Phosphorus in PDB 190d: Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)

Protein crystallography data

The structure of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4), PDB code: 190d was solved by L.Chen, L.Cai, X.Zhang, A.Rich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.80
Space group I 2 3 1
Cell size a, b, c (Å), α, β, γ (°) 82.300, 82.300, 82.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / n/a

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) (pdb code 190d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 24 binding sites of Phosphorus where determined in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4), PDB code: 190d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 24 in 190d

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Phosphorus binding site 1 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:34.4
occ:1.00
P A:DC2 0.0 34.4 1.0
OP1 A:DC2 1.5 34.8 1.0
OP2 A:DC2 1.5 34.2 1.0
O5' A:DC2 1.6 32.8 1.0
O3' A:DC1 1.6 32.5 1.0
C5' A:DC2 2.7 31.1 1.0
C3' A:DC1 2.7 29.9 1.0
H3' A:DC1 2.7 0.0 1.0
H5' A:DC2 2.9 0.0 1.0
H5'' A:DC2 3.0 0.0 1.0
H2' A:DC1 3.6 0.0 1.0
C2' A:DC1 3.6 27.8 1.0
H2'' A:DC1 3.8 0.0 1.0
H3' A:DC2 3.8 0.0 1.0
C4' A:DC2 3.9 29.7 1.0
C4' A:DC1 4.0 29.0 1.0
H5'' A:DC1 4.0 0.0 1.0
HO5' A:DC1 4.1 0.0 1.0
O4' A:DC2 4.1 27.2 1.0
H1 C:HOH69 4.2 0.0 1.0
H4' A:DC1 4.3 0.0 1.0
C3' A:DC2 4.4 30.6 1.0
H6 A:DC2 4.4 0.0 1.0
C5' A:DC1 4.5 29.1 1.0
H4' A:DC2 4.7 0.0 1.0
O3' A:DC2 4.8 34.2 1.0
O5' A:DC1 4.8 30.3 1.0
C1' A:DC1 4.9 25.5 1.0
HO3' D:DC16 4.9 0.0 1.0

Phosphorus binding site 2 out of 24 in 190d

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Phosphorus binding site 2 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:36.0
occ:1.00
P A:DC3 0.0 36.0 1.0
OP2 A:DC3 1.5 36.5 1.0
OP1 A:DC3 1.5 37.7 1.0
O3' A:DC2 1.6 34.2 1.0
O5' A:DC3 1.6 34.9 1.0
H5' A:DC3 2.7 0.0 1.0
C5' A:DC3 2.7 31.2 1.0
C3' A:DC2 2.7 30.6 1.0
H2'' A:DC2 3.0 0.0 1.0
C2' A:DC2 3.3 27.8 1.0
H5'' A:DC3 3.4 0.0 1.0
H3' A:DC2 3.4 0.0 1.0
H4' A:DC2 3.6 0.0 1.0
H2' A:DC2 3.6 0.0 1.0
C4' A:DC2 3.6 29.7 1.0
H4' A:DC3 3.7 0.0 1.0
C4' A:DC3 3.7 28.6 1.0
H5'' A:DC2 3.8 0.0 1.0
O4' A:DC3 4.2 25.4 1.0
O A:HOH72 4.2 45.2 1.0
C5' A:DC2 4.3 31.1 1.0
H1 A:HOH72 4.3 0.0 1.0
C1' A:DC2 4.6 25.1 1.0
O4' A:DC2 4.7 27.2 1.0
H1' D:DC15 4.9 0.0 1.0
O5' A:DC2 4.9 32.8 1.0
C3' A:DC3 5.0 28.5 1.0
H3' A:DC3 5.0 0.0 1.0

