Phosphorus in PDB 178d: Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs

Protein crystallography data

The structure of Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs, PDB code: 178d was solved by K.E.Mcauley-Hecht, G.A.Leonard, N.J.Gibson, J.B.Thomson, W.P.Watson, W.N.Hunter, T.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.670, 40.490, 65.140, 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 Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs (pdb code 178d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs, PDB code: 178d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 178d

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Phosphorus binding site 1 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:22.3
occ:1.00
P A:DG2 0.0 22.3 1.0
OP2 A:DG2 1.5 21.1 1.0
OP1 A:DG2 1.5 19.5 1.0
O5' A:DG2 1.6 20.1 1.0
O3' A:DC1 1.6 19.6 1.0
C5' A:DG2 2.6 14.7 1.0
C3' A:DC1 2.7 16.8 1.0
C2' A:DC1 3.6 13.8 1.0
C4' A:DC1 3.9 16.0 1.0
C4' A:DG2 3.9 16.1 1.0
C2' A:DG2 4.1 14.7 1.0
C3' A:DG2 4.1 17.8 1.0
C1' A:DC1 4.2 11.7 1.0
O A:HOH85 4.3 41.2 1.0
O4' A:DC1 4.5 14.5 1.0
O4' A:DG2 4.6 17.0 1.0
C8 A:DG2 4.7 13.4 1.0
C1' A:DG2 4.9 13.4 1.0

Phosphorus binding site 2 out of 22 in 178d

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Phosphorus binding site 2 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:22.9
occ:1.00
P A:DC3 0.0 22.9 1.0
OP2 A:DC3 1.5 24.4 1.0
OP1 A:DC3 1.5 24.6 1.0
O5' A:DC3 1.6 21.1 1.0
O3' A:DG2 1.6 23.8 1.0
C5' A:DC3 2.6 21.0 1.0
C3' A:DG2 2.7 17.8 1.0
C2' A:DG2 3.4 14.7 1.0
C4' A:DC3 3.8 19.6 1.0
C4' A:DG2 4.0 16.1 1.0
C1' A:DG2 4.1 13.4 1.0
O4' A:DC3 4.1 19.2 1.0
O A:HOH26 4.1 9.2 1.0
C3' A:DC3 4.3 21.4 1.0
O4' A:DG2 4.5 17.0 1.0
C6 A:DC3 4.9 20.6 1.0

Phosphorus binding site 3 out of 22 in 178d

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Phosphorus binding site 3 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:32.2
occ:1.00
P A:DA4 0.0 32.2 1.0
OP2 A:DA4 1.5 30.4 1.0
OP1 A:DA4 1.5 34.4 1.0
O5' A:DA4 1.6 25.8 1.0
O3' A:DC3 1.6 27.5 1.0
C5' A:DA4 2.6 28.0 1.0
C3' A:DC3 2.6 21.4 1.0
C2' A:DC3 3.3 20.3 1.0
O A:HOH31 3.8 34.4 1.0
C4' A:DA4 3.8 26.8 1.0
C4' A:DC3 4.0 19.6 1.0
C3' A:DA4 4.3 26.5 1.0
O4' A:DA4 4.3 23.1 1.0
C2' A:DA4 4.3 21.0 1.0
C1' A:DC3 4.6 17.8 1.0
C8 A:DA4 4.6 10.3 1.0
C5' A:DC3 4.7 21.0 1.0
O5' A:DC3 4.8 21.1 1.0
O A:HOH67 4.8 51.4 1.0
C1' A:DA4 4.9 15.6 1.0
O4' A:DC3 4.9 19.2 1.0

