Phosphorus in PDB 187d: Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition

Protein crystallography data

The structure of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition, PDB code: 187d was solved by M.Eisenstein, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.360, 43.360, 24.830, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition (pdb code 187d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 7 binding sites of Phosphorus where determined in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition, PDB code: 187d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7;

Phosphorus binding site 1 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 1 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:25.4
occ:1.00
P A:DC2 0.0 25.4 1.0
OP1 A:DC2 1.5 27.5 1.0
OP2 A:DC2 1.5 24.9 1.0
O5' A:DC2 1.6 23.4 1.0
O3' A:DC1 1.6 24.8 1.0
C5' A:DC2 2.6 23.5 1.0
C3' A:DC1 2.6 24.4 1.0
C2' A:DC1 3.6 24.3 1.0
C4' A:DC2 3.8 25.1 1.0
C4' A:DC1 3.8 23.5 1.0
O A:HOH23 3.9 18.2 1.0
O4' A:DC2 4.0 25.4 1.0
C6 A:DC2 4.3 24.1 1.0
C5' A:DC1 4.3 23.2 1.0
C3' A:DC2 4.4 25.3 1.0
O A:HOH22 4.9 18.6 1.0
O A:HOH24 4.9 67.5 1.0
O A:HOH29 4.9 52.9 1.0
C1' A:DC1 4.9 23.3 1.0
O5' A:DC1 4.9 23.6 1.0
O4' A:DC1 5.0 22.8 1.0
C5 A:DC2 5.0 23.6 1.0

Phosphorus binding site 2 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 2 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:26.1
occ:1.00
P A:DC3 0.0 26.1 1.0
OP2 A:DC3 1.5 25.8 1.0
OP1 A:DC3 1.5 26.8 1.0
O3' A:DC2 1.6 26.0 1.0
O5' A:DC3 1.6 25.7 1.0
C5' A:DC3 2.6 24.9 1.0
C3' A:DC2 2.6 25.3 1.0
C2' A:DC2 3.4 24.1 1.0
C4' A:DC3 3.8 23.4 1.0
C4' A:DC2 4.0 25.1 1.0
O A:HOH30 4.0 46.7 1.0
O4' A:DC3 4.1 23.1 1.0
C3' A:DC3 4.4 22.2 1.0
C6 A:DC3 4.4 17.9 1.0
C5' A:DC2 4.6 23.5 1.0
O5' A:DC2 4.7 23.4 1.0
C1' A:DC2 4.7 24.5 1.0
O4' A:DC2 5.0 25.4 1.0

Phosphorus binding site 3 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 3 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:24.1
occ:1.00
P A:DC4 0.0 24.1 1.0
OP1 A:DC4 1.5 24.9 1.0
OP2 A:DC4 1.5 25.6 1.0
O3' A:DC3 1.6 23.1 1.0
O5' A:DC4 1.6 21.8 1.0
C5' A:DC4 2.6 19.2 1.0
C3' A:DC3 2.7 22.2 1.0
C2' A:DC3 3.4 21.8 1.0
C4' A:DC3 3.9 23.4 1.0
C4' A:DC4 4.0 17.8 1.0
O A:HOH45 4.0 61.1 1.0
O A:HOH46 4.0 98.3 1.0
O A:HOH14 4.2 41.1 1.0
O4' A:DC4 4.4 16.6 1.0
C3' A:DC4 4.6 17.9 1.0
C5' A:DC3 4.6 24.9 1.0
C6 A:DC4 4.7 13.6 1.0
C1' A:DC3 4.8 20.8 1.0
O5' A:DC3 5.0 25.7 1.0

Phosphorus binding site 4 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 4 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:19.4
occ:1.00
P A:DG5 0.0 19.4 1.0
OP1 A:DG5 1.5 21.1 1.0
OP2 A:DG5 1.5 19.2 1.0
O5' A:DG5 1.6 19.9 1.0
O3' A:DC4 1.6 19.8 1.0
C3' A:DC4 2.5 17.9 1.0
C5' A:DG5 2.6 20.3 1.0
C2' A:DC4 3.3 17.3 1.0
O A:HOH21 3.5 44.1 1.0
O A:HOH32 3.8 81.0 1.0
C4' A:DC4 3.9 17.8 1.0
C4' A:DG5 3.9 20.2 1.0
O4' A:DG5 4.3 20.6 1.0
O A:HOH45 4.4 61.1 1.0
C5' A:DC4 4.4 19.2 1.0
O A:HOH40 4.5 77.7 1.0
C1' A:DC4 4.7 14.8 1.0
O5' A:DC4 4.8 21.8 1.0
O4' A:DC4 4.9 16.6 1.0

