Phosphorus in PDB 144d: Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex

Protein crystallography data

The structure of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex, PDB code: 144d was solved by Y.-G.Gao, M.Sriram, W.A.Denny, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.480, 36.110, 69.600, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex (pdb code 144d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex, PDB code: 144d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 144d

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Phosphorus binding site 1 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:14.0
occ:1.00
P A:DG2 0.0 14.0 1.0
OP2 A:DG2 1.5 14.4 1.0
OP1 A:DG2 1.5 13.9 1.0
O5' A:DG2 1.6 13.6 1.0
O3' A:DC1 1.7 12.5 1.0
C5' A:DG2 2.6 13.1 1.0
C3' A:DC1 2.7 12.2 1.0
C2' A:DC1 3.5 12.2 1.0
C4' A:DG2 3.6 12.8 1.0
C3' A:DG2 3.6 12.8 1.0
C2' A:DG2 3.7 12.6 1.0
C1' A:DC1 3.9 11.9 1.0
C4' A:DC1 3.9 12.2 1.0
O4' A:DC1 4.2 12.2 1.0
O4' A:DG2 4.3 12.8 1.0
C8 A:DG2 4.5 12.0 1.0
C1' A:DG2 4.6 12.4 1.0
O3' A:DG2 4.9 12.6 1.0
N9 A:DG2 4.9 12.2 1.0

Phosphorus binding site 2 out of 22 in 144d

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Phosphorus binding site 2 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:10.9
occ:1.00
P A:DC3 0.0 10.9 1.0
OP2 A:DC3 1.4 11.3 1.0
OP1 A:DC3 1.5 11.1 1.0
O5' A:DC3 1.6 9.5 1.0
O3' A:DG2 1.6 12.6 1.0
C5' A:DC3 2.6 8.3 1.0
C3' A:DG2 2.7 12.8 1.0
C2' A:DG2 3.1 12.6 1.0
C4' A:DC3 3.8 7.8 1.0
C1' A:DG2 3.8 12.4 1.0
C2' A:DC3 3.8 7.4 1.0
C6 A:DC3 3.9 6.2 1.0
C4' A:DG2 3.9 12.8 1.0
O4' A:DC3 4.1 7.5 1.0
C3' A:DC3 4.1 7.6 1.0
O4' A:DG2 4.4 12.8 1.0
C1' A:DC3 4.4 6.8 1.0
N1 A:DC3 4.6 6.3 1.0
C5 A:DC3 4.7 5.8 1.0

Phosphorus binding site 3 out of 22 in 144d

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Phosphorus binding site 3 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:10.9
occ:1.00
P A:G364 0.0 10.9 1.0
O1P A:G364 1.5 10.1 1.0
O2P A:G364 1.5 10.0 1.0
O5' A:G364 1.6 10.2 1.0
O3' A:DC3 1.6 7.9 1.0
C3' A:DC3 2.6 7.6 1.0
C5' A:G364 2.6 10.3 1.0
C2' A:DC3 3.4 7.4 1.0
C4' A:DC3 3.8 7.8 1.0
C4' A:G364 3.9 10.3 1.0
C2' A:G364 4.0 10.2 1.0
C3' A:G364 4.1 10.4 1.0
C1' A:DC3 4.2 6.8 1.0
O4' A:DC3 4.5 7.5 1.0
O4' A:G364 4.7 10.1 1.0
C1' A:G364 4.9 9.9 1.0
C5' A:DC3 4.9 8.3 1.0
C8 A:G364 5.0 9.5 1.0

Phosphorus binding site 4 out of 22 in 144d

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Phosphorus binding site 4 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:11.7
occ:1.00
P A:DA5 0.0 11.7 1.0
OP2 A:DA5 1.5 9.8 1.0
OP1 A:DA5 1.5 10.7 1.0
O3' A:G364 1.6 10.9 1.0
O5' A:DA5 1.6 10.9 1.0
C5' A:DA5 2.6 11.0 1.0
C3' A:G364 2.8 10.4 1.0
C4' A:DA5 3.1 11.0 1.0
O4' A:DA5 3.4 10.8 1.0
C2' A:G364 3.5 10.2 1.0
C4' A:G364 4.0 10.3 1.0
C1' A:G364 4.0 9.9 1.0
O4' A:G364 4.3 10.1 1.0
C3' A:DA5 4.6 11.1 1.0
C8 A:DA5 4.7 10.5 1.0
C1' A:DA5 4.7 10.7 1.0
O A:HOH81 4.8 16.1 1.0
O A:HOH87 4.8 47.8 1.0

Phosphorus binding site 5 out of 22 in 144d

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Phosphorus binding site 5 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:13.7
occ:1.00
P A:DA6 0.0 13.7 1.0
OP2 A:DA6 1.5 12.9 1.0
OP1 A:DA6 1.5 11.9 1.0
O3' A:DA5 1.6 11.2 1.0
O5' A:DA6 1.6 9.8 1.0
C5' A:DA6 2.6 8.9 1.0
C3' A:DA5 2.7 11.1 1.0
C2' A:DA5 3.7 11.0 1.0
C4' A:DA6 3.8 8.6 1.0
C4' A:DA5 3.9 11.0 1.0
O A:HOH87 3.9 47.8 1.0
O4' A:DA6 4.1 8.3 1.0
O A:HOH73 4.2 43.3 1.0
C3' A:DA6 4.3 8.4 1.0
C2' A:DA6 4.6 8.3 1.0
O4' A:DA5 4.7 10.8 1.0
C1' A:DA5 4.7 10.7 1.0
C5' A:DA5 4.9 11.0 1.0

