:HOH3401 2.3 79.0 1.0 N7 I:DG134 2.5 90.2 1.0 C8 I:DG134 3.4 91.2 1.0 C5 I:DG134 3.5 90.6 1.0 O6 I:DG134 3.6 88.0 1.0 C6 I:DG134 3.9 89.5 1.0 C8 I:DA133 3.9 77.2 1.0 N7 I:DA133 4.1 76.0 1.0 N9 I:DG134 4.6 92.0 1.0 C4 I:DG134 4.7 91.1 1.0 O6 I:DG135 4.7 95.2 1.0 OP2 I:DA133 4.8 72.9 1.0 N9 I:DA133 4.9 77.6 1.0

Manganese binding site 3 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2006 b:0.1 occ:0.71 N7 I:DG100 2.2 78.2 1.0 O I:HOH3832 2.3 86.7 1.0 O I:HOH3526 3.1 95.6 1.0 C8 I:DG100 3.2 77.4 1.0 C5 I:DG100 3.2 78.1 1.0 O6 I:DG100 3.4 80.0 1.0 C6 I:DG100 3.6 78.6 1.0 O I:HOH3817 3.9 71.9 1.0 O I:HOH3527 4.2 86.2 1.0 N9 I:DG100 4.4 77.4 1.0 C4 I:DG100 4.4 77.5 1.0 O I:HOH3525 4.5 92.1 1.0 C8 I:DA99 4.7 90.3 1.0 N7 I:DA99 4.8 89.9 1.0 N4 I:DC101 4.9 80.9 1.0

Manganese binding site 4 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2007 b:89.7 occ:0.81 O6 I:DG40 2.2 82.0 1.0 N7 I:DG39 2.3 83.2 1.0 O I:HOH3153 2.6 61.9 1.0 C6 I:DG40 3.1 81.1 1.0 C8 I:DG39 3.2 82.6 1.0 C5 I:DG39 3.3 83.2 1.0 O6 I:DG39 3.6 83.5 1.0 C5 I:DG40 3.8 80.5 1.0 C6 I:DG39 3.8 83.4 1.0 N7 I:DG40 4.0 79.6 1.0 N1 I:DG40 4.0 80.5 1.0 N4 J:DC253 4.3 0.6 1.0 OP2 I:DG39 4.4 81.7 1.0 N9 I:DG39 4.4 82.0 1.0 C2' I:DT38 4.4 87.6 1.0 C4 I:DG39 4.4 83.0 1.0 O3' I:DT38 4.8 84.4 1.0 C4 I:DG40 5.0 80.4 1.0

Manganese binding site 5 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2009 b:0.4 occ:0.66 N7 I:DG121 2.3 92.0 1.0 C8 I:DG121 3.2 91.3 1.0 C5 I:DG121 3.3 92.3 1.0 O6 I:DG121 3.6 92.2 1.0 C6 I:DG121 3.8 92.5 1.0 C2' I:DT120 4.3 0.8 1.0 N9 I:DG121 4.4 91.5 1.0 O6 I:DG122 4.5 90.4 1.0 C6 I:DT120 4.5 0.9 1.0 C4 I:DG121 4.5 92.1 1.0 O I:HOH3584 4.5 73.9 1.0 C7 I:DT120 4.9 0.8 1.0 C5 I:DT120 4.9 0.6 1.0

Manganese binding site 6 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2012 b:60.5 occ:0.80 O J:HOH3820 2.0 41.8 0.9 O I:HOH3821 2.0 44.9 0.9 O I:HOH3827 2.3 56.3 0.0 O J:HOH3833 2.3 63.3 1.0 O J:HOH3295 2.5 45.6 0.9 O J:HOH3002 3.7 63.1 1.0 O I:HOH3166 4.1 57.1 1.0 O J:HOH3001 4.1 63.2 1.0 O4' J:DT208 4.2 47.8 1.0 O2 I:DT86 4.2 65.4 1.0 C2 J:DA207 4.3 51.6 1.0 O2 J:DT208 4.4 55.0 1.0 O4' I:DG87 4.4 63.1 1.0 O4' I:DC88 4.4 67.3 1.0 N3 J:DA207 4.4 49.0 1.0 C4' I:DC88 4.6 67.3 1.0 O I:HOH3128 4.6 65.0 1.0 C5' I:DC88 4.6 66.2 1.0 C4' J:DT208 4.7 50.0 1.0 C1' J:DT208 4.7 49.3 1.0 C4' I:DG87 4.8 64.2 1.0 N3 I:DG87 4.9 68.8 1.0

