Phosphorus in PDB 113d: The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution

Protein crystallography data

The structure of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution, PDB code: 113d was solved by W.N.Hunter, T.Brown, G.Kneale, N.N.Anand, D.Rabinovich, O.Kennard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.530, 41.220, 65.630, 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 The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution (pdb code 113d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution, PDB code: 113d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 113d

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Phosphorus binding site 1 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:41.0
occ:1.00
P A:DG2 0.0 41.0 1.0
OP1 A:DG2 1.5 41.0 1.0
OP2 A:DG2 1.5 41.0 1.0
O3' A:DC1 1.6 36.0 1.0
O5' A:DG2 1.6 31.0 1.0
C5' A:DG2 2.6 31.0 1.0
C3' A:DC1 2.7 36.0 1.0
C2' A:DC1 3.3 36.0 1.0
O A:HOH74 3.9 66.0 1.0
C4' A:DC1 3.9 36.0 1.0
C4' A:DG2 4.0 31.0 1.0
O A:HOH56 4.0 53.0 1.0
O A:HOH94 4.2 72.0 1.0
C1' A:DC1 4.4 36.0 1.0
C3' A:DG2 4.4 31.0 1.0
C2' A:DG2 4.6 31.0 1.0
O4' A:DG2 4.7 31.0 1.0
O5' A:DC1 4.7 36.0 1.0
O4' A:DC1 4.7 36.0 1.0
C5' A:DC1 5.0 36.0 1.0

Phosphorus binding site 2 out of 22 in 113d

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Phosphorus binding site 2 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:38.0
occ:1.00
P A:DC3 0.0 38.0 1.0
OP1 A:DC3 1.5 38.0 1.0
OP2 A:DC3 1.5 38.0 1.0
O5' A:DC3 1.6 24.0 1.0
O3' A:DG2 1.6 31.0 1.0
C3' A:DG2 2.6 31.0 1.0
C5' A:DC3 2.7 24.0 1.0
C2' A:DG2 3.3 31.0 1.0
C4' A:DC3 3.8 24.0 1.0
O A:HOH55 3.9 51.0 1.0
O4' A:DC3 3.9 24.0 1.0
C4' A:DG2 4.0 31.0 1.0
C1' A:DG2 4.3 31.0 1.0
C3' A:DC3 4.5 24.0 1.0
O4' A:DG2 4.7 31.0 1.0
C6 A:DC3 4.9 20.0 1.0
O A:HOH94 5.0 72.0 1.0

Phosphorus binding site 3 out of 22 in 113d

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Phosphorus binding site 3 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:38.0
occ:1.00
P A:DG4 0.0 38.0 1.0
OP2 A:DG4 1.5 38.0 1.0
OP1 A:DG4 1.5 38.0 1.0
O5' A:DG4 1.6 30.0 1.0
O3' A:DC3 1.6 24.0 1.0
C3' A:DC3 2.6 24.0 1.0
C5' A:DG4 2.7 30.0 1.0
C2' A:DC3 3.4 24.0 1.0
O4' A:DG4 3.7 30.0 1.0
C4' A:DG4 3.7 30.0 1.0
C4' A:DC3 3.9 24.0 1.0
O A:HOH93 4.1 68.0 1.0
C3' A:DG4 4.4 30.0 1.0
C5' A:DC3 4.4 24.0 1.0
O A:HOH39 4.5 49.0 1.0
O A:HOH41 4.5 54.0 1.0
C2' A:DG4 4.6 30.0 1.0
C8 A:DG4 4.7 17.0 1.0
C1' A:DG4 4.7 30.0 1.0
C1' A:DC3 4.8 24.0 1.0
O5' A:DC3 4.8 24.0 1.0
O4' A:DC3 4.9 24.0 1.0

