Phosphorus in PDB 100d: Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing

Protein crystallography data

The structure of Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing, PDB code: 100d was solved by C.Ban, B.Ramakrishnan, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 23.980, 40.770, 44.840, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing (pdb code 100d). 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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing, PDB code: 100d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 100d

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Phosphorus binding site 1 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:24.9
occ:1.00
P A:DC2 0.0 24.9 1.0
OP2 A:DC2 1.5 24.6 1.0
OP1 A:DC2 1.5 26.0 1.0
O5' A:DC2 1.6 24.1 1.0
O3' A:C1 1.6 21.0 1.0
C5' A:DC2 2.6 19.7 1.0
C3' A:C1 2.7 23.6 1.0
C2' A:C1 3.5 23.7 1.0
O A:HOH67 3.6 71.0 1.0
C4' A:DC2 3.9 18.0 1.0
O2' A:C1 3.9 23.9 1.0
C4' A:C1 4.0 24.4 1.0
O A:HOH83 4.0 91.1 1.0
O A:HOH42 4.0 54.8 1.0
O A:HOH68 4.0 35.3 1.0
O4' A:DC2 4.1 17.2 1.0
C6 A:DC2 4.4 11.9 1.0
O A:HOH46 4.5 32.5 1.0
C5' A:C1 4.5 27.4 1.0
C3' A:DC2 4.5 19.0 1.0
O5' A:C1 4.7 28.7 1.0
C1' A:C1 4.8 20.6 1.0
O A:HOH25 4.8 21.9 1.0

Phosphorus binding site 2 out of 18 in 100d

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Phosphorus binding site 2 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:21.1
occ:1.00
P A:DG3 0.0 21.1 1.0
OP2 A:DG3 1.5 14.5 1.0
OP1 A:DG3 1.5 21.5 1.0
O5' A:DG3 1.6 19.9 1.0
O3' A:DC2 1.6 18.4 1.0
C5' A:DG3 2.6 17.6 1.0
C3' A:DC2 2.6 19.0 1.0
C2' A:DC2 3.3 17.3 1.0
C4' A:DG3 3.8 17.6 1.0
O4' A:DG3 3.9 16.8 1.0
C4' A:DC2 3.9 18.0 1.0
O A:HOH58 4.2 55.8 1.0
C3' A:DG3 4.4 16.3 1.0
C8 A:DG3 4.5 10.8 1.0
O A:HOH62 4.5 60.9 1.0
C5' A:DC2 4.6 19.7 1.0
O A:HOH86 4.6 76.7 1.0
C1' A:DC2 4.7 15.4 1.0
O5' A:DC2 4.9 24.1 1.0
C1' A:DG3 4.9 16.3 1.0
O4' A:DC2 4.9 17.2 1.0

Phosphorus binding site 3 out of 18 in 100d

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Phosphorus binding site 3 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:19.1
occ:1.00
P A:DG4 0.0 19.1 1.0
OP1 A:DG4 1.5 21.8 1.0
OP2 A:DG4 1.5 20.4 1.0
O3' A:DG3 1.6 18.9 1.0
O5' A:DG4 1.6 19.7 1.0
C3' A:DG3 2.6 16.3 1.0
C5' A:DG4 2.8 14.7 1.0
C2' A:DG3 3.3 17.7 1.0
O A:HOH64 3.7 28.0 1.0
O A:HOH60 3.7 46.4 1.0
C4' A:DG4 4.0 15.7 1.0
C4' A:DG3 4.0 17.6 1.0
O A:HOH43 4.0 68.3 1.0
C3' A:DG4 4.2 14.9 1.0
C8 A:DG4 4.3 8.1 1.0
O A:HOH39 4.4 36.4 1.0
O4' A:DG4 4.4 15.7 1.0
OP2 A:DC5 4.5 19.8 1.0
O A:HOH62 4.6 60.9 1.0
C5' A:DG3 4.6 17.6 1.0
C1' A:DG3 4.7 16.3 1.0
O3' A:DG4 4.8 20.2 1.0
O5' A:DG3 5.0 19.9 1.0
O4' A:DG3 5.0 16.8 1.0

