Phosphorus in PDB 107d: Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Phosphorus atom in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex (pdb code 107d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 12 binding sites of Phosphorus where determined in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex, PDB code: 107d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 12 in 107d

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Phosphorus binding site 1 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.6
occ:1.00
P A:DC2 0.0 0.6 1.0
OP2 A:DC2 1.5 0.7 1.0
OP1 A:DC2 1.5 0.6 1.0
O3' A:DC1 1.6 0.4 1.0
O5' A:DC2 1.6 0.7 1.0
C3' A:DC1 2.7 0.3 1.0
C5' A:DC2 2.7 0.7 1.0
HO5' A:DC1 2.7 0.5 1.0
H5' A:DC2 2.8 0.7 1.0
H3' A:DC1 2.9 0.3 1.0
H4' A:DC1 3.2 0.4 1.0
H5'' A:DC2 3.2 0.9 1.0
C4' A:DC1 3.4 0.4 1.0
H6 A:DC2 3.5 0.6 1.0
O5' A:DC1 3.6 0.6 1.0
C2' A:DC1 3.9 0.3 1.0
C4' A:DC2 3.9 0.6 1.0
H2'' A:DC1 4.1 0.4 1.0
H3' A:DC2 4.1 0.8 1.0
C5' A:DC1 4.1 0.5 1.0
H2' A:DC2 4.2 0.7 1.0
H1' A:DC1 4.3 0.3 1.0
O4' A:DC2 4.4 0.6 1.0
C6 A:DC2 4.5 0.6 1.0
C1' A:DC1 4.6 0.2 1.0
C3' A:DC2 4.6 0.7 1.0
O4' A:DC1 4.6 0.3 1.0
H2' A:DC1 4.7 0.4 1.0
H5' A:DC1 4.7 0.6 1.0
H4' A:DC2 4.8 0.7 1.0
C2' A:DC2 4.8 0.7 1.0
H5'' A:DC1 4.9 0.7 1.0
H5 A:DC2 5.0 0.6 1.0

Phosphorus binding site 2 out of 12 in 107d

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Phosphorus binding site 2 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.7
occ:1.00
P A:DT3 0.0 0.7 1.0
OP1 A:DT3 1.5 0.9 1.0
OP2 A:DT3 1.5 0.8 1.0
O5' A:DT3 1.6 0.6 1.0
O3' A:DC2 1.6 0.9 1.0
C5' A:DT3 2.6 0.5 1.0
C3' A:DC2 2.7 0.7 1.0
H5' A:DT3 2.7 0.6 1.0
H3' A:DC2 2.7 0.8 1.0
H4' A:DC2 3.0 0.7 1.0
H5'' A:DT3 3.4 0.6 1.0
C4' A:DC2 3.6 0.6 1.0
C4' A:DT3 3.7 0.4 1.0
O4' A:DT3 3.7 0.4 1.0
H2'' A:DC2 3.8 0.7 1.0
C2' A:DC2 3.8 0.7 1.0
H2' A:DT3 4.0 0.4 1.0
H5'' A:DC2 4.0 0.9 1.0
H3' A:DT3 4.3 0.4 1.0
H6 A:DT3 4.4 0.5 1.0
C5' A:DC2 4.4 0.7 1.0
C3' A:DT3 4.5 0.4 1.0
H2' A:DC2 4.5 0.7 1.0
H4' A:DT3 4.5 0.4 1.0
H1' A:DC2 4.6 0.6 1.0
C2' A:DT3 4.6 0.4 1.0
C1' A:DC2 4.6 0.6 1.0
O4' A:DC2 4.7 0.6 1.0
C1' A:DT3 4.7 0.3 1.0
C6 A:DT3 5.0 0.4 1.0

