Phosphorus in PDB 126d: Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models

Protein crystallography data

The structure of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models, PDB code: 126d was solved by D.S.Goodsell, M.L.Kopka, D.Cascio, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.600, 42.490, 34.690, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models (pdb code 126d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models, PDB code: 126d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 126d

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Phosphorus binding site 1 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:48.6
occ:1.00
P A:DA2 0.0 48.6 1.0
OP1 A:DA2 1.5 53.2 1.0
OP2 A:DA2 1.6 26.7 1.0
O3' A:DC1 1.6 30.2 1.0
O5' A:DA2 1.7 36.6 1.0
C3' A:DC1 2.6 24.8 1.0
C5' A:DA2 2.8 34.4 1.0
C2' A:DC1 3.2 32.0 1.0
C4' A:DC1 3.9 17.0 1.0
C1' A:DC1 4.0 21.5 1.0
O A:HOH37 4.1 32.9 1.0
C4' A:DA2 4.1 18.3 1.0
O4' A:DC1 4.4 22.8 1.0
C3' A:DA2 4.6 19.4 1.0
C8 A:DA2 4.8 17.6 1.0
C2' A:DA2 4.8 9.6 1.0
O4' A:DA2 4.9 15.7 1.0
O5' A:DC1 5.0 27.8 1.0

Phosphorus binding site 2 out of 18 in 126d

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Phosphorus binding site 2 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:21.4
occ:1.00
P A:DT3 0.0 21.4 1.0
OP2 A:DT3 1.4 33.4 1.0
OP1 A:DT3 1.4 28.6 1.0
O3' A:DA2 1.6 16.6 1.0
O5' A:DT3 1.8 29.4 1.0
C3' A:DA2 2.6 19.4 1.0
C5' A:DT3 2.9 22.2 1.0
C2' A:DA2 3.3 9.6 1.0
O A:HOH41 3.6 28.7 1.0
O A:HOH21 3.9 23.7 1.0
C4' A:DA2 4.0 18.3 1.0
C1' A:DA2 4.1 11.6 1.0
C4' A:DT3 4.2 20.2 1.0
O A:HOH49 4.4 28.2 1.0
O4' A:DA2 4.5 15.7 1.0
O4' A:DT3 4.5 15.6 1.0
C3' A:DT3 4.6 14.7 1.0
C2' A:DT3 4.6 7.2 1.0

Phosphorus binding site 3 out of 18 in 126d

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Phosphorus binding site 3 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:16.9
occ:1.00
P A:DG4 0.0 16.9 1.0
OP2 A:DG4 1.5 32.2 1.0
OP1 A:DG4 1.5 21.1 1.0
O3' A:DT3 1.6 15.5 1.0
O5' A:DG4 1.7 22.8 1.0
C5' A:DG4 2.6 14.0 1.0
C3' A:DT3 2.6 14.7 1.0
C4' A:DT3 3.6 20.2 1.0
C4' A:DG4 3.7 14.8 1.0
C2' A:DT3 3.8 7.2 1.0
C8 A:DG4 3.9 10.3 1.0
C2' A:DG4 4.1 9.3 1.0
O4' A:DG4 4.2 13.9 1.0
C3' A:DG4 4.2 18.5 1.0
N9 A:DG4 4.4 11.1 1.0
C1' A:DT3 4.4 12.8 1.0
C5' A:DT3 4.4 22.2 1.0
N7 A:DG4 4.5 9.4 1.0
O4' A:DT3 4.6 15.6 1.0
C1' A:DG4 4.6 9.3 1.0

Phosphorus binding site 4 out of 18 in 126d

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Phosphorus binding site 4 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:29.0
occ:1.00
P A:DG5 0.0 29.0 1.0
OP2 A:DG5 1.5 24.4 1.0
O5' A:DG5 1.5 22.2 1.0
OP1 A:DG5 1.6 34.4 1.0
O3' A:DG4 1.7 28.4 1.0
C5' A:DG5 2.4 40.2 1.0
C3' A:DG4 2.9 18.5 1.0
C2' A:DG4 3.5 9.3 1.0
C4' A:DG5 3.7 37.7 1.0
C1' A:DG4 4.0 9.3 1.0
C4' A:DG4 4.1 14.8 1.0
C3' A:DG5 4.2 32.7 1.0
O4' A:DG4 4.3 13.9 1.0
C2' A:DG5 4.7 27.3 1.0
O4' A:DG5 4.7 26.4 1.0

Phosphorus binding site 5 out of 18 in 126d

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Phosphorus binding site 5 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:47.5
occ:1.00
P A:DC6 0.0 47.5 1.0
OP1 A:DC6 1.5 42.7 1.0
OP2 A:DC6 1.5 37.0 1.0
O5' A:DC6 1.6 28.6 1.0
O3' A:DG5 1.6 52.7 1.0
C5' A:DC6 2.6 24.8 1.0
C3' A:DG5 2.9 32.7 1.0
O A:HOH62 3.2 30.8 1.0
O A:HOH43 3.2 29.9 1.0
C4' A:DC6 3.7 24.0 1.0
C2' A:DG5 3.8 27.3 1.0
C4' A:DG5 4.0 37.7 1.0
O4' A:DC6 4.1 22.2 1.0
C3' A:DC6 4.3 18.1 1.0
C1' A:DG5 4.4 22.7 1.0
O4' A:DG5 4.5 26.4 1.0