Phosphorus binding site 4 out of 18 in 100d

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Phosphorus binding site 4 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:16.1
occ:1.00
P A:DC5 0.0 16.1 1.0
OP1 A:DC5 1.5 21.8 1.0
OP2 A:DC5 1.5 19.8 1.0
O5' A:DC5 1.6 19.5 1.0
O3' A:DG4 1.6 20.2 1.0
C3' A:DG4 2.7 14.9 1.0
C5' A:DC5 2.7 15.3 1.0
C2' A:DG4 3.4 13.4 1.0
O A:HOH55 3.8 21.3 1.0
C4' A:DC5 3.8 12.5 1.0
C4' A:DG4 4.0 15.7 1.0
C9 A:SPM21 4.0 28.5 1.0
O4' A:DC5 4.1 12.6 1.0
O A:HOH60 4.1 46.4 1.0
C5' A:DG4 4.5 14.7 1.0
N10 A:SPM21 4.6 28.4 1.0
O5' A:DG4 4.7 19.7 1.0
C8 A:SPM21 4.7 30.8 1.0
C7 A:SPM21 4.7 31.1 1.0
C1' A:DG4 4.8 13.1 1.0

Phosphorus binding site 5 out of 18 in 100d

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Phosphorus binding site 5 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:14.9
occ:1.00
P A:DG6 0.0 14.9 1.0
OP1 A:DG6 1.5 14.3 1.0
OP2 A:DG6 1.5 10.7 1.0
O3' A:DC5 1.6 14.2 1.0
O5' A:DG6 1.6 15.2 1.0
C3' A:DC5 2.6 12.0 1.0
C5' A:DG6 2.7 15.4 1.0
C2' A:DC5 3.6 10.6 1.0
C4' A:DC5 3.8 12.5 1.0
O A:HOH30 3.9 53.9 1.0
C4' A:DG6 4.0 15.3 1.0
N5 A:SPM21 4.1 32.9 1.0
C5' A:DC5 4.1 15.3 1.0
O4' A:DG6 4.4 16.5 1.0
C8 A:DG6 4.4 11.3 1.0
C3' A:DG6 4.5 16.5 1.0
C3 A:SPM21 4.5 36.7 1.0
OP2 A:DC7 4.6 20.1 1.0
C4 A:SPM21 4.6 35.0 1.0
C6 A:SPM21 4.6 32.9 1.0
C1' A:DC5 4.9 11.0 1.0
O4' A:DC5 5.0 12.6 1.0

Phosphorus binding site 6 out of 18 in 100d

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Phosphorus binding site 6 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:17.8
occ:1.00
P A:DC7 0.0 17.8 1.0
OP1 A:DC7 1.5 17.8 1.0
OP2 A:DC7 1.5 20.1 1.0
O5' A:DC7 1.6 17.3 1.0
O3' A:DG6 1.6 18.6 1.0
C5' A:DC7 2.7 16.4 1.0
C3' A:DG6 2.7 16.5 1.0
C2' A:DG6 3.8 17.8 1.0
C4' A:DG6 3.9 15.3 1.0
C4' A:DC7 4.0 15.8 1.0
O A:HOH56 4.2 39.1 1.0
C5' A:DG6 4.2 15.4 1.0
O4' A:DC7 4.3 16.3 1.0
O A:HOH30 4.4 53.9 1.0
O A:HOH44 4.5 49.8 1.0
C3' A:DC7 4.6 14.8 1.0
O5' A:DG6 4.6 15.2 1.0
C6 A:DC7 4.7 6.5 1.0

Phosphorus binding site 7 out of 18 in 100d

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Phosphorus binding site 7 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:18.8
occ:1.00
P A:DC8 0.0 18.8 1.0
OP2 A:DC8 1.5 20.2 1.0
OP1 A:DC8 1.5 20.0 1.0
O3' A:DC7 1.6 16.2 1.0
O5' A:DC8 1.6 18.8 1.0
C3' A:DC7 2.6 14.8 1.0
C5' A:DC8 2.7 12.8 1.0
C2' A:DC7 3.4 11.2 1.0
C4' A:DC8 3.9 14.4 1.0
C4' A:DC7 4.0 15.8 1.0
O4' A:DC8 4.1 10.9 1.0
O A:HOH32 4.5 37.7 1.0
C5' A:DC7 4.5 16.4 1.0
C3' A:DC8 4.6 14.9 1.0
C6 A:DC8 4.6 9.2 1.0
C1' A:DC7 4.8 10.6 1.0
O5' A:DC7 4.8 17.3 1.0