Phosphorus binding site 5 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 5 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:22.6
occ:1.00
P A:DG6 0.0 22.6 1.0
OP2 A:DG6 1.5 21.8 1.0
OP1 A:DG6 1.5 20.9 1.0
O3' A:DG5 1.6 21.4 1.0
O5' A:DG6 1.6 21.7 1.0
C5' A:DG6 2.7 20.0 1.0
C3' A:DG5 2.7 19.9 1.0
C2' A:DG5 3.5 18.2 1.0
O A:HOH42 3.6 68.0 1.0
C4' A:DG6 3.9 20.9 1.0
O A:HOH25 3.9 61.6 1.0
C4' A:DG5 4.0 20.2 1.0
O A:HOH13 4.0 71.7 1.0
O4' A:DG6 4.1 18.4 1.0
O A:HOH16 4.1 51.6 1.0
C8 A:DG6 4.2 13.5 1.0
C3' A:DG6 4.6 23.2 1.0
O A:HOH15 4.6 52.6 1.0
C5' A:DG5 4.7 20.3 1.0
C1' A:DG5 4.8 15.2 1.0
OP2 A:DG7 4.9 29.7 1.0

Phosphorus binding site 6 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 6 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:29.1
occ:1.00
P A:DG7 0.0 29.1 1.0
OP2 A:DG7 1.5 29.7 1.0
OP1 A:DG7 1.5 31.0 1.0
O3' A:DG6 1.6 27.1 1.0
O5' A:DG7 1.6 27.0 1.0
C3' A:DG6 2.6 23.2 1.0
C5' A:DG7 2.6 21.9 1.0
C2' A:DG6 3.5 20.4 1.0
C4' A:DG6 3.8 20.9 1.0
C4' A:DG7 3.9 19.8 1.0
O4' A:DG7 4.0 17.2 1.0
O A:HOH16 4.3 51.6 1.0
C5' A:DG6 4.3 20.0 1.0
C1' A:DG6 4.7 17.3 1.0
C3' A:DG7 4.7 20.2 1.0
O5' A:DG6 4.8 21.7 1.0
O A:HOH13 4.9 71.7 1.0
O4' A:DG6 4.9 18.4 1.0
C8 A:DG7 4.9 16.2 1.0

Phosphorus binding site 7 out of 7 in 187d

Go back to Phosphorus Binding Sites List in 187d
Phosphorus binding site 7 out of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:24.9
occ:1.00
P A:DG8 0.0 24.9 1.0
OP1 A:DG8 1.5 24.7 1.0
OP2 A:DG8 1.5 24.3 1.0
O5' A:DG8 1.6 25.7 1.0
O3' A:DG7 1.6 22.7 1.0
C3' A:DG7 2.6 20.2 1.0
C5' A:DG8 2.7 27.6 1.0
C2' A:DG7 3.2 19.0 1.0
C4' A:DG8 3.9 28.7 1.0
C4' A:DG7 3.9 19.8 1.0
O4' A:DG8 4.3 27.7 1.0
C3' A:DG8 4.3 29.4 1.0
C8 A:DG8 4.4 23.3 1.0
C1' A:DG7 4.6 17.0 1.0
C2' A:DG8 4.6 27.5 1.0
C5' A:DG7 4.6 21.9 1.0
O4' A:DG7 4.9 17.2 1.0
C1' A:DG8 5.0 26.1 1.0

Reference:

M.Eisenstein, Z.Shakked. Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition. J.Mol.Biol. V. 248 662 1995.
ISSN: ISSN 0022-2836
PubMed: 7752232
DOI: 10.1006/JMBI.1995.0250
Page generated: Fri Sep 25 11:48:02 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy