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Bromine in PDB 115d: Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution

Protein crystallography data

The structure of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution, PDB code: 115d was solved by O.Kennard, W.B.T.Cruse, J.Nachman, T.Prange, Z.Shakked, D.Rabinovich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 45.084, 45.084, 41.720, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Bromine Binding Sites:

The binding sites of Bromine atom in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution (pdb code 115d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution, PDB code: 115d:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 115d

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Bromine binding site 1 out of 4 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3

b:14.6
occ:1.00
BR A:BRU3 0.0 14.6 1.0
C5 A:BRU3 1.8 14.6 1.0
C6 A:BRU3 2.8 14.6 1.0
C4 A:BRU3 2.8 14.6 1.0
O4 A:BRU3 3.1 14.6 1.0
OP2 A:BRU3 3.7 17.8 1.0
O A:HOH33 3.7 33.4 1.0
O A:HOH70 3.7 33.4 1.0
N7 A:DG2 3.8 14.6 1.0
C8 A:DG2 3.8 14.6 1.0
O A:HOH34 3.8 33.4 1.0
O A:HOH20 3.8 33.4 1.0
C5 A:DG2 3.9 14.6 1.0
N9 A:DG2 3.9 14.6 1.0
O A:HOH61 3.9 33.4 1.0
C4 A:DG2 4.0 14.6 1.0
N3 A:BRU3 4.1 14.6 1.0
N1 A:BRU3 4.1 14.6 1.0
C3' A:DG2 4.2 16.2 1.0
O A:HOH101 4.2 33.4 1.0
C2' A:DG2 4.4 16.2 1.0
O5' A:BRU3 4.4 16.2 1.0
C6 A:DG2 4.5 14.6 1.0
P A:BRU3 4.6 17.8 1.0
N3 A:DG2 4.6 14.6 1.0
C2 A:BRU3 4.7 14.6 1.0
C1' A:DG2 4.7 16.2 1.0
O A:HOH29 4.8 33.4 1.0
O5' A:DG2 4.8 16.2 1.0
O3' A:DG2 4.9 16.2 1.0

Bromine binding site 2 out of 4 in 115d

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Bromine binding site 2 out of 4 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br5

b:14.6
occ:1.00
BR A:BRU5 0.0 14.6 1.0
C5 A:BRU5 1.8 14.6 1.0
C6 A:BRU5 2.8 14.6 1.0
C4 A:BRU5 2.8 14.6 1.0
O4 A:BRU5 3.1 14.6 1.0
O A:HOH40 3.5 33.4 1.0
O A:HOH56 3.7 33.4 1.0
OP2 A:BRU5 3.7 17.8 1.0
C8 A:DA4 3.7 14.6 1.0
O A:HOH86 3.8 33.4 1.0
O A:HOH49 3.8 33.4 1.0
N7 A:DA4 3.8 14.6 1.0
O A:HOH31 3.8 33.4 1.0
O A:HOH24 4.0 33.4 1.0
N3 A:BRU5 4.1 14.6 1.0
N1 A:BRU5 4.1 14.6 1.0
N9 A:DA4 4.2 14.6 1.0
C3' A:DA4 4.2 16.2 1.0
C5 A:DA4 4.2 14.6 1.0
O A:HOH20 4.2 33.4 1.0
C4 A:DA4 4.5 14.6 1.0
C2' A:DA4 4.5 16.2 1.0
O5' A:BRU5 4.5 16.2 1.0
P A:BRU5 4.6 17.8 1.0
C2 A:BRU5 4.6 14.6 1.0
O5' A:DA4 4.7 16.2 1.0
C1' A:DA4 4.9 16.2 1.0
OP2 A:DA4 4.9 17.8 1.0
O3' A:DA4 4.9 16.2 1.0
C6 A:DA4 4.9 14.6 1.0