Phosphorus binding site 4 out of 22 in 178d

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Phosphorus binding site 4 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:38.4
occ:1.00
P A:DA5 0.0 38.4 1.0
OP2 A:DA5 1.5 34.1 1.0
OP1 A:DA5 1.5 38.8 1.0
O5' A:DA5 1.6 32.9 1.0
O3' A:DA4 1.6 31.1 1.0
C5' A:DA5 2.6 26.0 1.0
C3' A:DA4 2.7 26.5 1.0
C2' A:DA4 3.3 21.0 1.0
O A:HOH60 3.8 49.0 1.0
C4' A:DA5 3.9 20.3 1.0
C4' A:DA4 4.0 26.8 1.0
C1' A:DA4 4.0 15.6 1.0
O4' A:DA5 4.1 18.2 1.0
O A:HOH59 4.3 44.7 1.0
O A:HOH61 4.4 21.4 1.0
O4' A:DA4 4.6 23.1 1.0
C3' A:DA5 4.6 19.6 1.0
C8 A:DA5 4.8 12.2 1.0
C2' A:DA5 4.9 17.5 1.0

Phosphorus binding site 5 out of 22 in 178d

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Phosphorus binding site 5 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:25.1
occ:1.00
P A:DA6 0.0 25.1 1.0
OP2 A:DA6 1.5 29.0 1.0
OP1 A:DA6 1.5 19.1 1.0
O5' A:DA6 1.6 24.3 1.0
O3' A:DA5 1.6 21.9 1.0
C5' A:DA6 2.6 18.8 1.0
C3' A:DA5 2.7 19.6 1.0
C2' A:DA5 3.3 17.5 1.0
O A:HOH33 3.6 20.9 1.0
C4' A:DA6 3.9 16.2 1.0
C4' A:DA5 4.0 20.3 1.0
C3' A:DA6 4.3 14.1 1.0
C1' A:DA5 4.3 16.5 1.0
O4' A:DA6 4.5 14.8 1.0
C2' A:DA6 4.5 12.8 1.0
O4' A:DA5 4.8 18.2 1.0
C5' A:DA5 5.0 26.0 1.0

Phosphorus binding site 6 out of 22 in 178d

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Phosphorus binding site 6 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:16.1
occ:1.00
P A:DT7 0.0 16.1 1.0
OP2 A:DT7 1.5 14.3 1.0
OP1 A:DT7 1.5 16.3 1.0
O5' A:DT7 1.6 9.2 1.0
O3' A:DA6 1.6 15.3 1.0
C5' A:DT7 2.6 13.6 1.0
C3' A:DA6 2.7 14.1 1.0
C2' A:DA6 3.4 12.8 1.0
C4' A:DT7 3.8 16.3 1.0
C4' A:DA6 4.0 16.2 1.0
C1' A:DA6 4.2 12.2 1.0
O A:HOH29 4.3 32.7 1.0
O4' A:DT7 4.4 18.7 1.0
C3' A:DT7 4.4 14.0 1.0
O4' A:DA6 4.7 14.8 1.0
C2' A:DT7 4.9 12.8 1.0

Phosphorus binding site 7 out of 22 in 178d

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Phosphorus binding site 7 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:25.4
occ:1.00
P A:DT8 0.0 25.4 1.0
OP2 A:DT8 1.5 22.5 1.0
OP1 A:DT8 1.5 17.3 1.0
O3' A:DT7 1.6 15.4 1.0
O5' A:DT8 1.6 21.5 1.0
C5' A:DT8 2.6 21.3 1.0
C3' A:DT7 2.7 14.0 1.0
C2' A:DT7 3.4 12.8 1.0
C4' A:DT8 3.8 19.4 1.0
C4' A:DT7 3.9 16.3 1.0
O4' A:DT8 4.1 20.0 1.0
C1' A:DT7 4.4 14.3 1.0
C3' A:DT8 4.4 21.2 1.0
C2' A:DT8 4.8 20.3 1.0
O4' A:DT7 4.8 18.7 1.0
O A:HOH90 4.9 46.9 1.0
C5' A:DT7 4.9 13.6 1.0

