Phosphorus 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

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus 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 Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Refinement of Netropsin Bound to Dna: Bias and Feedback in Electron Density Map Interpretation, PDB code: 101d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 101d

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Phosphorus binding site 1 out of 22 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 Phosphorus with other atoms in the P 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:P2

b:16.5
occ:1.00
P A:DG2 0.0 16.5 1.0
OP2 A:DG2 1.5 15.1 1.0
OP1 A:DG2 1.5 19.7 1.0
O5' A:DG2 1.6 11.5 1.0
O3' A:DC1 1.6 9.7 1.0
C3' A:DC1 2.6 8.0 1.0
C5' A:DG2 2.7 12.5 1.0
C2' A:DC1 3.3 6.6 1.0
O A:HOH48 3.3 14.3 1.0
C4' A:DG2 3.9 9.0 1.0
C4' A:DC1 3.9 8.8 1.0
C3' A:DG2 4.1 6.7 1.0
C1' A:DC1 4.3 1.1 1.0
C2' A:DG2 4.6 5.0 1.0
O4' A:DG2 4.6 8.8 1.0
O4' A:DC1 4.7 4.4 1.0
O A:HOH34 4.8 15.1 1.0
C5' A:DC1 4.8 8.0 1.0

Phosphorus binding site 2 out of 22 in 101d

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Phosphorus binding site 2 out of 22 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 Phosphorus with other atoms in the P 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
A:P3

b:13.8
occ:1.00
P A:DC3 0.0 13.8 1.0
OP2 A:DC3 1.5 1.7 1.0
OP1 A:DC3 1.5 10.7 1.0
O3' A:DG2 1.6 12.6 1.0
O5' A:DC3 1.6 0.3 1.0
C5' A:DC3 2.7 8.4 1.0
C3' A:DG2 2.8 6.7 1.0
C2' A:DG2 3.5 5.0 1.0
C4' A:DC3 3.8 2.4 1.0
O4' A:DC3 4.0 5.4 1.0
C4' A:DG2 4.0 9.0 1.0
C1' A:DG2 4.3 1.7 1.0
C3' A:DC3 4.5 11.8 1.0
O A:HOH39 4.5 27.9 1.0
O4' A:DG2 4.7 8.8 1.0

Phosphorus binding site 3 out of 22 in 101d

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Phosphorus binding site 3 out of 22 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 Phosphorus with other atoms in the P binding site number 3 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:P4

b:6.0
occ:1.00
P A:DG4 0.0 6.0 1.0
OP1 A:DG4 1.5 20.3 1.0
OP2 A:DG4 1.5 9.3 1.0
O3' A:DC3 1.6 9.1 1.0
O5' A:DG4 1.6 12.4 1.0
C3' A:DC3 2.6 11.8 1.0
C5' A:DG4 2.7 0.0 1.0
C2' A:DC3 3.2 3.9 1.0
C4' A:DG4 3.9 6.1 1.0
C4' A:DC3 4.0 2.4 1.0
C8 A:DG4 4.0 0.0 1.0
O A:HOH39 4.3 27.9 1.0
O4' A:DG4 4.4 0.0 1.0
O A:HOH33 4.4 16.8 1.0
C2' A:DG4 4.5 3.0 1.0
C5' A:DC3 4.6 8.4 1.0
C1' A:DC3 4.6 0.0 1.0
C3' A:DG4 4.6 3.2 1.0
N9 A:DG4 4.6 0.0 1.0
O A:HOH35 4.6 4.9 1.0
C1' A:DG4 4.8 0.0 1.0
N7 A:DG4 4.8 0.0 1.0
O4' A:DC3 4.9 5.4 1.0

Phosphorus binding site 4 out of 22 in 101d

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Phosphorus binding site 4 out of 22 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 Phosphorus with other atoms in the P binding site number 4 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:P5

b:7.5
occ:1.00
P A:DA5 0.0 7.5 1.0
OP2 A:DA5 1.5 10.2 1.0
OP1 A:DA5 1.5 14.4 1.0
O3' A:DG4 1.6 0.0 1.0
O5' A:DA5 1.6 10.8 1.0
C3' A:DG4 2.6 3.2 1.0
C5' A:DA5 2.6 9.6 1.0
C2' A:DG4 3.2 3.0 1.0
C4' A:DG4 3.9 6.1 1.0
C4' A:DA5 3.9 6.2 1.0
C1' A:DG4 3.9 0.0 1.0
C3' A:DA5 4.3 6.9 1.0
O4' A:DG4 4.3 0.0 1.0
C2' A:DA5 4.3 6.2 1.0
C8 A:DA5 4.4 0.0 1.0
O4' A:DA5 4.7 5.3 1.0
C1' A:DA5 5.0 0.4 1.0

Phosphorus binding site 5 out of 22 in 101d

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Phosphorus binding site 5 out of 22 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 Phosphorus with other atoms in the P binding site number 5 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:P6

b:4.6
occ:1.00
P A:DA6 0.0 4.6 1.0
OP2 A:DA6 1.4 7.7 1.0
OP1 A:DA6 1.5 10.9 1.0
O5' A:DA6 1.6 13.1 1.0
O3' A:DA5 1.6 7.9 1.0
C5' A:DA6 2.5 2.5 1.0
C3' A:DA5 2.7 6.9 1.0
C2' A:DA5 3.3 6.2 1.0
C4' A:DA6 3.9 0.8 1.0
C4' A:DA5 4.0 6.2 1.0
C1' A:DA5 4.0 0.4 1.0
C3' A:DA6 4.3 3.8 1.0
O4' A:DA5 4.5 5.3 1.0
O4' A:DA6 4.5 0.4 1.0
C2' A:DA6 4.7 3.5 1.0