Phosphorus binding site 6 out of 18 in 126d

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Phosphorus binding site 6 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:27.5
occ:1.00
P A:DC7 0.0 27.5 1.0
OP1 A:DC7 1.5 20.8 1.0
OP2 A:DC7 1.5 15.8 1.0
O5' A:DC7 1.6 18.7 1.0
O3' A:DC6 1.7 23.6 1.0
C3' A:DC6 2.6 18.1 1.0
C5' A:DC7 2.9 15.8 1.0
C2' A:DC6 3.4 20.0 1.0
C4' A:DC6 3.9 24.0 1.0
O A:HOH65 3.9 37.0 1.0
C4' A:DC7 4.1 15.0 1.0
C3' A:DC7 4.3 16.8 1.0
O4' A:DC7 4.4 17.2 1.0
C1' A:DC6 4.4 17.3 1.0
C2' A:DC7 4.6 13.8 1.0
C5' A:DC6 4.8 24.8 1.0
O4' A:DC6 4.9 22.2 1.0

Phosphorus binding site 7 out of 18 in 126d

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Phosphorus binding site 7 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:22.9
occ:1.00
P A:DA8 0.0 22.9 1.0
OP1 A:DA8 1.5 24.4 1.0
OP2 A:DA8 1.5 32.9 1.0
O3' A:DC7 1.5 17.4 1.0
O5' A:DA8 1.7 25.2 1.0
C5' A:DA8 2.7 25.4 1.0
C3' A:DC7 2.7 16.8 1.0
C8 A:DA8 3.7 11.1 1.0
C2' A:DC7 3.7 13.8 1.0
C4' A:DC7 3.8 15.0 1.0
O A:HOH24 3.8 13.5 1.0
C4' A:DA8 3.8 20.3 1.0
O4' A:DA8 4.0 21.5 1.0
N9 A:DA8 4.2 8.0 1.0
C2' A:DA8 4.3 11.3 1.0
C3' A:DA8 4.4 20.8 1.0
N7 A:DA8 4.4 16.0 1.0
O A:HOH23 4.4 25.8 1.0
C1' A:DA8 4.5 10.1 1.0
C1' A:DC7 4.5 12.6 1.0
O A:HOH56 4.5 30.3 1.0
O A:HOH48 4.6 28.3 1.0
O4' A:DC7 4.7 17.2 1.0
C5' A:DC7 4.8 15.8 1.0

Phosphorus binding site 8 out of 18 in 126d

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Phosphorus binding site 8 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:22.0
occ:1.00
P A:DT9 0.0 22.0 1.0
OP1 A:DT9 1.4 25.5 1.0
OP2 A:DT9 1.5 25.8 1.0
O3' A:DA8 1.6 26.1 1.0
O5' A:DT9 1.7 22.4 1.0
C3' A:DA8 2.6 20.8 1.0
C5' A:DT9 2.8 19.0 1.0
C2' A:DA8 3.3 11.3 1.0
C4' A:DA8 3.8 20.3 1.0
C4' A:DT9 4.0 15.2 1.0
C1' A:DA8 4.1 10.1 1.0
O4' A:DT9 4.3 23.0 1.0
O4' A:DA8 4.4 21.5 1.0
C3' A:DT9 4.8 28.0 1.0
C5' A:DA8 4.9 25.4 1.0

Phosphorus binding site 9 out of 18 in 126d

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Phosphorus binding site 9 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:29.3
occ:1.00
P A:DG10 0.0 29.3 1.0
OP1 A:DG10 1.5 32.9 1.0
O5' A:DG10 1.5 28.9 1.0
OP2 A:DG10 1.6 23.1 1.0
O3' A:DT9 1.6 29.9 1.0
C3' A:DT9 2.6 28.0 1.0
C5' A:DG10 2.6 21.0 1.0
C2' A:DT9 3.3 25.8 1.0
C4' A:DT9 3.9 15.2 1.0
C4' A:DG10 3.9 25.3 1.0
O4' A:DG10 4.2 24.8 1.0
C1' A:DT9 4.5 19.1 1.0
C3' A:DG10 4.6 26.6 1.0
C5' A:DT9 4.6 19.0 1.0
C2' A:DG10 4.7 19.4 1.0
O4' A:DT9 4.8 23.0 1.0
C8 A:DG10 4.8 18.6 1.0
C1' A:DG10 5.0 21.9 1.0

Phosphorus binding site 10 out of 18 in 126d

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Phosphorus binding site 10 out of 18 in the Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal Structure of Catggccatg and Its Implications For A- Tract Bending Models within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:37.4
occ:1.00
P B:DA12 0.0 37.4 1.0
OP2 B:DA12 1.5 36.0 1.0
OP1 B:DA12 1.5 34.4 1.0
O3' B:DC11 1.6 35.3 1.0
O5' B:DA12 1.7 20.9 1.0
C3' B:DC11 2.7 43.5 1.0
C5' B:DA12 2.7 22.8 1.0
C2' B:DC11 3.3 24.3 1.0
C4' B:DA12 3.9 19.7 1.0
C4' B:DC11 4.1 42.9 1.0
C3' B:DA12 4.1 19.6 1.0
C1' B:DC11 4.1 26.9 1.0
C2' B:DA12 4.2 18.2 1.0
O4' B:DC11 4.4 40.5 1.0
C8 B:DA12 4.7 22.5 1.0
O4' B:DA12 4.9 24.4 1.0
C1' B:DA12 5.0 18.8 1.0

Reference:

D.S.Goodsell, M.L.Kopka, D.Cascio, R.E.Dickerson. Crystal Structure of Catggccatg and Its Implications For A-Tract Bending Models. Proc.Natl.Acad.Sci.Usa V. 90 2930 1993.
ISSN: ISSN 0027-8424
PubMed: 8464909
DOI: 10.1073/PNAS.90.7.2930
Page generated: Fri Sep 25 11:15:26 2020

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