Phosphorus binding site 8 out of 22 in 178d

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Phosphorus binding site 8 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:31.8
occ:1.00
P A:8OG9 0.0 31.8 1.0
OP2 A:8OG9 1.5 29.7 1.0
OP1 A:8OG9 1.5 33.5 1.0
O5' A:8OG9 1.6 31.1 1.0
O3' A:DT8 1.6 25.3 1.0
C5' A:8OG9 2.6 29.0 1.0
C3' A:DT8 2.7 21.2 1.0
C2' A:DT8 3.4 20.3 1.0
C4' A:8OG9 3.8 25.1 1.0
C4' A:DT8 4.0 19.4 1.0
C3' A:8OG9 4.1 26.8 1.0
C1' A:DT8 4.3 18.8 1.0
O A:HOH72 4.6 45.9 1.0
C2' A:8OG9 4.6 26.8 1.0
O4' A:8OG9 4.7 27.1 1.0
O4' A:DT8 4.8 20.0 1.0
N3 A:8OG9 4.8 28.4 1.0
N2 A:8OG9 5.0 28.3 1.0
C5' A:DT8 5.0 21.3 1.0

Phosphorus binding site 9 out of 22 in 178d

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Phosphorus binding site 9 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:34.8
occ:1.00
P A:DG10 0.0 34.8 1.0
OP2 A:DG10 1.5 23.9 1.0
OP1 A:DG10 1.5 32.1 1.0
O5' A:DG10 1.6 31.8 1.0
O3' A:8OG9 1.6 30.8 1.0
C5' A:DG10 2.6 33.8 1.0
C3' A:8OG9 2.7 26.8 1.0
C2' A:8OG9 3.5 26.8 1.0
C4' A:DG10 3.8 29.6 1.0
C4' A:8OG9 3.9 25.1 1.0
O4' A:DG10 4.1 29.7 1.0
C1' A:8OG9 4.3 27.7 1.0
C3' A:DG10 4.4 29.4 1.0
C2' A:DG10 4.4 29.1 1.0
O4' A:8OG9 4.7 27.1 1.0
O5' A:8OG9 4.8 31.1 1.0
C1' A:DG10 4.8 26.0 1.0
C5' A:8OG9 5.0 29.0 1.0

Phosphorus binding site 10 out of 22 in 178d

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Phosphorus binding site 10 out of 22 in the Crystal Structure of A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs


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 A Dna Duplex Containing 8- Hydroxydeoxyguanine.Adenine Base-Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:39.3
occ:1.00
P A:DC11 0.0 39.3 1.0
OP2 A:DC11 1.5 32.5 1.0
OP1 A:DC11 1.5 34.4 1.0
O5' A:DC11 1.6 32.8 1.0
O3' A:DG10 1.6 32.8 1.0
C5' A:DC11 2.6 31.0 1.0
C3' A:DG10 2.7 29.4 1.0
O A:HOH38 3.2 23.8 1.0
C4' A:DG10 3.4 29.6 1.0
O A:HOH70 3.6 43.6 1.0
C4' A:DC11 3.8 28.6 1.0
C6 A:DC11 3.9 26.6 1.0
C2' A:DG10 4.0 29.1 1.0
O4' A:DC11 4.1 29.3 1.0
C5' A:DG10 4.4 33.8 1.0
O4' A:DG10 4.4 29.7 1.0
C1' A:DG10 4.4 26.0 1.0
C3' A:DC11 4.5 27.8 1.0
C2' A:DC11 4.6 26.0 1.0
C5 A:DC11 4.6 24.7 1.0
C1' A:DC11 4.8 25.1 1.0
N1 A:DC11 4.8 25.1 1.0

Reference:

K.E.Mcauley-Hecht, G.A.Leonard, N.J.Gibson, J.B.Thomson, W.P.Watson, W.N.Hunter, T.Brown. Crystal Structure of A Dna Duplex Containing 8-Hydroxydeoxyguanine-Adenine Base Pairs. Biochemistry V. 33 10266 1994.
ISSN: ISSN 0006-2960
PubMed: 8068665
DOI: 10.1021/BI00200A006
Page generated: Fri Sep 25 11:44:02 2020

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