Phosphorus in PDB 175d: The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution (pdb code 175d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution, PDB code: 175d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 175d

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Phosphorus binding site 1 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution 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
OP1 A:DC2 1.5 0.0 1.0
OP2 A:DC2 1.5 0.0 1.0
O5' A:DC2 1.6 0.0 1.0
O3' A:DG1 1.6 0.0 1.0
C5' A:DC2 2.7 0.0 1.0
C3' A:DG1 2.7 0.0 1.0
H5'' A:DC2 2.9 0.0 1.0
H3' A:DG1 2.9 0.0 1.0
H2'' A:DG1 2.9 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 3.8 0.0 1.0
C4' A:DG1 4.0 0.0 1.0
C4' A:DC2 4.0 0.0 1.0
H2' A:DC2 4.0 0.0 1.0
H3' A:DC2 4.0 0.0 1.0
H4' A:DG1 4.0 0.0 1.0
C1' A:DG1 4.1 0.0 1.0
H2' A:DG1 4.1 0.0 1.0
H6 A:DC2 4.2 0.0 1.0
O4' A:DC2 4.5 0.0 1.0
C3' A:DC2 4.5 0.0 1.0
O4' A:DG1 4.7 0.0 1.0
C2' A:DC2 4.7 0.0 1.0
H4' A:DC2 4.8 0.0 1.0

Phosphorus binding site 2 out of 18 in 175d

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Phosphorus binding site 2 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DG3 0.0 0.0 1.0
OP1 A:DG3 1.5 0.0 1.0
OP2 A:DG3 1.5 0.0 1.0
O5' A:DG3 1.6 0.0 1.0
O3' A:DC2 1.6 0.0 1.0
C5' A:DG3 2.7 0.0 1.0
C3' A:DC2 2.7 0.0 1.0
H5' A:DG3 2.9 0.0 1.0
H3' A:DC2 2.9 0.0 1.0
H5'' A:DG3 3.0 0.0 1.0
H2'' A:DC2 3.0 0.0 1.0
C2' A:DC2 3.3 0.0 1.0
H1' A:DC2 3.7 0.0 1.0
C4' A:DG3 4.0 0.0 1.0
C4' A:DC2 4.0 0.0 1.0
H3' A:DG3 4.0 0.0 1.0
H4' A:DC2 4.0 0.0 1.0
C1' A:DC2 4.1 0.0 1.0
H2' A:DC2 4.2 0.0 1.0
H2' A:DG3 4.3 0.0 1.0
O4' A:DG3 4.4 0.0 1.0
C3' A:DG3 4.5 0.0 1.0
O4' A:DC2 4.7 0.0 1.0
H4' A:DG3 4.8 0.0 1.0
H8 A:DG3 4.8 0.0 1.0
C2' A:DG3 4.9 0.0 1.0
H5'' A:DC2 4.9 0.0 1.0

Phosphorus binding site 3 out of 18 in 175d

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Phosphorus binding site 3 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DA4 0.0 0.0 1.0
OP2 A:DA4 1.5 0.0 1.0
OP1 A:DA4 1.5 0.0 1.0
O5' A:DA4 1.6 0.0 1.0
O3' A:DG3 1.6 0.0 1.0
C3' A:DG3 2.7 0.0 1.0
C5' A:DA4 2.7 0.0 1.0
H3' A:DG3 2.8 0.0 1.0
H5' A:DA4 2.9 0.0 1.0
H5'' A:DA4 2.9 0.0 1.0
H4' A:DG3 3.2 0.0 1.0
H8 A:DA4 3.4 0.0 1.0
C4' A:DG3 3.5 0.0 1.0
H2' A:DA4 3.8 0.0 1.0
H5'' A:DG3 3.9 0.0 1.0
C2' A:DG3 3.9 0.0 1.0
C4' A:DA4 4.0 0.0 1.0
H2'' A:DG3 4.0 0.0 1.0
H3' A:DA4 4.1 0.0 1.0
C5' A:DG3 4.3 0.0 1.0
C8 A:DA4 4.4 0.0 1.0
O4' A:DA4 4.4 0.0 1.0
H1' A:DG3 4.4 0.0 1.0
C3' A:DA4 4.5 0.0 1.0
C2' A:DA4 4.6 0.0 1.0
O4' A:DG3 4.6 0.0 1.0
C1' A:DG3 4.6 0.0 1.0
H2' A:DG3 4.6 0.0 1.0
H4' A:DA4 4.8 0.0 1.0
C1' A:DA4 5.0 0.0 1.0