Phosphorus binding site 3 out of 12 in 107d

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Phosphorus binding site 3 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.4
occ:1.00
P A:DT4 0.0 0.4 1.0
OP1 A:DT4 1.5 0.5 1.0
OP2 A:DT4 1.5 0.6 1.0
O5' A:DT4 1.6 0.5 1.0
O3' A:DT3 1.6 0.4 1.0
C3' A:DT3 2.7 0.4 1.0
C5' A:DT4 2.7 0.4 1.0
H2'' A:DT3 2.8 0.4 1.0
H5' A:DT4 2.9 0.4 1.0
H3' A:DT3 3.0 0.4 1.0
C2' A:DT3 3.2 0.4 1.0
H3' A:DT4 3.3 0.4 1.0
C4' A:DT4 3.5 0.4 1.0
H6 A:DT4 3.5 0.4 1.0
H5'' A:DT4 3.5 0.4 1.0
H1' A:DT3 3.6 0.4 1.0
O4' A:DT4 3.7 0.4 1.0
H4' A:DT3 4.0 0.4 1.0
C4' A:DT3 4.0 0.4 1.0
C1' A:DT3 4.0 0.3 1.0
C3' A:DT4 4.0 0.4 1.0
H2' A:DT3 4.0 0.4 1.0
H2' A:DT4 4.5 0.4 1.0
C6 A:DT4 4.5 0.3 1.0
H4' A:DT4 4.5 0.4 1.0
O4' A:DT3 4.7 0.4 1.0
C2' A:DT4 4.7 0.4 1.0
C1' A:DT4 4.8 0.3 1.0
H73 A:DT4 4.8 0.7 1.0
H5'' A:DT3 4.9 0.6 1.0

Phosphorus binding site 4 out of 12 in 107d

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Phosphorus binding site 4 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.4
occ:1.00
P A:DT5 0.0 0.4 1.0
OP1 A:DT5 1.5 0.5 1.0
OP2 A:DT5 1.5 0.6 1.0
O5' A:DT5 1.6 0.3 1.0
O3' A:DT4 1.6 0.4 1.0
C5' A:DT5 2.6 0.3 1.0
C3' A:DT4 2.7 0.4 1.0
H5' A:DT5 2.8 0.4 1.0
H5'' A:DT5 3.0 0.4 1.0
H2'' A:DT4 3.0 0.4 1.0
H3' A:DT4 3.1 0.4 1.0
C2' A:DT4 3.3 0.4 1.0
H6 A:DT5 3.5 0.2 1.0
H4' A:DT4 3.6 0.4 1.0
H2' A:DT4 3.8 0.4 1.0
H2' A:DT5 3.9 0.3 1.0
C4' A:DT5 3.9 0.2 1.0
C4' A:DT4 4.0 0.4 1.0
H3' A:DT5 4.2 0.3 1.0
H73 A:DT5 4.3 0.5 1.0
O4' A:DT5 4.4 0.2 1.0
H5'' A:DT4 4.5 0.4 1.0
C6 A:DT5 4.5 0.2 1.0
C3' A:DT5 4.5 0.2 1.0
O35 B:DUO15 4.5 0.5 1.0
C1' A:DT4 4.6 0.3 1.0
C2' A:DT5 4.6 0.2 1.0
H1' A:DT4 4.7 0.3 1.0
C5' A:DT4 4.7 0.4 1.0
H4' A:DT5 4.7 0.3 1.0
H72 A:DT5 4.9 0.5 1.0
O4' A:DT4 4.9 0.4 1.0

Phosphorus binding site 5 out of 12 in 107d

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Phosphorus binding site 5 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.2
occ:1.00
P A:DT6 0.0 0.2 1.0
OP2 A:DT6 1.5 0.3 1.0
OP1 A:DT6 1.5 0.3 1.0
O3' A:DT5 1.6 0.2 1.0
O5' A:DT6 1.6 0.3 1.0
C5' A:DT6 2.6 0.2 1.0
C3' A:DT5 2.7 0.2 1.0
H5' A:DT6 2.7 0.3 1.0
H3' A:DT5 2.8 0.3 1.0
H5'' A:DT6 3.1 0.4 1.0
H2'' A:DT5 3.4 0.3 1.0
C2' A:DT5 3.6 0.2 1.0
H4' A:DT5 3.6 0.3 1.0
H7 B:DUO15 3.7 0.2 1.0
C4' A:DT5 3.8 0.2 1.0
C4' A:DT6 3.9 0.2 1.0
H3' A:DT6 4.1 0.4 1.0
C7 B:DUO15 4.1 0.2 1.0
H1' A:DT5 4.2 0.2 1.0
O4' A:DT6 4.2 0.2 1.0
H2' A:DT5 4.4 0.3 1.0
C1' A:DT5 4.5 0.2 1.0
H5'' A:DT5 4.6 0.4 1.0
H4' A:DT6 4.6 0.3 1.0
C3' A:DT6 4.7 0.3 1.0
C8 B:DUO15 4.7 0.2 1.0
O30 B:DUO15 4.7 0.4 1.0
C6 B:DUO15 4.7 0.3 1.0
O4' A:DT5 4.7 0.2 1.0
O31 B:DUO15 4.7 0.3 1.0
C14 B:DUO15 4.8 0.3 1.0
C5' A:DT5 4.8 0.3 1.0
N13 B:DUO15 5.0 0.2 1.0