Phosphorus binding site 3 out of 24 in 190d

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Phosphorus binding site 3 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:33.0
occ:1.00
P A:DC4 0.0 33.0 1.0
OP1 A:DC4 1.5 33.2 1.0
OP2 A:DC4 1.5 33.1 1.0
O3' A:DC3 1.6 31.4 1.0
O5' A:DC4 1.6 30.7 1.0
H2 A:HOH53 2.6 0.0 1.0
C3' A:DC3 2.7 28.5 1.0
C5' A:DC4 2.7 27.5 1.0
H3' A:DC3 2.7 0.0 1.0
H5' A:DC4 2.9 0.0 1.0
H5'' A:DC4 3.2 0.0 1.0
H2'' A:DC3 3.3 0.0 1.0
H2'' D:DC14 3.5 0.0 1.0
O A:HOH53 3.5 36.6 1.0
C2' A:DC3 3.6 25.9 1.0
H5' D:DC15 3.8 0.0 1.0
H1 A:HOH53 3.8 0.0 1.0
C4' A:DC3 3.8 28.6 1.0
H4' D:DC14 3.8 0.0 1.0
H4' A:DC3 3.9 0.0 1.0
C4' A:DC4 3.9 25.4 1.0
H4' A:DC4 4.0 0.0 1.0
H1' D:DC14 4.1 0.0 1.0
H2' A:DC3 4.3 0.0 1.0
O4' A:DC4 4.3 22.9 1.0
H5' A:DC3 4.4 0.0 1.0
C2' D:DC14 4.4 16.6 1.0
H1' A:DC3 4.4 0.0 1.0
C1' A:DC3 4.5 23.5 1.0
C5' A:DC3 4.6 31.2 1.0
H5'' A:DC3 4.7 0.0 1.0
C1' D:DC14 4.7 15.3 1.0
C4' D:DC14 4.7 17.2 1.0
H4' D:DC15 4.8 0.0 1.0
O4' A:DC3 4.8 25.4 1.0
C5' D:DC15 4.8 17.4 1.0
O3' D:DC14 5.0 17.9 1.0
O4' D:DC14 5.0 17.1 1.0

Phosphorus binding site 4 out of 24 in 190d

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Phosphorus binding site 4 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P6

b:22.4
occ:1.00
P B:DC6 0.0 22.4 1.0
OP2 B:DC6 1.5 23.0 1.0
OP1 B:DC6 1.5 23.3 1.0
O5' B:DC6 1.6 22.6 1.0
O3' B:DC5 1.6 22.3 1.0
C3' B:DC5 2.7 20.8 1.0
C5' B:DC6 2.7 20.4 1.0
H3' B:DC5 2.8 0.0 1.0
HO3' C:DC12 2.9 0.0 1.0
H2'' C:DC12 3.0 0.0 1.0
H5'' B:DC6 3.0 0.0 1.0
H5' B:DC6 3.1 0.0 1.0
H2'' B:DC5 3.5 0.0 1.0
H4' B:DC5 3.6 0.0 1.0
C2' B:DC5 3.6 19.3 1.0
H4' C:DC12 3.7 0.0 1.0
C4' B:DC5 3.8 20.6 1.0
O3' C:DC12 3.8 16.8 1.0
H1 B:HOH58 3.9 0.0 1.0
C4' B:DC6 3.9 18.9 1.0
C2' C:DC12 3.9 16.3 1.0
O B:HOH58 4.0 40.1 1.0
H4' B:DC6 4.1 0.0 1.0
H1' C:DC12 4.1 0.0 1.0
HO5' B:DC5 4.1 0.0 1.0
H1' B:DC5 4.2 0.0 1.0
C3' C:DC12 4.3 17.2 1.0
O4' B:DC6 4.3 17.8 1.0
C1' B:DC5 4.4 17.7 1.0
C4' C:DC12 4.4 18.2 1.0
O4' B:DC5 4.5 18.8 1.0
H2' B:DC5 4.5 0.0 1.0
C1' C:DC12 4.5 16.7 1.0
H2' C:DC12 4.7 0.0 1.0
O4' C:DC12 4.9 17.8 1.0
O5' B:DC5 4.9 25.6 1.0
C5' B:DC5 4.9 21.7 1.0

Phosphorus binding site 5 out of 24 in 190d

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Phosphorus binding site 5 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P7

b:23.8
occ:1.00
P B:DC7 0.0 23.8 1.0
OP2 B:DC7 1.5 24.0 1.0
OP1 B:DC7 1.5 25.1 1.0
O5' B:DC7 1.6 23.1 1.0
O3' B:DC6 1.6 22.8 1.0
C5' B:DC7 2.7 23.1 1.0
C3' B:DC6 2.7 19.7 1.0
H5' B:DC7 2.8 0.0 1.0
H3' B:DC6 2.9 0.0 1.0
H5'' B:DC7 3.1 0.0 1.0
H2'' B:DC6 3.3 0.0 1.0
C2' B:DC6 3.4 18.0 1.0
H2' B:DC6 3.6 0.0 1.0
C4' B:DC7 3.8 22.7 1.0
C4' B:DC6 3.9 18.9 1.0
H4' B:DC7 4.0 0.0 1.0
H5' B:DC6 4.0 0.0 1.0
H4' B:DC6 4.0 0.0 1.0
O4' B:DC7 4.3 22.1 1.0
C5' B:DC6 4.5 20.4 1.0
H4' C:DC11 4.7 0.0 1.0
C1' B:DC6 4.8 16.5 1.0
H5'' B:DC6 4.9 0.0 1.0
O4' B:DC6 5.0 17.8 1.0
H3' B:DC7 5.0 0.0 1.0
C3' B:DC7 5.0 23.7 1.0