Phosphorus binding site 4 out of 18 in 175d

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Phosphorus binding site 4 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DA5 0.0 0.0 1.0
OP2 A:DA5 1.5 0.0 1.0
OP1 A:DA5 1.5 0.0 1.0
O5' A:DA5 1.6 0.0 1.0
O3' A:DA4 1.6 0.0 1.0
C5' A:DA5 2.7 0.0 1.0
C3' A:DA4 2.7 0.0 1.0
H3' A:DA4 2.8 0.0 1.0
H5' A:DA5 2.9 0.0 1.0
H5'' A:DA5 3.0 0.0 1.0
H2'' A:DA4 3.1 0.0 1.0
C2' A:DA4 3.4 0.0 1.0
C4' A:DA5 4.0 0.0 1.0
C4' A:DA4 4.0 0.0 1.0
H4' A:DA4 4.0 0.0 1.0
H8 A:DA5 4.1 0.0 1.0
H1' A:DA4 4.2 0.0 1.0
H2' A:DA4 4.2 0.0 1.0
H2' A:DA5 4.2 0.0 1.0
H3' A:DA5 4.3 0.0 1.0
O4' A:DA5 4.3 0.0 1.0
C1' A:DA4 4.3 0.0 1.0
C3' A:DA5 4.6 0.0 1.0
O4' A:DA4 4.7 0.0 1.0
H4' A:DA5 4.7 0.0 1.0
C2' A:DA5 4.9 0.0 1.0
C8 A:DA5 4.9 0.0 1.0

Phosphorus binding site 5 out of 18 in 175d

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Phosphorus binding site 5 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution 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
O5' A:DT6 1.6 0.0 1.0
O3' A:DA5 1.6 0.0 1.0
C5' A:DT6 2.6 0.0 1.0
C3' A:DA5 2.7 0.0 1.0
H5' A:DT6 2.8 0.0 1.0
H2'' A:DA5 2.9 0.0 1.0
H3' A:DA5 2.9 0.0 1.0
H5'' A:DT6 3.0 0.0 1.0
C2' A:DA5 3.3 0.0 1.0
H1' A:DA5 4.0 0.0 1.0
C4' A:DT6 4.0 0.0 1.0
C4' A:DA5 4.0 0.0 1.0
H4' A:DA5 4.0 0.0 1.0
H2' A:DA5 4.1 0.0 1.0
H2' A:DT6 4.2 0.0 1.0
C1' A:DA5 4.2 0.0 1.0
H6 A:DT6 4.3 0.0 1.0
O4' A:DT6 4.3 0.0 1.0
H3' A:DT6 4.3 0.0 1.0
C3' A:DT6 4.6 0.0 1.0
O4' A:DA5 4.7 0.0 1.0
H4' A:DT6 4.7 0.0 1.0
C2' A:DT6 4.9 0.0 1.0
H5'' A:DA5 4.9 0.0 1.0

Phosphorus binding site 6 out of 18 in 175d

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Phosphorus binding site 6 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:DG7 0.0 0.0 1.0
OP1 A:DG7 1.5 0.0 1.0
OP2 A:DG7 1.5 0.0 1.0
O5' A:DG7 1.6 0.0 1.0
O3' A:DT6 1.6 0.0 1.0
C5' A:DG7 2.7 0.0 1.0
C3' A:DT6 2.7 0.0 1.0
H5' A:DG7 2.9 0.0 1.0
H3' A:DT6 2.9 0.0 1.0
H5'' A:DG7 3.0 0.0 1.0
H2'' A:DT6 3.0 0.0 1.0
C2' A:DT6 3.3 0.0 1.0
H1' A:DT6 3.8 0.0 1.0
C4' A:DG7 4.0 0.0 1.0
C4' A:DT6 4.0 0.0 1.0
H3' A:DG7 4.0 0.0 1.0
H4' A:DT6 4.0 0.0 1.0
H2' A:DT6 4.2 0.0 1.0
C1' A:DT6 4.2 0.0 1.0
H2' A:DG7 4.3 0.0 1.0
O4' A:DG7 4.3 0.0 1.0
C3' A:DG7 4.5 0.0 1.0
O4' A:DT6 4.7 0.0 1.0
H4' A:DG7 4.8 0.0 1.0
H8 A:DG7 4.8 0.0 1.0
H5'' A:DT6 4.9 0.0 1.0
C2' A:DG7 4.9 0.0 1.0

Phosphorus binding site 7 out of 18 in 175d

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Phosphorus binding site 7 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution 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
O5' A:DA8 1.6 0.0 1.0
O3' A:DG7 1.6 0.0 1.0
C3' A:DG7 2.6 0.0 1.0
C5' A:DA8 2.7 0.0 1.0
H3' A:DG7 2.8 0.0 1.0
H5'' A:DA8 2.9 0.0 1.0
H5' A:DA8 2.9 0.0 1.0
H4' A:DG7 3.1 0.0 1.0
C4' A:DG7 3.4 0.0 1.0
H8 A:DA8 3.4 0.0 1.0
H5'' A:DG7 3.7 0.0 1.0
H2' A:DA8 3.9 0.0 1.0
C2' A:DG7 3.9 0.0 1.0
C4' A:DA8 4.0 0.0 1.0
H2'' A:DG7 4.1 0.0 1.0
H3' A:DA8 4.1 0.0 1.0
C5' A:DG7 4.1 0.0 1.0
O4' A:DA8 4.4 0.0 1.0
H1' A:DG7 4.4 0.0 1.0
C8 A:DA8 4.5 0.0 1.0
C3' A:DA8 4.5 0.0 1.0
O4' A:DG7 4.6 0.0 1.0
C2' A:DA8 4.6 0.0 1.0
C1' A:DG7 4.6 0.0 1.0
H2' A:DG7 4.7 0.0 1.0
H4' A:DA8 4.8 0.0 1.0
H5' A:DG7 4.9 0.0 1.0
H61 B:DA14 4.9 0.0 1.0
O5' A:DG7 4.9 0.0 1.0
C1' A:DA8 5.0 0.0 1.0