Phosphorus binding site 6 out of 12 in 107d

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Phosphorus binding site 6 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.7
occ:1.00
P A:DC7 0.0 0.7 1.0
OP2 A:DC7 1.5 0.9 1.0
OP1 A:DC7 1.5 0.9 1.0
O3' A:DT6 1.6 0.5 1.0
O5' A:DC7 1.6 0.5 1.0
C5' A:DC7 2.7 0.5 1.0
C3' A:DT6 2.7 0.3 1.0
H2'' A:DT6 2.9 0.3 1.0
H5' A:DC7 2.9 0.6 1.0
H5'' A:DC7 3.0 0.6 1.0
H3' A:DT6 3.2 0.4 1.0
C2' A:DT6 3.2 0.3 1.0
H2' A:DT6 3.7 0.3 1.0
H3' A:DC7 3.8 0.4 1.0
H4' A:DT6 3.9 0.3 1.0
H6 A:DC7 3.9 0.2 1.0
C4' A:DT6 4.0 0.2 1.0
C4' A:DC7 4.0 0.4 1.0
O4' A:DC7 4.3 0.4 1.0
H5'' A:DT6 4.4 0.4 1.0
C3' A:DC7 4.4 0.4 1.0
C1' A:DT6 4.5 0.3 1.0
H1' A:DT6 4.6 0.3 1.0
C5' A:DT6 4.8 0.2 1.0
H4' A:DC7 4.8 0.6 1.0
C6 A:DC7 4.9 0.2 1.0
O4' A:DT6 4.9 0.2 1.0

Phosphorus binding site 7 out of 12 in 107d

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Phosphorus binding site 7 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:0.3
occ:1.00
P B:DA9 0.0 0.3 1.0
OP1 B:DA9 1.5 0.4 1.0
OP2 B:DA9 1.5 0.5 1.0
O5' B:DA9 1.6 0.5 1.0
O3' B:DG8 1.6 0.4 1.0
C5' B:DA9 2.7 0.4 1.0
C3' B:DG8 2.7 0.4 1.0
H5'' B:DA9 2.9 0.5 1.0
H3' B:DG8 3.0 0.5 1.0
H5' B:DA9 3.0 0.5 1.0
H2'' B:DG8 3.1 0.4 1.0
H8 B:DA9 3.2 0.4 1.0
C2' B:DG8 3.3 0.4 1.0
H2' B:DA9 3.5 0.5 1.0
H1' B:DG8 3.8 0.4 1.0
H3' B:DA9 3.9 0.6 1.0
C4' B:DA9 4.0 0.4 1.0
C4' B:DG8 4.0 0.5 1.0
H4' B:DG8 4.1 0.6 1.0
C1' B:DG8 4.1 0.3 1.0
H2' B:DG8 4.2 0.5 1.0
C8 B:DA9 4.2 0.3 1.0
C3' B:DA9 4.4 0.5 1.0
C2' B:DA9 4.4 0.4 1.0
O4' B:DA9 4.5 0.4 1.0
HO5' B:DG8 4.6 1.4 1.0
O4' B:DG8 4.6 0.4 1.0
H4' B:DA9 4.8 0.5 1.0
C1' B:DA9 4.9 0.3 1.0
N9 B:DA9 5.0 0.3 1.0

Phosphorus binding site 8 out of 12 in 107d

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Phosphorus binding site 8 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:0.6
occ:1.00
P B:DA10 0.0 0.6 1.0
OP2 B:DA10 1.5 1.0 1.0
OP1 B:DA10 1.5 0.7 1.0
O5' B:DA10 1.6 0.7 1.0
O3' B:DA9 1.6 0.6 1.0
C5' B:DA10 2.7 0.5 1.0
C3' B:DA9 2.7 0.5 1.0
H5'' B:DA10 2.9 0.5 1.0
H2'' B:DA9 2.9 0.5 1.0
H3' B:DA9 3.1 0.6 1.0
H5' B:DA10 3.2 0.7 1.0
C2' B:DA9 3.2 0.4 1.0
H2' B:DA10 3.4 0.3 1.0
H1' B:DA9 3.4 0.4 1.0
H3' B:DA10 3.7 0.4 1.0
H4' B:DA9 3.8 0.5 1.0
C4' B:DA9 3.9 0.4 1.0
C1' B:DA9 3.9 0.3 1.0
C4' B:DA10 3.9 0.4 1.0
H8 B:DA10 3.9 0.4 1.0
H2' B:DA9 4.2 0.5 1.0
C3' B:DA10 4.2 0.3 1.0
C2' B:DA10 4.2 0.2 1.0
O4' B:DA9 4.4 0.4 1.0
O4' B:DA10 4.4 0.4 1.0
H4' B:DA10 4.7 0.4 1.0
C8 B:DA10 4.8 0.3 1.0
C1' B:DA10 5.0 0.3 1.0
H2'' B:DA10 5.0 0.2 1.0

