Phosphorus in PDB 132d: Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Phosphorus atom in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site (pdb code 132d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 24 binding sites of Phosphorus where determined in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site, PDB code: 132d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 24 in 132d

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Phosphorus binding site 1 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1

b:0.0
occ:1.00
P A:DG1 0.0 0.0 1.0
OP3 A:DG1 1.5 0.0 1.0
OP1 A:DG1 1.5 0.0 1.0
O5' A:DG1 1.6 0.0 1.0
OP2 A:DG1 1.6 0.0 1.0
C5' A:DG1 2.6 0.0 1.0
H5' A:DG1 2.9 0.0 1.0
H5'' A:DG1 2.9 0.0 1.0
C4' A:DG1 3.9 0.0 1.0
H4' A:DG1 4.0 0.0 1.0
H3' A:DG1 4.6 0.0 1.0
C3' A:DG1 4.9 0.0 1.0
O4' A:DG1 4.9 0.0 1.0

Phosphorus binding site 2 out of 24 in 132d

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Phosphorus binding site 2 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:DC2 0.0 0.0 1.0
OP2 A:DC2 1.5 0.0 1.0
OP1 A:DC2 1.5 0.0 1.0
O3' A:DG1 1.6 0.0 1.0
O5' A:DC2 1.6 0.0 1.0
C5' A:DC2 2.6 0.0 1.0
C3' A:DG1 2.7 0.0 1.0
H5'' A:DC2 2.8 0.0 1.0
H2'' A:DG1 2.8 0.0 1.0
H3' A:DG1 3.0 0.0 1.0
H5' A:DC2 3.0 0.0 1.0
C2' A:DG1 3.3 0.0 1.0
H1' A:DG1 3.7 0.0 1.0
H3' A:DC2 3.9 0.0 1.0
H4' A:DG1 3.9 0.0 1.0
C4' A:DC2 3.9 0.0 1.0
C4' A:DG1 3.9 0.0 1.0
H2' A:DG1 4.0 0.0 1.0
C1' A:DG1 4.0 0.0 1.0
H6 A:DC2 4.0 0.0 1.0
C3' A:DC2 4.4 0.0 1.0
O4' A:DC2 4.5 0.0 1.0
O4' A:DG1 4.6 0.0 1.0
H4' A:DC2 4.7 0.0 1.0
H2' A:DC2 4.8 0.0 1.0

Phosphorus binding site 3 out of 24 in 132d

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Phosphorus binding site 3 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DC3 0.0 0.0 1.0
OP1 A:DC3 1.5 0.0 1.0
OP2 A:DC3 1.5 0.0 1.0
O3' A:DC2 1.5 0.0 1.0
O5' A:DC3 1.6 0.0 1.0
C5' A:DC3 2.6 0.0 1.0
C3' A:DC2 2.7 0.0 1.0
H2'' A:DC2 2.8 0.0 1.0
H5'' A:DC3 2.8 0.0 1.0
H5' A:DC3 3.0 0.0 1.0
H3' A:DC2 3.1 0.0 1.0
C2' A:DC2 3.3 0.0 1.0
H4' A:DC2 3.8 0.0 1.0
H3' A:DC3 3.8 0.0 1.0
C4' A:DC2 3.9 0.0 1.0
H1' A:DC2 3.9 0.0 1.0
C4' A:DC3 3.9 0.0 1.0
C1' A:DC2 4.0 0.0 1.0
H2' A:DC2 4.2 0.0 1.0
H6 A:DC3 4.2 0.0 1.0
C3' A:DC3 4.4 0.0 1.0
O4' A:DC3 4.6 0.0 1.0
O4' A:DC2 4.6 0.0 1.0
H2' A:DC3 4.8 0.0 1.0
H4' A:DC3 4.8 0.0 1.0
H5'' A:DC2 4.8 0.0 1.0
C5' A:DC2 5.0 0.0 1.0

Phosphorus binding site 4 out of 24 in 132d

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Phosphorus binding site 4 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DG4 0.0 0.0 1.0
OP1 A:DG4 1.5 0.0 1.0
OP2 A:DG4 1.5 0.0 1.0
O3' A:DC3 1.5 0.0 1.0
O5' A:DG4 1.6 0.0 1.0
C5' A:DG4 2.6 0.0 1.0
C3' A:DC3 2.7 0.0 1.0
H2'' A:DC3 2.8 0.0 1.0
H5'' A:DG4 2.8 0.0 1.0
H5' A:DG4 2.8 0.0 1.0
H3' A:DC3 3.1 0.0 1.0
C2' A:DC3 3.3 0.0 1.0
H1' A:DC3 3.8 0.0 1.0
H4' A:DC3 3.8 0.0 1.0
C4' A:DC3 3.9 0.0 1.0
C4' A:DG4 4.0 0.0 1.0
C1' A:DC3 4.0 0.0 1.0
H3' A:DG4 4.1 0.0 1.0
H2' A:DC3 4.1 0.0 1.0
C3' A:DG4 4.6 0.0 1.0
O4' A:DC3 4.6 0.0 1.0
H4' A:DG4 4.7 0.0 1.0
O4' A:DG4 4.7 0.0 1.0
H5'' A:DC3 4.8 0.0 1.0
H8 A:DG4 5.0 0.0 1.0
H2' A:DG4 5.0 0.0 1.0
C5' A:DC3 5.0 0.0 1.0

