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Bromine in PDB 1i3w: Actinomycin D Binding to Cgatcgatcg

Protein crystallography data

The structure of Actinomycin D Binding to Cgatcgatcg, PDB code: 1i3w was solved by H.Robinson, Y.-G.Gao, X.-L.Yang, R.Sanishvili, A.Joachimiak, A.H.-J.Wang, 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 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.013, 47.013, 160.368, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 27.9

Bromine Binding Sites:

The binding sites of Bromine atom in the Actinomycin D Binding to Cgatcgatcg (pdb code 1i3w). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Actinomycin D Binding to Cgatcgatcg, PDB code: 1i3w:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 1i3w

Go back to Bromine Binding Sites List in 1i3w
Bromine binding site 1 out of 4 in the Actinomycin D Binding to Cgatcgatcg


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Actinomycin D Binding to Cgatcgatcg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br8

b:51.3
occ:1.00
BR A:BRU8 0.0 51.3 1.0
C5 A:BRU8 1.9 40.0 1.0
C6 A:BRU8 2.8 25.2 1.0
C4 A:BRU8 2.8 32.7 1.0
O A:HOH2009 2.9 37.6 1.0
O4 A:BRU8 3.0 34.3 1.0
C8 A:DA7 3.6 25.6 1.0
O A:HOH2027 3.7 25.3 1.0
N7 A:DA7 3.8 33.6 1.0
N3 A:BRU8 4.1 36.0 1.0
N1 A:BRU8 4.1 39.4 1.0
N4 A:DC9 4.1 34.3 1.0
N9 A:DA7 4.2 29.6 1.0
O A:HOH2012 4.2 49.0 1.0
C2' A:DA7 4.4 37.5 1.0
C5 A:DA7 4.4 28.7 1.0
C4 A:DA7 4.6 20.2 1.0
C2' D:DT34 4.6 26.0 1.0
C2 A:BRU8 4.7 33.3 1.0
C1' A:DA7 4.8 37.0 1.0
C4 A:DC9 5.0 30.8 1.0
OP1 D:DC35 5.0 35.7 1.0

Bromine binding site 2 out of 4 in 1i3w

Go back to Bromine Binding Sites List in 1i3w
Bromine binding site 2 out of 4 in the Actinomycin D Binding to Cgatcgatcg


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Actinomycin D Binding to Cgatcgatcg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br18

b:37.6
occ:1.00
BR B:BRU18 0.0 37.6 1.0
C5 B:BRU18 1.9 23.3 1.0
C6 B:BRU18 2.8 23.0 1.0
C4 B:BRU18 2.8 22.1 1.0
O4 B:BRU18 3.0 25.1 1.0
O B:HOH2009 3.0 42.1 1.0
C2' B:DA17 3.5 29.9 1.0
O C:HOH2013 3.6 48.1 1.0
C8 B:DA17 3.6 25.6 1.0
O B:HOH2029 3.6 40.4 1.0
O B:HOH2037 3.7 43.6 1.0
O B:HOH2039 3.7 27.5 1.0
N9 B:DA17 3.8 26.9 1.0
N4 B:DC19 3.9 27.6 1.0
O B:HOH2033 3.9 23.1 0.5
N7 B:DA17 3.9 22.0 1.0
N3 B:BRU18 4.1 20.5 1.0
N1 B:BRU18 4.1 26.7 1.0
C5 B:DA17 4.1 21.8 1.0
C4 B:DA17 4.2 26.9 1.0
C1' B:DA17 4.2 33.0 1.0
O B:HOH2035 4.4 48.1 1.0
OP2 B:BRU18 4.5 44.1 1.0
C2 B:BRU18 4.6 28.4 1.0
C4 B:DC19 4.7 23.1 1.0
C2' C:DT24 4.8 20.9 1.0
C3' B:DA17 4.8 41.1 1.0
N3 B:DA17 4.9 23.2 1.0
C5 B:DC19 4.9 29.5 1.0

Bromine binding site 3 out of 4 in 1i3w

Go back to Bromine Binding Sites List in 1i3w
Bromine binding site 3 out of 4 in the Actinomycin D Binding to Cgatcgatcg


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Actinomycin D Binding to Cgatcgatcg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br28

b:45.8
occ:1.00
BR C:BRU28 0.0 45.8 1.0
C5 C:BRU28 1.9 24.9 1.0
O B:HOH2004 2.3 35.9 1.0
C6 C:BRU28 2.8 25.4 1.0
C4 C:BRU28 2.9 21.8 1.0
O4 C:BRU28 3.2 24.3 1.0
C8 C:DA27 3.5 29.8 1.0
O C:HOH2026 3.6 22.4 1.0
O C:HOH2025 3.8 40.9 1.0
N7 C:DA27 3.8 34.2 1.0
N9 C:DA27 4.0 29.0 1.0
N1 C:BRU28 4.1 28.5 1.0
N3 C:BRU28 4.1 27.8 1.0
N4 C:DC29 4.3 25.4 1.0
C5 C:DA27 4.3 32.2 1.0
C2' C:DA27 4.3 39.4 1.0
O B:HOH2001 4.4 46.3 1.0
C4 C:DA27 4.5 32.5 1.0
C2' B:DT14 4.5 22.4 1.0
OP1 B:DC15 4.6 41.8 1.0
C1' C:DA27 4.6 41.1 1.0
C2 C:BRU28 4.6 22.1 1.0
C3' B:DT14 4.8 22.3 1.0

Bromine binding site 4 out of 4 in 1i3w

Go back to Bromine Binding Sites List in 1i3w
Bromine binding site 4 out of 4 in the Actinomycin D Binding to Cgatcgatcg


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Actinomycin D Binding to Cgatcgatcg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br38

b:43.0
occ:1.00
BR D:BRU38 0.0 43.0 1.0
C5 D:BRU38 1.9 20.7 1.0
C4 D:BRU38 2.8 26.7 1.0
C6 D:BRU38 2.8 26.8 1.0
O4 D:BRU38 3.0 27.2 1.0
O A:HOH2018 3.5 37.5 1.0
C8 D:DA37 3.5 29.9 1.0
O D:HOH2036 3.6 31.2 1.0
O D:HOH2030 3.8 38.9 1.0
C2' D:DA37 3.8 35.5 1.0
N9 D:DA37 3.8 31.4 1.0
N7 D:DA37 3.9 21.7 1.0
O D:HOH2038 4.0 45.9 1.0
N3 D:BRU38 4.1 25.6 1.0
N1 D:BRU38 4.1 35.0 1.0
C5 D:DA37 4.1 22.2 1.0
C4 D:DA37 4.2 20.4 1.0
N4 D:DC39 4.4 23.9 1.0
C1' D:DA37 4.4 32.2 1.0
O D:HOH2031 4.5 41.9 1.0
C2 D:BRU38 4.7 32.4 1.0
C4 D:DC39 5.0 28.8 1.0

Reference:

H.Robinson, Y.G.Gao, X.Yang, R.Sanishvili, A.Joachimiak, A.H.Wang. Crystallographic Analysis of A Novel Complex of Actinomycin D Bound to the Dna Decamer Cgatcgatcg. Biochemistry V. 40 5587 2001.
ISSN: ISSN 0006-2960
PubMed: 11341823
DOI: 10.1021/BI002859Z
Page generated: Wed Jul 10 16:40:07 2024

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