Phosphorus in PDB 180d: Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)

Protein crystallography data

The structure of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg), PDB code: 180d was solved by C.Sadasivan, N.Gautham, 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 1 1 21
Cell size a, b, c (Å), α, β, γ (°) 17.750, 17.760, 42.770, 90.00, 90.00, 120.05
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) (pdb code 180d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 10 binding sites of Phosphorus where determined in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg), PDB code: 180d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 10 in 180d

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Phosphorus binding site 1 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:7.4
occ:1.00
 P A:DG2 0.0 7.4 1.0
OP2 A:DG2 1.5 8.0 1.0
OP1 A:DG2 1.5 14.9 1.0
O3' A:DC1 1.6 13.2 1.0
O5' A:DG2 1.7 6.5 1.0
C5' A:DG2 2.7 5.7 1.0
C3' A:DC1 2.7 9.2 1.0
O4' A:DG2 3.6 4.0 1.0
C2' A:DC1 3.7 8.6 1.0
C4' A:DG2 3.7 5.0 1.0
C4' A:DC1 3.9 7.2 1.0
C1' A:DC1 4.2 7.1 1.0
O4' A:DC1 4.3 10.7 1.0
N3 A:DG2 4.6 18.1 1.0
C3' A:DG2 4.8 5.6 1.0
C1' A:DG2 5.0 5.7 1.0

Phosphorus binding site 2 out of 10 in 180d

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Phosphorus binding site 2 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:35.4
occ:1.00
 P A:DC3 0.0 35.4 1.0
O3' A:DG2 1.5 16.4 1.0
OP2 A:DC3 1.5 32.5 1.0
OP1 A:DC3 1.6 29.7 1.0
O5' A:DC3 1.7 28.6 1.0
C5' A:DC3 2.5 33.6 1.0
C3' A:DG2 2.8 5.6 1.0
C2' A:DG2 3.5 2.6 1.0
O A:HOH16 3.6 17.9 1.0
C4' A:DC3 3.9 32.2 1.0
C4' A:DG2 3.9 5.0 1.0
O A:HOH21 4.1 4.2 1.0
C3' A:DC3 4.3 27.4 1.0
N6 A:DA4 4.5 26.0 1.0
C5' A:DG2 4.7 5.7 1.0
C1' A:DG2 4.8 5.7 1.0
N7 A:DA4 4.8 14.8 1.0
C2' A:DC3 4.8 21.6 1.0
O4' A:DC3 4.8 26.9 1.0
O A:HOH29 4.8 5.1 1.0
C6 A:DA4 4.9 22.4 1.0
C5 A:DA4 4.9 18.0 1.0
C6 A:DC3 5.0 20.2 1.0
O4' A:DG2 5.0 4.0 1.0

Phosphorus binding site 3 out of 10 in 180d

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Phosphorus binding site 3 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:13.5
occ:1.00
 P A:DA4 0.0 13.5 1.0
OP1 A:DA4 1.4 22.9 1.0
OP2 A:DA4 1.5 3.8 1.0
O3' A:DC3 1.6 21.4 1.0
O5' A:DA4 1.7 9.2 1.0
C5' A:DA4 2.5 3.0 1.0
C3' A:DC3 2.8 27.4 1.0
C4' A:DA4 3.8 16.7 1.0
C4' A:DC3 3.8 32.2 1.0
C2' A:DC3 3.9 21.6 1.0
O4' A:DA4 4.3 10.4 1.0
O4' A:DC3 4.6 26.9 1.0
C1' A:DC3 4.6 21.9 1.0
O5' A:DC3 4.9 28.6 1.0
N3 A:DA4 5.0 28.9 1.0
C5' A:DC3 5.0 33.6 1.0

Phosphorus binding site 4 out of 10 in 180d

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Phosphorus binding site 4 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:33.7
occ:1.00
 P A:DC5 0.0 33.7 1.0
OP2 A:DC5 1.5 20.7 1.0
OP1 A:DC5 1.5 27.3 1.0
O5' A:DC5 1.6 18.5 1.0
O3' A:DA4 1.7 31.9 1.0
C5' A:DC5 2.6 13.3 1.0
C3' A:DA4 3.0 25.2 1.0
O A:HOH20 3.4 2.8 1.0
C4' A:DA4 3.8 16.7 1.0
C4' A:DC5 3.9 19.6 1.0
C2' A:DA4 4.1 17.1 1.0
C3' A:DC5 4.4 21.5 1.0
C5' A:DA4 4.6 3.0 1.0
O A:HOH19 4.8 14.0 1.0
O4' A:DA4 4.9 10.4 1.0
O4' A:DC5 5.0 27.1 1.0

Phosphorus binding site 5 out of 10 in 180d

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Phosphorus binding site 5 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:32.4
occ:1.00
 P A:DG6 0.0 32.4 1.0
OP2 A:DG6 1.5 28.1 1.0
OP1 A:DG6 1.5 33.2 1.0
O3' A:DC5 1.5 17.1 1.0
O5' A:DG6 1.7 20.1 1.0
C5' A:DG6 2.6 10.0 1.0
C3' A:DC5 2.9 21.5 1.0
C2' A:DC5 3.7 26.1 1.0
C4' A:DC5 3.8 19.6 1.0
C4' A:DG6 3.8 2.9 1.0
O A:HOH25 3.9 4.3 1.0
C1' A:DC5 4.0 27.9 1.0
O4' A:DG6 4.0 12.5 1.0
O4' A:DC5 4.1 27.1 1.0
C3' A:DG6 4.4 3.9 1.0