Phosphorus binding site 9 out of 12 in 107d

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Phosphorus binding site 9 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:0.3
occ:1.00
P B:DA11 0.0 0.3 1.0
OP2 B:DA11 1.5 0.6 1.0
OP1 B:DA11 1.5 0.5 1.0
O3' B:DA10 1.6 0.2 1.0
O5' B:DA11 1.6 0.3 1.0
C3' B:DA10 2.6 0.3 1.0
C5' B:DA11 2.7 0.2 1.0
H5' B:DA11 2.7 0.3 1.0
H3' B:DA10 2.8 0.4 1.0
H4' B:DA10 2.9 0.4 1.0
C4' B:DA10 3.4 0.4 1.0
H5'' B:DA11 3.4 0.3 1.0
C4' B:DA11 3.7 0.2 1.0
H3' B:DA11 3.7 0.3 1.0
H8 B:DA11 3.8 0.2 1.0
O4' B:DA11 3.8 0.2 1.0
C2' B:DA10 3.9 0.2 1.0
H2'' B:DA10 4.1 0.2 1.0
H1' B:DA10 4.2 0.3 1.0
H5'' B:DA10 4.2 0.5 1.0
C3' B:DA11 4.3 0.2 1.0
O4' B:DA10 4.4 0.4 1.0
C5' B:DA10 4.4 0.5 1.0
C1' B:DA10 4.4 0.3 1.0
H253 B:DUO15 4.5 0.4 1.0
H4' B:DA11 4.6 0.2 1.0
H2' B:DA11 4.7 0.2 1.0
H2' B:DA10 4.7 0.3 1.0
C8 B:DA11 4.8 0.2 1.0
C2' B:DA11 5.0 0.2 1.0
C1' B:DA11 5.0 0.2 1.0

Phosphorus binding site 10 out of 12 in 107d

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Phosphorus binding site 10 out of 12 in the Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex


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 Covalent Duocarmycin A-Dna Duplex Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:0.3
occ:1.00
P B:DA12 0.0 0.3 1.0
OP2 B:DA12 1.5 0.4 1.0
OP1 B:DA12 1.5 0.5 1.0
O5' B:DA12 1.6 0.3 1.0
O3' B:DA11 1.6 0.3 1.0
C5' B:DA12 2.6 0.3 1.0
C3' B:DA11 2.7 0.2 1.0
H3' B:DA11 2.9 0.3 1.0
H5'' B:DA12 2.9 0.4 1.0
H5' B:DA12 2.9 0.4 1.0
H2'' B:DA11 3.1 0.3 1.0
C2' B:DA11 3.4 0.2 1.0
H293 B:DUO15 3.6 0.6 1.0
H2' B:DA12 3.8 0.3 1.0
H291 B:DUO15 3.8 0.7 1.0
H3' B:DA12 3.9 0.3 1.0
H2' B:DA11 3.9 0.2 1.0
C4' B:DA11 3.9 0.2 1.0
H4' B:DA11 4.0 0.2 1.0
C4' B:DA12 4.0 0.3 1.0
C29 B:DUO15 4.2 0.4 1.0
H5'' B:DA11 4.3 0.3 1.0
C3' B:DA12 4.4 0.3 1.0
O4' B:DA12 4.6 0.3 1.0
C2' B:DA12 4.6 0.2 1.0
C1' B:DA11 4.6 0.2 1.0
C5' B:DA11 4.7 0.2 1.0
H8 B:DA12 4.7 0.2 1.0
H1' B:DA11 4.7 0.3 1.0
H292 B:DUO15 4.7 0.4 1.0
H4' B:DA12 4.7 0.4 1.0
H273 B:DUO15 4.9 0.5 1.0
O4' B:DA11 4.9 0.2 1.0
O5' B:DA11 5.0 0.3 1.0

Reference:

C.H.Lin, D.J.Patel. Solution Structure of the Covalent Duocarmycin A-Dna Duplex Complex. J.Mol.Biol. V. 248 162 1995.
ISSN: ISSN 0022-2836
PubMed: 7731041
DOI: 10.1006/JMBI.1995.0209
Page generated: Fri Sep 25 11:05:42 2020

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