Phosphorus binding site 6 out of 22 in 101d

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Phosphorus binding site 6 out of 22 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 Phosphorus with other atoms in the P binding site number 6 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:P7

b:1.5
occ:1.00
P A:DT7 0.0 1.5 1.0
OP2 A:DT7 1.5 3.1 1.0
O5' A:DT7 1.6 5.2 1.0
OP1 A:DT7 1.6 8.0 1.0
O3' A:DA6 1.6 8.2 1.0
C3' A:DA6 2.7 3.8 1.0
C5' A:DT7 2.7 2.6 1.0
C2' A:DA6 3.3 3.5 1.0
C4' A:DT7 3.8 0.1 1.0
C4' A:DA6 4.0 0.8 1.0
O4' A:DT7 4.1 0.0 1.0
C1' A:DA6 4.1 0.0 1.0
C3' A:DT7 4.1 0.0 1.0
O4' A:DA6 4.5 0.4 1.0
C2' A:DT7 4.7 1.2 1.0

Phosphorus binding site 7 out of 22 in 101d

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Phosphorus binding site 7 out of 22 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 Phosphorus with other atoms in the P binding site number 7 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:P8

b:4.2
occ:1.00
P A:DT8 0.0 4.2 1.0
OP2 A:DT8 1.5 10.5 1.0
OP1 A:DT8 1.5 8.4 1.0
O5' A:DT8 1.6 4.4 1.0
O3' A:DT7 1.6 11.8 1.0
C5' A:DT8 2.7 0.0 1.0
C3' A:DT7 2.8 0.0 1.0
C2' A:DT7 3.5 1.2 1.0
C4' A:DT8 3.8 5.6 1.0
C4' A:DT7 3.9 0.1 1.0
O4' A:DT8 4.1 0.0 1.0
C3' A:DT8 4.2 0.0 1.0
O A:HOH53 4.2 12.8 1.0
C1' A:DT7 4.3 2.5 1.0
O A:HOH52 4.3 22.0 1.0
C8 B:NT25 4.5 31.1 1.0
O4' A:DT7 4.8 0.0 1.0
O3' A:DT8 5.0 12.8 1.0
C5' A:DT7 5.0 2.6 1.0

Phosphorus binding site 8 out of 22 in 101d

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Phosphorus binding site 8 out of 22 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 Phosphorus with other atoms in the P binding site number 8 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:P9

b:10.9
occ:1.00
P A:CBR9 0.0 10.9 1.0
OP1 A:CBR9 1.5 13.2 1.0
OP2 A:CBR9 1.5 24.4 1.0
O5' A:CBR9 1.6 23.5 1.0
O3' A:DT8 1.6 12.8 1.0
C5' A:CBR9 2.7 18.3 1.0
C3' A:DT8 2.9 0.0 1.0
C2' A:DT8 3.4 0.1 1.0
C4' A:CBR9 3.9 20.8 1.0
C4' A:DT8 4.0 5.6 1.0
O A:HOH53 4.3 12.8 1.0
C3' A:CBR9 4.3 18.4 1.0
O4' A:CBR9 4.5 15.3 1.0
C1' A:DT8 4.6 0.0 1.0
C5' A:DT8 4.8 0.0 1.0
O5' A:DT8 5.0 4.4 1.0
O4' A:DT8 5.0 0.0 1.0

Phosphorus binding site 9 out of 22 in 101d

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Phosphorus binding site 9 out of 22 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 Phosphorus with other atoms in the P binding site number 9 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:P10

b:22.6
occ:1.00
P A:DG10 0.0 22.6 1.0
OP1 A:DG10 1.5 30.3 1.0
OP2 A:DG10 1.5 22.3 1.0
O3' A:CBR9 1.6 21.6 1.0
O5' A:DG10 1.6 28.8 1.0
C3' A:CBR9 2.8 18.4 1.0
C5' A:DG10 2.8 28.1 1.0
C2' A:CBR9 3.4 18.7 1.0
C4' A:CBR9 3.9 20.8 1.0
C4' A:DG10 4.0 25.9 1.0
C2' A:DG10 4.0 15.2 1.0
C3' A:DG10 4.2 21.5 1.0
C1' A:CBR9 4.4 15.9 1.0
O4' A:DG10 4.4 18.4 1.0
C5' A:CBR9 4.8 18.3 1.0
C1' A:DG10 4.8 8.6 1.0
O4' A:CBR9 4.8 15.3 1.0
C8 A:DG10 5.0 3.1 1.0

Phosphorus binding site 10 out of 22 in 101d

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Phosphorus binding site 10 out of 22 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 Phosphorus with other atoms in the P binding site number 10 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:P11

b:31.2
occ:1.00
P A:DC11 0.0 31.2 1.0
OP1 A:DC11 1.5 31.8 1.0
OP2 A:DC11 1.5 34.3 1.0
O5' A:DC11 1.6 26.2 1.0
O3' A:DG10 1.6 30.0 1.0
C5' A:DC11 2.6 22.5 1.0
C3' A:DG10 2.8 21.5 1.0
C4' A:DG10 3.6 25.9 1.0
O4' A:DC11 3.8 23.3 1.0
C4' A:DC11 3.8 17.1 1.0
C2' A:DG10 4.0 15.2 1.0
C6 A:DC11 4.3 8.8 1.0
C1' A:DG10 4.5 8.6 1.0
C3' A:DC11 4.5 13.8 1.0
O4' A:DG10 4.6 18.4 1.0
C5' A:DG10 4.7 28.1 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: Fri Sep 25 11:01:49 2020

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