Phosphorus binding site 4 out of 22 in 113d

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Phosphorus binding site 4 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:44.0
occ:1.00
P A:DA5 0.0 44.0 1.0
OP2 A:DA5 1.5 44.0 1.0
OP1 A:DA5 1.5 44.0 1.0
O5' A:DA5 1.6 35.0 1.0
O3' A:DG4 1.6 30.0 1.0
C3' A:DG4 2.7 30.0 1.0
C5' A:DA5 2.7 35.0 1.0
C2' A:DG4 3.4 30.0 1.0
C4' A:DA5 3.9 35.0 1.0
C4' A:DG4 4.0 30.0 1.0
O A:HOH50 4.1 63.0 1.0
O A:HOH76 4.2 64.0 1.0
C1' A:DG4 4.3 30.0 1.0
C3' A:DA5 4.4 35.0 1.0
O4' A:DA5 4.6 35.0 1.0
C2' A:DA5 4.7 35.0 1.0
C8 A:DA5 4.7 19.0 1.0
O4' A:DG4 4.9 30.0 1.0
C5' A:DG4 4.9 30.0 1.0

Phosphorus binding site 5 out of 22 in 113d

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Phosphorus binding site 5 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:42.0
occ:1.00
P A:DA6 0.0 42.0 1.0
OP1 A:DA6 1.5 42.0 1.0
OP2 A:DA6 1.5 42.0 1.0
O3' A:DA5 1.6 35.0 1.0
O5' A:DA6 1.6 30.0 1.0
C5' A:DA6 2.6 30.0 1.0
C3' A:DA5 2.6 35.0 1.0
C2' A:DA5 3.2 35.0 1.0
C4' A:DA6 3.8 30.0 1.0
C4' A:DA5 4.0 35.0 1.0
C1' A:DA5 4.1 35.0 1.0
C3' A:DA6 4.2 30.0 1.0
C2' A:DA6 4.4 30.0 1.0
O A:HOH54 4.5 60.0 1.0
O4' A:DA5 4.6 35.0 1.0
O A:HOH61 4.6 66.0 1.0
O4' A:DA6 4.6 30.0 1.0
C8 A:DA6 4.8 12.0 1.0
O A:HOH70 4.9 59.0 1.0

Phosphorus binding site 6 out of 22 in 113d

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Phosphorus binding site 6 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:36.0
occ:1.00
P A:DT7 0.0 36.0 1.0
OP1 A:DT7 1.5 36.0 1.0
OP2 A:DT7 1.5 36.0 1.0
O3' A:DA6 1.6 30.0 1.0
O5' A:DT7 1.6 30.0 1.0
C5' A:DT7 2.6 30.0 1.0
C3' A:DA6 2.7 30.0 1.0
C2' A:DA6 3.3 30.0 1.0
O A:HOH65 3.8 47.0 1.0
C4' A:DT7 3.9 30.0 1.0
C4' A:DA6 3.9 30.0 1.0
O A:HOH61 4.0 66.0 1.0
C1' A:DA6 4.1 30.0 1.0
C3' A:DT7 4.4 30.0 1.0
O4' A:DA6 4.5 30.0 1.0
O4' A:DT7 4.5 30.0 1.0

Phosphorus binding site 7 out of 22 in 113d

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Phosphorus binding site 7 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:34.0
occ:1.00
P A:DT8 0.0 34.0 1.0
OP2 A:DT8 1.5 34.0 1.0
OP1 A:DT8 1.5 34.0 1.0
O3' A:DT7 1.6 30.0 1.0
O5' A:DT8 1.6 33.0 1.0
C5' A:DT8 2.7 33.0 1.0
C3' A:DT7 2.7 30.0 1.0
C2' A:DT7 3.2 30.0 1.0
O A:HOH86 3.7 58.0 1.0
C4' A:DT8 3.9 33.0 1.0
C4' A:DT7 3.9 30.0 1.0
O A:HOH89 4.2 66.0 1.0
O4' A:DT8 4.2 33.0 1.0
C1' A:DT7 4.3 30.0 1.0
C3' A:DT8 4.6 33.0 1.0
O4' A:DT7 4.7 30.0 1.0