Phosphorus binding site 6 out of 10 in 180d

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Phosphorus binding site 6 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:29.9
occ:1.00
 P B:DG8 0.0 29.9 1.0
OP2 B:DG8 1.5 31.9 1.0
OP1 B:DG8 1.5 32.8 1.0
O3' B:DC7 1.6 39.0 1.0
O5' B:DG8 1.7 23.6 1.0
C5' B:DG8 2.6 24.8 1.0
C3' B:DC7 2.8 33.7 1.0
C2' B:DC7 3.3 25.2 1.0
C1' B:DC7 3.6 30.3 1.0
C4' B:DG8 3.8 23.3 1.0
C4' B:DC7 3.9 32.4 1.0
O4' B:DC7 3.9 34.9 1.0
O B:HOH15 4.0 3.5 1.0
O4' B:DG8 4.3 26.3 1.0
O B:HOH28 4.5 11.2 1.0
N3 B:DG8 4.6 24.6 1.0
O B:HOH31 4.9 5.5 1.0
N2 B:DG8 5.0 19.8 1.0
C2 B:DG8 5.0 20.6 1.0
O2 B:DC7 5.0 14.5 1.0
N1 B:DC7 5.0 21.7 1.0

Phosphorus binding site 7 out of 10 in 180d

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Phosphorus binding site 7 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:41.2
occ:1.00
 P B:DT9 0.0 41.2 1.0
OP1 B:DT9 1.5 29.4 1.0
OP2 B:DT9 1.5 44.0 1.0
O5' B:DT9 1.6 52.3 1.0
O3' B:DG8 1.7 9.5 1.0
C3' B:DG8 2.6 14.9 1.0
C5' B:DT9 2.7 50.2 1.0
C2' B:DG8 3.6 12.4 1.0
C4' B:DG8 3.8 23.3 1.0
C4' B:DT9 4.0 37.1 1.0
O B:HOH28 4.5 11.2 1.0
C5' B:DG8 4.7 24.8 1.0
C3' B:DT9 4.7 28.3 1.0
C1' B:DG8 4.8 16.9 1.0
O4' B:DG8 4.8 26.3 1.0

Phosphorus binding site 8 out of 10 in 180d

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Phosphorus binding site 8 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:18.7
occ:1.00
 P B:DG10 0.0 18.7 1.0
OP1 B:DG10 1.5 18.8 1.0
OP2 B:DG10 1.5 20.9 1.0
O3' B:DT9 1.6 23.3 1.0
O5' B:DG10 1.6 6.9 1.0
C5' B:DG10 2.6 16.7 1.0
C3' B:DT9 2.9 28.3 1.0
C4' B:DT9 3.9 37.1 1.0
C4' B:DG10 3.9 20.0 1.0
C2' B:DT9 3.9 23.9 1.0
O4' B:DG10 4.0 13.8 1.0
O B:HOH28 4.2 11.2 1.0
C1' B:DT9 4.4 15.1 1.0
N3 B:DG10 4.4 10.2 1.0
O4' B:DT9 4.5 30.8 1.0
N2 B:DG10 4.6 4.3 1.0
C2 B:DG10 4.7 10.4 1.0
O A:HOH25 4.9 4.3 1.0

Phosphorus binding site 9 out of 10 in 180d

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Phosphorus binding site 9 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:42.3
occ:1.00
 P B:DC11 0.0 42.3 1.0
OP1 B:DC11 1.5 26.6 1.0
OP2 B:DC11 1.5 29.4 1.0
O3' B:DG10 1.6 26.7 1.0
O5' B:DC11 1.7 31.8 1.0
C5' B:DC11 2.5 31.9 1.0
C3' B:DG10 2.7 21.3 1.0
C2' B:DG10 3.4 6.7 1.0
O B:HOH22 3.8 13.4 1.0
C4' B:DC11 3.9 28.8 1.0
C4' B:DG10 3.9 20.0 1.0
O4' B:DC11 4.4 17.3 1.0
C3' B:DC11 4.5 27.3 1.0
C5' B:DG10 4.7 16.7 1.0
C1' B:DG10 4.8 5.8 1.0
O4' B:DG10 5.0 13.8 1.0

Phosphorus binding site 10 out of 10 in 180d

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Phosphorus binding site 10 out of 10 in the Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:21.1
occ:1.00
 P B:DG12 0.0 21.1 1.0
OP1 B:DG12 1.5 5.8 1.0
OP2 B:DG12 1.5 17.1 1.0
O5' B:DG12 1.6 2.0 1.0
O3' B:DC11 1.7 27.5 1.0
C5' B:DG12 2.6 3.2 1.0
C3' B:DC11 2.7 27.3 1.0
C4' B:DC11 3.8 28.8 1.0
C2' B:DC11 3.8 18.1 1.0
C4' B:DG12 3.8 3.8 1.0
O B:HOH22 4.0 13.4 1.0
O B:HOH17 4.1 20.9 1.0
O4' B:DG12 4.2 2.6 1.0
C5' B:DC11 4.5 31.9 1.0
C1' B:DC11 4.7 19.8 1.0
N3 B:DG12 4.8 30.5 1.0
O4' B:DC11 4.9 17.3 1.0

Reference:

C.Sadasivan, N.Gautham. Sequence-Dependent Microheterogeneity of Z-Dna: the Crystal and Molecular Structures of D(Cacgcg).D(Cgcgtg) and D(Cgcacg).D(Cgtgcg). J.Mol.Biol. V. 248 918 1995.
ISSN: ISSN 0022-2836
PubMed: 7760333
DOI: 10.1006/JMBI.1995.9894
Page generated: Fri Sep 25 11:45:23 2020

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