Phosphorus binding site 5 out of 24 in 132d

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Phosphorus binding site 5 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DT5 0.0 0.0 1.0
O3' A:DG4 1.5 0.0 1.0
OP2 A:DT5 1.5 0.0 1.0
OP1 A:DT5 1.5 0.0 1.0
O5' A:DT5 1.6 0.0 1.0
C3' A:DG4 2.7 0.0 1.0
C5' A:DT5 2.7 0.0 1.0
H5'' A:DT5 2.7 0.0 1.0
H2'' A:DG4 2.8 0.0 1.0
C2' A:DG4 3.2 0.0 1.0
H3' A:DG4 3.2 0.0 1.0
H1' A:DG4 3.3 0.0 1.0
H5' A:DT5 3.3 0.0 1.0
H4' A:DG4 3.5 0.0 1.0
H3' A:DT5 3.6 0.0 1.0
C1' A:DG4 3.7 0.0 1.0
C4' A:DG4 3.7 0.0 1.0
C4' A:DT5 3.9 0.0 1.0
H2' A:DG4 4.2 0.0 1.0
O4' A:DG4 4.2 0.0 1.0
C3' A:DT5 4.3 0.0 1.0
H6 A:DT5 4.4 0.0 1.0
O4' A:DT5 4.4 0.0 1.0
H5'' A:DG4 4.6 0.0 1.0
H2' A:DT5 4.6 0.0 1.0
H4' A:DT5 4.7 0.0 1.0
C5' A:DG4 4.9 0.0 1.0

Phosphorus binding site 6 out of 24 in 132d

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Phosphorus binding site 6 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:DT6 0.0 0.0 1.0
OP1 A:DT6 1.5 0.0 1.0
OP2 A:DT6 1.5 0.0 1.0
O3' A:DT5 1.5 0.0 1.0
O5' A:DT6 1.7 0.0 1.0
C3' A:DT5 2.6 0.0 1.0
C5' A:DT6 2.7 0.0 1.0
H5'' A:DT6 2.7 0.0 1.0
H2'' A:DT5 2.7 0.0 1.0
H5' A:DT6 3.1 0.0 1.0
H3' A:DT5 3.2 0.0 1.0
C2' A:DT5 3.2 0.0 1.0
H4' A:DT5 3.6 0.0 1.0
H3' A:DT6 3.7 0.0 1.0
H1' A:DT5 3.8 0.0 1.0
C4' A:DT5 3.8 0.0 1.0
C1' A:DT5 3.9 0.0 1.0
C4' A:DT6 3.9 0.0 1.0
H2' A:DT5 4.1 0.0 1.0
H6 A:DT6 4.3 0.0 1.0
C3' A:DT6 4.3 0.0 1.0
H5'' A:DT5 4.5 0.0 1.0
O4' A:DT5 4.6 0.0 1.0
O4' A:DT6 4.6 0.0 1.0
H4' A:DT6 4.7 0.0 1.0
C5' A:DT5 4.8 0.0 1.0
H2' A:DT6 4.9 0.0 1.0

Phosphorus binding site 7 out of 24 in 132d

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Phosphorus binding site 7 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:DA7 0.0 0.0 1.0
O3' A:DT6 1.5 0.0 1.0
OP2 A:DA7 1.5 0.0 1.0
OP1 A:DA7 1.5 0.0 1.0
O5' A:DA7 1.6 0.0 1.0
C5' A:DA7 2.7 0.0 1.0
C3' A:DT6 2.7 0.0 1.0
H2'' A:DT6 2.7 0.0 1.0
H5'' A:DA7 2.8 0.0 1.0
H5' A:DA7 3.0 0.0 1.0
H3' A:DT6 3.2 0.0 1.0
C2' A:DT6 3.2 0.0 1.0
H4' A:DT6 3.6 0.0 1.0
H1' A:DT6 3.7 0.0 1.0
C4' A:DT6 3.7 0.0 1.0
C1' A:DT6 3.9 0.0 1.0
C4' A:DA7 4.0 0.0 1.0
H3' A:DA7 4.0 0.0 1.0
H2' A:DT6 4.1 0.0 1.0
H5'' A:DT6 4.4 0.0 1.0
O4' A:DT6 4.5 0.0 1.0
C3' A:DA7 4.6 0.0 1.0
O4' A:DA7 4.7 0.0 1.0
H4' A:DA7 4.7 0.0 1.0
H2' A:DA7 4.8 0.0 1.0
C5' A:DT6 4.8 0.0 1.0