Phosphorus binding site 8 out of 22 in 113d

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Phosphorus binding site 8 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:41.0
occ:1.00
P A:DT9 0.0 41.0 1.0
OP1 A:DT9 1.5 41.0 1.0
OP2 A:DT9 1.5 41.0 1.0
O5' A:DT9 1.6 35.0 1.0
O3' A:DT8 1.6 33.0 1.0
C5' A:DT9 2.6 35.0 1.0
C3' A:DT8 2.7 33.0 1.0
C2' A:DT8 3.4 33.0 1.0
O A:HOH85 3.7 74.0 1.0
O A:HOH82 3.8 65.0 1.0
O A:HOH42 3.8 40.0 1.0
C4' A:DT9 3.9 35.0 1.0
C4' A:DT8 4.0 33.0 1.0
O A:HOH69 4.1 66.0 1.0
O4' A:DT9 4.2 35.0 1.0
C1' A:DT8 4.4 33.0 1.0
C3' A:DT9 4.5 35.0 1.0
O4' A:DT8 4.8 33.0 1.0
C5' A:DT8 4.9 33.0 1.0

Phosphorus binding site 9 out of 22 in 113d

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Phosphorus binding site 9 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:44.0
occ:1.00
P A:DG10 0.0 44.0 1.0
OP2 A:DG10 1.5 44.0 1.0
OP1 A:DG10 1.5 44.0 1.0
O3' A:DT9 1.6 35.0 1.0
O5' A:DG10 1.6 35.0 1.0
C3' A:DT9 2.7 35.0 1.0
C5' A:DG10 2.7 35.0 1.0
C2' A:DT9 3.5 35.0 1.0
O A:HOH82 3.7 65.0 1.0
C4' A:DT9 3.9 35.0 1.0
C4' A:DG10 4.0 35.0 1.0
C2' A:DG10 4.4 35.0 1.0
O4' A:DG10 4.4 35.0 1.0
C5' A:DT9 4.5 35.0 1.0
C3' A:DG10 4.5 35.0 1.0
C8 A:DG10 4.8 21.0 1.0
O A:HOH85 4.8 74.0 1.0
C1' A:DG10 4.8 35.0 1.0
O5' A:DT9 4.8 35.0 1.0
C1' A:DT9 4.9 35.0 1.0
O4' A:DT9 5.0 35.0 1.0

Phosphorus binding site 10 out of 22 in 113d

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Phosphorus binding site 10 out of 22 in the The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:50.0
occ:1.00
P A:DC11 0.0 50.0 1.0
OP1 A:DC11 1.5 50.0 1.0
OP2 A:DC11 1.5 50.0 1.0
O5' A:DC11 1.6 42.0 1.0
O3' A:DG10 1.6 35.0 1.0
C5' A:DC11 2.6 42.0 1.0
C3' A:DG10 2.7 35.0 1.0
O A:HOH31 3.3 65.0 1.0
C4' A:DG10 3.4 35.0 1.0
C6 A:DC11 3.9 28.0 1.0
C4' A:DC11 3.9 42.0 1.0
C2' A:DG10 3.9 35.0 1.0
O4' A:DG10 4.3 35.0 1.0
C1' A:DG10 4.4 35.0 1.0
O4' A:DC11 4.4 42.0 1.0
C3' A:DC11 4.5 42.0 1.0
C2' A:DC11 4.5 42.0 1.0
C5 A:DC11 4.6 28.0 1.0
C5' A:DG10 4.6 35.0 1.0
N1 A:DC11 4.8 28.0 1.0
C1' A:DC11 4.8 42.0 1.0

Reference:

W.N.Hunter, T.Brown, G.Kneale, N.N.Anand, D.Rabinovich, O.Kennard. The Structure of Guanosine-Thymidine Mismatches in B-Dna at 2.5-A Resolution. J.Biol.Chem. V. 262 9962 1987.
ISSN: ISSN 0021-9258
PubMed: 3611072
Page generated: Fri Sep 25 11:09:07 2020

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