Phosphorus binding site 8 out of 18 in 175d

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Phosphorus binding site 8 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DG9 0.0 0.0 1.0
OP1 A:DG9 1.5 0.0 1.0
OP2 A:DG9 1.5 0.0 1.0
O5' A:DG9 1.6 0.0 1.0
O3' A:DA8 1.6 0.0 1.0
C5' A:DG9 2.6 0.0 1.0
C3' A:DA8 2.7 0.0 1.0
H5' A:DG9 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:DG9 3.0 0.0 1.0
C2' A:DA8 3.3 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
C4' A:DA8 4.0 0.0 1.0
H1' A:DA8 4.0 0.0 1.0
H4' A:DA8 4.1 0.0 1.0
H2' A:DG9 4.1 0.0 1.0
H2' A:DA8 4.1 0.0 1.0
H8 A:DG9 4.2 0.0 1.0
C1' A:DA8 4.3 0.0 1.0
O4' A:DG9 4.3 0.0 1.0
H3' A:DG9 4.4 0.0 1.0
C3' A:DG9 4.6 0.0 1.0
O4' A:DA8 4.7 0.0 1.0
H4' A:DG9 4.7 0.0 1.0
C2' A:DG9 4.8 0.0 1.0
H5'' A:DA8 5.0 0.0 1.0

Phosphorus binding site 9 out of 18 in 175d

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Phosphorus binding site 9 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:DC10 0.0 0.0 1.0
OP2 A:DC10 1.5 0.0 1.0
OP1 A:DC10 1.5 0.0 1.0
O5' A:DC10 1.6 0.0 1.0
O3' A:DG9 1.6 0.0 1.0
C5' A:DC10 2.7 0.0 1.0
C3' A:DG9 2.7 0.0 1.0
H5' A:DC10 2.9 0.0 1.0
H2'' A:DG9 2.9 0.0 1.0
H3' A:DG9 2.9 0.0 1.0
H5'' A:DC10 3.0 0.0 1.0
C2' A:DG9 3.3 0.0 1.0
H1' A:DG9 3.8 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
C4' A:DC10 4.0 0.0 1.0
H6 A:DC10 4.0 0.0 1.0
H4' A:DG9 4.0 0.0 1.0
C1' A:DG9 4.1 0.0 1.0
H2' A:DG9 4.2 0.0 1.0
H3' A:DC10 4.2 0.0 1.0
H2' A:DC10 4.3 0.0 1.0
O4' A:DC10 4.3 0.0 1.0
C3' A:DC10 4.6 0.0 1.0
O4' A:DG9 4.7 0.0 1.0
H4' A:DC10 4.8 0.0 1.0
C2' A:DC10 4.9 0.0 1.0

Phosphorus binding site 10 out of 18 in 175d

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Phosphorus binding site 10 out of 18 in the The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G:A Pairs in Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:0.0
occ:1.00
P B:DC12 0.0 0.0 1.0
OP1 B:DC12 1.5 0.0 1.0
OP2 B:DC12 1.5 0.0 1.0
O3' B:DG11 1.6 0.0 1.0
O5' B:DC12 1.6 0.0 1.0
C5' B:DC12 2.7 0.0 1.0
C3' B:DG11 2.7 0.0 1.0
H5'' B:DC12 2.9 0.0 1.0
H3' B:DG11 2.9 0.0 1.0
H2'' B:DG11 2.9 0.0 1.0
H5' B:DC12 3.0 0.0 1.0
C2' B:DG11 3.3 0.0 1.0
H1' B:DG11 3.8 0.0 1.0
C4' B:DG11 4.0 0.0 1.0
C4' B:DC12 4.0 0.0 1.0
H2' B:DC12 4.0 0.0 1.0
H3' B:DC12 4.0 0.0 1.0
H4' B:DG11 4.0 0.0 1.0
C1' B:DG11 4.1 0.0 1.0
H2' B:DG11 4.1 0.0 1.0
H6 B:DC12 4.2 0.0 1.0
O4' B:DC12 4.5 0.0 1.0
C3' B:DC12 4.5 0.0 1.0
O4' B:DG11 4.7 0.0 1.0
C2' B:DC12 4.7 0.0 1.0
H4' B:DC12 4.8 0.0 1.0

Reference:

S.H.Chou, J.W.Cheng, O.Fedoroff, B.R.Reid. Dna Sequence Gcgaatgagc Containing the Human Centromere Core Sequence Gaat Forms A Self-Complementary Duplex with Sheared G.A Pairs in Solution. J.Mol.Biol. V. 241 467 1994.
ISSN: ISSN 0022-2836
PubMed: 8064859
DOI: 10.1006/JMBI.1994.1521
Page generated: Fri Sep 25 11:42:12 2020

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