Phosphorus binding site 8 out of 18 in 100d

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Phosphorus binding site 8 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:14.6
occ:1.00
P A:DG9 0.0 14.6 1.0
OP1 A:DG9 1.5 17.8 1.0
OP2 A:DG9 1.5 16.3 1.0
O3' A:DC8 1.6 15.2 1.0
O5' A:DG9 1.6 13.7 1.0
C3' A:DC8 2.6 14.9 1.0
C5' A:DG9 2.7 10.0 1.0
C2' A:DC8 3.5 9.3 1.0
C4' A:DC8 3.9 14.4 1.0
C4' A:DG9 3.9 8.6 1.0
O4' A:DG9 4.1 9.9 1.0
C5' A:DC8 4.3 12.8 1.0
O A:HOH32 4.4 37.7 1.0
C3' A:DG9 4.5 11.5 1.0
C8 A:DG9 4.5 7.3 1.0
O5' A:DC8 4.6 18.8 1.0
C1' A:DC8 4.8 8.8 1.0
O A:HOH54 4.8 61.8 1.0
O A:HOH50 4.8 32.2 1.0
O4' A:DC8 4.9 10.9 1.0

Phosphorus binding site 9 out of 18 in 100d

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Phosphorus binding site 9 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:18.0
occ:1.00
P A:G10 0.0 18.0 1.0
OP1 A:G10 1.5 19.6 1.0
OP2 A:G10 1.5 21.6 1.0
O3' A:DG9 1.6 12.3 1.0
O5' A:G10 1.6 18.2 1.0
C3' A:DG9 2.6 11.5 1.0
C5' A:G10 2.8 18.2 1.0
O A:HOH28 3.5 20.3 1.0
C2' A:DG9 3.6 7.9 1.0
O A:HOH29 3.7 19.8 1.0
O A:HOH54 3.8 61.8 1.0
C4' A:DG9 3.9 8.6 1.0
C4' A:G10 4.1 17.4 1.0
O A:HOH50 4.2 32.2 1.0
C5' A:DG9 4.2 10.0 1.0
O5' A:DG9 4.5 13.7 1.0
O4' A:G10 4.6 15.1 1.0
C3' A:G10 4.6 17.9 1.0
C8 A:G10 4.6 15.0 1.0
C1' A:DG9 4.8 8.6 1.0
O4' A:DG9 4.9 9.9 1.0

Phosphorus binding site 10 out of 18 in 100d

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Phosphorus binding site 10 out of 18 in the Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing


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 the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G)-Spermine Complex-Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:21.4
occ:1.00
P B:DC12 0.0 21.4 1.0
OP2 B:DC12 1.5 22.1 1.0
OP1 B:DC12 1.5 21.3 1.0
O3' B:C11 1.6 18.8 1.0
O5' B:DC12 1.7 20.8 1.0
C3' B:C11 2.6 18.0 1.0
C5' B:DC12 2.7 19.8 1.0
C2' B:C11 3.4 14.1 1.0
O B:HOH57 3.7 32.4 1.0
C4' B:C11 3.9 17.2 1.0
O2' B:C11 4.0 13.6 1.0
C4' B:DC12 4.0 18.6 1.0
O B:HOH45 4.3 32.1 1.0
C5' B:C11 4.4 17.6 1.0
C3' B:DC12 4.4 18.0 1.0
O4' B:DC12 4.5 19.8 1.0
O5' B:C11 4.5 18.5 1.0
C6 B:DC12 4.6 15.7 1.0
C1' B:C11 4.7 14.1 1.0
O4' B:C11 4.9 16.6 1.0
O3' B:DC12 4.9 19.1 1.0

Reference:

C.Ban, B.Ramakrishnan, M.Sundaralingam. Crystal Structure of the Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G).Spermine Complex--Spermine Binding to Phosphate Only and Minor Groove Tertiary Base-Pairing. Nucleic Acids Res. V. 22 5466 1994.
ISSN: ISSN 0305-1048
PubMed: 7816639
DOI: 10.1093/NAR/22.24.5466
Page generated: Fri Sep 25 11:01:49 2020

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