Bromine binding site 3 out of 4 in 115d

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Bromine binding site 3 out of 4 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br11

b:14.6
occ:1.00
BR B:BRU11 0.0 14.6 1.0
C5 B:BRU11 1.8 14.6 1.0
C6 B:BRU11 2.8 14.6 1.0
C4 B:BRU11 2.8 14.6 1.0
O4 B:BRU11 3.1 14.6 1.0
O B:HOH65 3.2 33.4 1.0
N7 B:DG10 3.6 14.6 1.0
C8 B:DG10 3.7 14.6 1.0
O B:HOH22 3.8 33.4 1.0
O B:HOH73 3.8 33.4 1.0
C5 B:DG10 3.8 14.6 1.0
OP2 B:BRU11 3.8 17.8 1.0
N9 B:DG10 3.8 14.6 1.0
C4 B:DG10 3.9 14.6 1.0
O B:HOH17 4.0 33.4 1.0
N1 B:BRU11 4.0 14.6 1.0
N3 B:BRU11 4.1 14.6 1.0
C3' B:DG10 4.1 16.2 1.0
O B:HOH47 4.1 33.4 1.0
O B:HOH32 4.3 33.4 1.0
C6 B:DG10 4.4 14.6 1.0
O5' B:BRU11 4.4 16.2 1.0
C2' B:DG10 4.4 16.2 1.0
P B:BRU11 4.5 17.8 1.0
N3 B:DG10 4.6 14.6 1.0
C2 B:BRU11 4.6 14.6 1.0
O5' B:DG10 4.7 16.2 1.0
C1' B:DG10 4.7 16.2 1.0
O3' B:DG10 4.8 16.2 1.0
N7 B:DA12 4.9 14.6 1.0
O6 B:DG10 4.9 14.6 1.0
N1 B:DG10 4.9 14.6 1.0

Bromine binding site 4 out of 4 in 115d

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Bromine binding site 4 out of 4 in the Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Ordered Water Structure in An A-Dna Octamer at 1.7 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br13

b:14.6
occ:1.00
BR B:BRU13 0.0 14.6 1.0
C5 B:BRU13 1.8 14.6 1.0
C6 B:BRU13 2.8 14.6 1.0
C4 B:BRU13 2.8 14.6 1.0
O4 B:BRU13 3.1 14.6 1.0
O B:HOH97 3.5 33.4 1.0
C8 B:DA12 3.7 14.6 1.0
N7 B:DA12 3.7 14.6 1.0
OP2 B:BRU13 3.7 17.8 1.0
O B:HOH23 3.7 33.4 1.0
O B:HOH76 3.7 33.4 1.0
N9 B:DA12 3.9 14.6 1.0
O B:HOH25 3.9 33.4 1.0
C5 B:DA12 4.0 14.6 1.0
N3 B:BRU13 4.1 14.6 1.0
N1 B:BRU13 4.1 14.6 1.0
C3' B:DA12 4.1 16.2 1.0
O B:HOH17 4.1 33.4 1.0
C4 B:DA12 4.1 14.6 1.0
O B:HOH42 4.2 33.4 1.0
C2' B:DA12 4.4 16.2 1.0
O5' B:BRU13 4.6 16.2 1.0
P B:BRU13 4.6 17.8 1.0
C2 B:BRU13 4.6 14.6 1.0
C1' B:DA12 4.7 16.2 1.0
C6 B:DA12 4.7 14.6 1.0
O3' B:DA12 4.8 16.2 1.0
N3 B:DA12 4.9 14.6 1.0

Reference:

O.Kennard, W.B.Cruse, J.Nachman, T.Prange, Z.Shakked, D.Rabinovich. Ordered Water Structure in An A-Dna Octamer at 1.7 A Resolution. J.Biomol.Struct.Dyn. V. 3 623 1986.
ISSN: ISSN 0739-1102
PubMed: 3271041
Page generated: Sat Dec 12 01:59:29 2020

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