Phosphorus binding site 8 out of 24 in 132d

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Phosphorus binding site 8 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DA8 0.0 0.0 1.0
OP2 A:DA8 1.5 0.0 1.0
OP1 A:DA8 1.5 0.0 1.0
O3' A:DA7 1.6 0.0 1.0
O5' A:DA8 1.6 0.0 1.0
C5' A:DA8 2.6 0.0 1.0
C3' A:DA7 2.7 0.0 1.0
H2'' A:DA7 2.8 0.0 1.0
H5' A:DA8 2.8 0.0 1.0
H5'' A:DA8 2.9 0.0 1.0
H3' A:DA7 3.0 0.0 1.0
C2' A:DA7 3.4 0.0 1.0
H1' A:DA7 3.7 0.0 1.0
H4' A:DA7 3.8 0.0 1.0
C4' A:DA7 3.9 0.0 1.0
C4' A:DA8 3.9 0.0 1.0
C1' A:DA7 4.0 0.0 1.0
H3' A:DA8 4.1 0.0 1.0
H2' A:DA7 4.2 0.0 1.0
O4' A:DA8 4.5 0.0 1.0
C3' A:DA8 4.5 0.0 1.0
H5'' A:DA7 4.6 0.0 1.0
O4' A:DA7 4.6 0.0 1.0
H8 A:DA8 4.6 0.0 1.0
H2' A:DA8 4.6 0.0 1.0
H4' A:DA8 4.7 0.0 1.0
C5' A:DA7 5.0 0.0 1.0

Phosphorus binding site 9 out of 24 in 132d

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Phosphorus binding site 9 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DC9 0.0 0.0 1.0
OP2 A:DC9 1.5 0.0 1.0
OP1 A:DC9 1.5 0.0 1.0
O3' A:DA8 1.6 0.0 1.0
O5' A:DC9 1.6 0.0 1.0
C5' A:DC9 2.6 0.0 1.0
C3' A:DA8 2.7 0.0 1.0
H5' A:DC9 2.8 0.0 1.0
H3' A:DA8 2.9 0.0 1.0
H2'' A:DA8 3.0 0.0 1.0
H5'' A:DC9 3.0 0.0 1.0
C2' A:DA8 3.3 0.0 1.0
H1' A:DA8 3.9 0.0 1.0
H4' A:DA8 3.9 0.0 1.0
C4' A:DC9 3.9 0.0 1.0
C4' A:DA8 3.9 0.0 1.0
H2' A:DA8 4.1 0.0 1.0
H3' A:DC9 4.1 0.0 1.0
C1' A:DA8 4.1 0.0 1.0
H6 A:DC9 4.2 0.0 1.0
O4' A:DC9 4.3 0.0 1.0
C3' A:DC9 4.5 0.0 1.0
H2' A:DC9 4.6 0.0 1.0
O4' A:DA8 4.6 0.0 1.0
H4' A:DC9 4.7 0.0 1.0
H5'' A:DA8 4.9 0.0 1.0

Phosphorus binding site 10 out of 24 in 132d

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Phosphorus binding site 10 out of 24 in the Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Solution Structure of the Tn An Dna Duplex Gccgttaacggc Containing the Hpa I Restriction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:DG10 0.0 0.0 1.0
OP1 A:DG10 1.5 0.0 1.0
OP2 A:DG10 1.5 0.0 1.0
O3' A:DC9 1.5 0.0 1.0
O5' A:DG10 1.6 0.0 1.0
C5' A:DG10 2.7 0.0 1.0
C3' A:DC9 2.7 0.0 1.0
H2'' A:DC9 2.8 0.0 1.0
H5'' A:DG10 2.8 0.0 1.0
H3' A:DC9 3.1 0.0 1.0
H5' A:DG10 3.1 0.0 1.0
C2' A:DC9 3.3 0.0 1.0
H3' A:DG10 3.5 0.0 1.0
H1' A:DC9 3.7 0.0 1.0
H4' A:DC9 3.8 0.0 1.0
C4' A:DC9 3.9 0.0 1.0
C4' A:DG10 3.9 0.0 1.0
C1' A:DC9 4.1 0.0 1.0
H2' A:DG10 4.2 0.0 1.0
C3' A:DG10 4.2 0.0 1.0
H2' A:DC9 4.3 0.0 1.0
C2' A:DG10 4.7 0.0 1.0
O4' A:DC9 4.7 0.0 1.0
H4' A:DG10 4.7 0.0 1.0
O4' A:DG10 4.8 0.0 1.0
H5'' A:DC9 4.8 0.0 1.0
C5' A:DC9 5.0 0.0 1.0

Reference:

S.G.Kim, B.R.Reid. Solution Structure of the Tnan Dna Duplex Gccgttaacgcg Containing the Hpai Restriction Site. Biochemistry V. 31 12103 1992.
ISSN: ISSN 0006-2960
PubMed: 1457407
DOI: 10.1021/BI00163A020
Page generated: Fri Sep 25 11:19:16 2020

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