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Bromine in PDB 101d: Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation

Protein crystallography data

The structure of Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation, PDB code: 101d was solved by D.S.Goodsell, M.L.Kopka, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.270, 39.620, 63.570, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 101d:

The structure of Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation (pdb code 101d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation, PDB code: 101d:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 101d

Go back to Bromine Binding Sites List in 101d
Bromine binding site 1 out of 2 in the Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br9

b:30.8
occ:1.00
BR A:CBR9 0.0 30.8 1.0
C5 A:CBR9 1.8 8.0 1.0
C6 A:CBR9 2.7 7.6 1.0
C4 A:CBR9 2.8 11.1 1.0
N4 A:CBR9 3.1 6.3 1.0
O A:HOH54 3.7 37.0 1.0
C6 A:DT8 3.9 1.9 1.0
C2' A:DT8 3.9 0.1 1.0
N1 A:CBR9 4.0 13.1 1.0
N3 A:CBR9 4.1 11.1 1.0
N1 A:DT8 4.2 0.4 1.0
C5 A:DT8 4.2 1.6 1.0
C7 A:DT8 4.6 0.0 1.0
C2 A:CBR9 4.6 5.0 1.0
O6 A:DG10 4.6 5.2 1.0
C1' A:DT8 4.7 0.0 1.0
C2 A:DT8 4.8 3.0 1.0
C4 A:DT8 4.8 0.0 1.0
C3' A:DT8 4.9 0.0 1.0

Bromine binding site 2 out of 2 in 101d

Go back to Bromine Binding Sites List in 101d
Bromine binding site 2 out of 2 in the Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br21

b:15.9
occ:1.00
BR B:CBR21 0.0 15.9 1.0
C5 B:CBR21 1.7 7.5 1.0
C6 B:CBR21 2.7 3.1 1.0
C4 B:CBR21 2.7 4.0 1.0
N4 B:CBR21 3.0 0.0 1.0
C2' B:DT20 3.7 0.0 1.0
C6 B:DT20 3.8 0.0 1.0
N1 B:CBR21 4.0 8.1 1.0
N3 B:CBR21 4.0 0.1 1.0
N1 B:DT20 4.0 2.4 1.0
O B:HOH36 4.1 7.7 1.0
C5 B:DT20 4.1 0.0 1.0
O B:HOH49 4.3 29.3 1.0
O B:HOH62 4.3 40.1 1.0
C1' B:DT20 4.4 0.0 1.0
O6 B:DG22 4.5 0.0 1.0
C2 B:CBR21 4.5 0.1 1.0
C7 B:DT20 4.6 0.0 1.0
C2 B:DT20 4.6 0.0 1.0
O B:HOH43 4.7 6.2 1.0
C4 B:DT20 4.7 0.0 1.0
N7 B:DG22 4.9 4.3 1.0
N3 B:DT20 4.9 0.0 1.0

Reference:

D.S.Goodsell, M.L.Kopka, R.E.Dickerson. Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation. Biochemistry V. 34 4983 1995.
ISSN: ISSN 0006-2960
PubMed: 7711020
DOI: 10.1021/BI00015A009
Page generated: Sat Dec 12 01:59:29 2020

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