Phosphorus binding site 6 out of 22 in 144d

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Phosphorus binding site 6 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:6.0
occ:1.00
P A:DT7 0.0 6.0 1.0
OP2 A:DT7 1.5 7.0 1.0
OP1 A:DT7 1.5 5.2 1.0
O5' A:DT7 1.6 6.8 1.0
O3' A:DA6 1.6 8.0 1.0
C5' A:DT7 2.6 6.8 1.0
C3' A:DA6 2.7 8.4 1.0
C2' A:DA6 3.1 8.3 1.0
C4' A:DT7 3.7 6.6 1.0
C1' A:DA6 3.9 8.0 1.0
C4' A:DA6 3.9 8.6 1.0
C3' A:DT7 4.1 6.7 1.0
C2' A:DT7 4.6 6.3 1.0
O4' A:DA6 4.6 8.3 1.0
O A:HOH37 4.6 18.0 1.0
O4' A:DT7 4.9 6.6 1.0

Phosphorus binding site 7 out of 22 in 144d

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Phosphorus binding site 7 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:8.3
occ:1.00
P A:DT8 0.0 8.3 1.0
OP2 A:DT8 1.4 6.8 1.0
OP1 A:DT8 1.5 9.5 1.0
O3' A:DT7 1.6 6.7 1.0
O5' A:DT8 1.7 9.1 1.0
C5' A:DT8 2.6 9.2 1.0
C3' A:DT7 2.7 6.7 1.0
C4' A:DT8 3.7 9.2 1.0
C4' A:DT7 3.8 6.6 1.0
C2' A:DT7 3.8 6.3 1.0
O4' A:DT8 4.1 9.2 1.0
O4' A:DT7 4.4 6.6 1.0
C1' A:DT7 4.5 6.3 1.0
C16 B:SN625 4.8 22.8 1.0

Phosphorus binding site 8 out of 22 in 144d

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Phosphorus binding site 8 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:9.9
occ:1.00
P A:DC9 0.0 9.9 1.0
OP2 A:DC9 1.5 10.1 1.0
OP1 A:DC9 1.5 12.0 1.0
O5' A:DC9 1.6 12.0 1.0
O3' A:DT8 1.6 9.2 1.0
C3' A:DT8 2.6 9.2 1.0
C5' A:DC9 2.7 12.1 1.0
C4' A:DT8 3.4 9.2 1.0
C2' A:DC9 3.6 12.0 1.0
C3' A:DC9 3.7 12.2 1.0
C4' A:DC9 3.7 12.2 1.0
C2' A:DT8 4.0 9.0 1.0
O4' A:DT8 4.2 9.2 1.0
C1' A:DT8 4.4 9.2 1.0
C6 A:DC9 4.4 11.0 1.0
C5' A:DT8 4.4 9.2 1.0
O4' A:DC9 4.5 11.9 1.0
C1' A:DC9 4.6 11.5 1.0
N1 A:DC9 4.9 11.2 1.0

Phosphorus binding site 9 out of 22 in 144d

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Phosphorus binding site 9 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:17.1
occ:1.00
P A:DG10 0.0 17.1 1.0
OP2 A:DG10 1.4 15.6 1.0
OP1 A:DG10 1.5 14.9 1.0
O5' A:DG10 1.6 12.8 1.0
O3' A:DC9 1.6 12.8 1.0
C5' A:DG10 2.5 12.5 1.0
C3' A:DC9 2.8 12.2 1.0
O A:HOH90 3.6 22.8 1.0
C4' A:DG10 3.6 12.6 1.0
C4' A:DC9 3.8 12.2 1.0
O4' A:DG10 4.0 12.3 1.0
C2' A:DC9 4.0 12.0 1.0
C3' A:DG10 4.2 12.6 1.0
C2' A:DG10 4.5 12.2 1.0
O5' A:DC9 4.6 12.0 1.0
O4' A:DC9 4.7 11.9 1.0
C1' A:DC9 4.7 11.5 1.0
C1' A:DG10 4.8 12.0 1.0
C5' A:DC9 4.9 12.1 1.0
C8 A:DG10 4.9 11.5 1.0

Phosphorus binding site 10 out of 22 in 144d

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Phosphorus binding site 10 out of 22 in the Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:16.3
occ:1.00
P A:DC11 0.0 16.3 1.0
OP2 A:DC11 1.5 14.6 1.0
OP1 A:DC11 1.5 15.4 1.0
O3' A:DG10 1.6 12.9 1.0
O5' A:DC11 1.7 15.3 1.0
C5' A:DC11 2.6 14.6 1.0
C3' A:DG10 2.7 12.6 1.0
C2' A:DG10 3.3 12.2 1.0
C6 A:DC11 3.8 12.9 1.0
C4' A:DG10 3.9 12.6 1.0
C4' A:DC11 4.0 14.5 1.0
C1' A:DG10 4.3 12.0 1.0
O A:HOH67 4.3 11.7 1.0
O A:HOH70 4.4 16.9 1.0
C5 A:DC11 4.5 12.7 1.0
O4' A:DC11 4.5 14.1 1.0
C2' A:DC11 4.5 14.1 1.0
C3' A:DC11 4.6 14.3 1.0
N1 A:DC11 4.7 13.2 1.0
O4' A:DG10 4.8 12.3 1.0
C1' A:DC11 4.8 13.7 1.0
C5' A:DG10 4.9 12.5 1.0
O5' A:DG10 5.0 12.8 1.0

Reference:

Y.G.Gao, M.Sriram, W.A.Denny, A.H.Wang. Minor Groove Binding of SN6999 to An Alkylated Dna: Molecular Structure of D(Cgc[E6G]Aattcgcg)-SN6999 Complex. Biochemistry V. 32 9639 1993.
ISSN: ISSN 0006-2960
PubMed: 8373768
DOI: 10.1021/BI00088A016
Page generated: Fri Sep 25 11:27:55 2020

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