Manganese binding site 7 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn2014 b:0.7 occ:0.59 N7 I:DG138 2.1 87.0 1.0 O I:HOH3233 2.4 85.3 1.0 C5 I:DG138 3.1 86.6 1.0 O6 I:DG138 3.2 85.3 1.0 C8 I:DG138 3.2 88.3 1.0 O I:HOH3004 3.5 86.3 1.0 C6 I:DG138 3.5 85.8 1.0 C8 I:DG137 3.6 0.1 1.0 N7 I:DG137 3.7 0.0 1.0 N6 I:DA139 4.2 75.8 1.0 C4 I:DG138 4.3 87.7 1.0 N9 I:DG137 4.3 0.9 1.0 N9 I:DG138 4.4 89.9 1.0 C5 I:DG137 4.5 99.7 1.0 C2' I:DG137 4.7 0.5 1.0 C4 I:DG137 4.8 0.5 1.0 N1 I:DG138 4.9 85.0 1.0

Manganese binding site 8 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn2002 b:72.3 occ:0.76 O J:HOH3395 2.1 72.6 1.0 O I:HOH3396 2.2 76.8 1.0 O J:HOH3399 2.2 76.3 1.0 O J:HOH3397 2.3 73.3 1.0 O J:HOH3398 2.4 86.3 1.0 N7 J:DG246 2.5 85.2 1.0 O J:HOH3807 3.3 92.0 1.0 C5 J:DG246 3.3 85.0 1.0 C8 J:DG246 3.4 85.2 1.0 O6 J:DG246 3.4 86.2 1.0 C6 J:DG246 3.7 85.0 1.0 O6 I:DG46 4.3 0.1 1.0 C4 J:DG246 4.5 85.2 1.0 N9 J:DG246 4.5 85.3 1.0 O J:HOH3665 4.8 84.0 1.0 C8 J:DA245 4.9 90.3 1.0

Manganese binding site 9 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn2005 b:77.4 occ:0.94 N7 J:DG280 1.9 0.7 1.0 O J:HOH3641 2.4 77.6 1.0 C5 J:DG280 2.6 0.8 1.0 O6 J:DG280 2.7 0.3 1.0 C6 J:DG280 2.9 0.0 1.0 C8 J:DG280 3.1 0.1 1.0 C4 J:DG280 3.9 0.7 1.0 C8 J:DA279 4.0 71.7 1.0 N7 J:DA279 4.0 71.0 1.0 N9 J:DG280 4.1 0.0 1.0 N1 J:DG280 4.3 0.6 1.0 O6 J:DG281 4.5 0.1 1.0 N9 J:DA279 4.9 72.7 1.0 C5 J:DA279 4.9 71.7 1.0

Manganese binding site 10 out of 14 in the Molecular Recognition of the Nucleosomal 'Supergroove'


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Molecular Recognition of the Nucleosomal 'Supergroove' within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn2008 b:0.8 occ:0.80 O J:HOH3411 2.3 86.8 1.0 N7 J:DG267 2.3 91.9 1.0 O J:HOH3047 2.4 0.7 1.0 C5 J:DG267 3.2 91.5 1.0 O6 J:DG267 3.2 92.5 1.0 C8 J:DG267 3.3 91.2 1.0 C6 J:DG267 3.5 91.9 1.0 C2' J:DT266 3.7 0.4 1.0 O J:HOH3643 4.2 98.9 1.0 C4 J:DG267 4.4 90.7 1.0 N9 J:DG267 4.5 90.2 1.0 O6 J:DG268 4.6 87.9 1.0 C1' J:DT266 4.7 0.1 1.0 O J:HOH3825 4.7 86.8 1.0 C6 J:DT266 4.8 0.9 1.0 C3' J:DT266 4.8 0.2 1.0 N1 J:DT266 4.8 0.1 1.0 OP2 J:DG267 4.8 96.0 1.0 N1 J:DG267 4.9 91.1 1.0

R.S.Edayathumangalam, P.Weyermann, J.M.Gottesfeld, P.B.Dervan, K.Luger. Molecular Recognition of the Nucleosomal 'Supergroove' Proc.Natl.Acad.Sci.Usa V. 101 6864 2004.
ISSN: ISSN 0027-8424
PubMed: 15100411
DOI: 10.1073/PNAS.0401743101