Phosphorus binding site 6 out of 24 in 190d

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Phosphorus binding site 6 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:30.1
occ:1.00
P B:DC8 0.0 30.1 1.0
OP1 B:DC8 1.5 30.6 1.0
OP2 B:DC8 1.5 28.7 1.0
O3' B:DC7 1.6 27.3 1.0
O5' B:DC8 1.6 28.2 1.0
C3' B:DC7 2.6 23.7 1.0
C5' B:DC8 2.6 24.9 1.0
H3' B:DC7 2.8 0.0 1.0
H5' B:DC8 2.8 0.0 1.0
H5'' B:DC8 2.9 0.0 1.0
H2'' B:DC7 3.3 0.0 1.0
C2' B:DC7 3.4 22.0 1.0
C4' B:DC7 3.6 22.7 1.0
H5' B:DC7 3.7 0.0 1.0
H4' B:DC7 3.8 0.0 1.0
H2' B:DC7 3.8 0.0 1.0
C4' B:DC8 3.9 22.3 1.0
C5' B:DC7 4.1 23.1 1.0
H4' B:DC8 4.2 0.0 1.0
O4' B:DC8 4.3 21.4 1.0
H5'' B:DC7 4.3 0.0 1.0
H4' C:DC10 4.4 0.0 1.0
H5' C:DC11 4.6 0.0 1.0
C1' B:DC7 4.7 20.3 1.0
O4' B:DC7 4.7 22.1 1.0
H1' C:DC10 4.9 0.0 1.0

Phosphorus binding site 7 out of 24 in 190d

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Phosphorus binding site 7 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P10

b:23.8
occ:1.00
P C:DC10 0.0 23.8 1.0
OP1 C:DC10 1.5 24.9 1.0
OP2 C:DC10 1.5 24.4 1.0
O3' C:DC9 1.6 23.8 1.0
O5' C:DC10 1.6 24.6 1.0
C3' C:DC9 2.7 22.7 1.0
C5' C:DC10 2.7 23.0 1.0
H5'' C:DC10 2.8 0.0 1.0
H4' C:DC9 2.9 0.0 1.0
H3' C:DC9 3.0 0.0 1.0
HO3' B:DC8 3.0 0.0 1.0
H5' C:DC10 3.2 0.0 1.0
H2'' B:DC8 3.3 0.0 1.0
H1 G:HOH51 3.3 0.0 1.0
H4' B:DC8 3.4 0.0 1.0
C4' C:DC9 3.4 22.9 1.0
C2' C:DC9 3.8 21.4 1.0
C4' C:DC10 3.8 21.9 1.0
H2'' C:DC9 3.8 0.0 1.0
H1' B:DC8 3.9 0.0 1.0
O3' B:DC8 4.0 21.0 1.0
O4' C:DC10 4.0 20.8 1.0
H4' C:DC10 4.1 0.0 1.0
H1' C:DC9 4.1 0.0 1.0
C2' B:DC8 4.1 20.2 1.0
C4' B:DC8 4.2 22.3 1.0
O G:HOH51 4.3 36.4 1.0
O4' C:DC9 4.3 21.7 1.0
O E:HOH62 4.3 25.7 1.0
C1' C:DC9 4.3 20.1 1.0
H2 E:HOH52 4.4 0.0 1.0
H5'' C:DC9 4.4 0.0 1.0
C3' B:DC8 4.4 20.8 1.0
H2 E:HOH62 4.4 0.0 1.0
C1' B:DC8 4.5 19.4 1.0
C5' C:DC9 4.6 24.7 1.0
H2' C:DC9 4.7 0.0 1.0
H2 G:HOH51 4.7 0.0 1.0
O4' B:DC8 4.8 21.4 1.0

Phosphorus binding site 8 out of 24 in 190d

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Phosphorus binding site 8 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P11

b:23.6
occ:1.00
P C:DC11 0.0 23.6 1.0
OP1 C:DC11 1.5 25.4 1.0
OP2 C:DC11 1.5 23.6 1.0
O5' C:DC11 1.6 23.1 1.0
O3' C:DC10 1.6 23.3 1.0
H41 G:DC27 2.7 0.0 1.0
C3' C:DC10 2.7 21.5 1.0
C5' C:DC11 2.7 20.9 1.0
H3' C:DC10 2.9 0.0 1.0
H5'' C:DC11 2.9 0.0 1.0
H1 C:HOH42 2.9 0.0 1.0
H5' C:DC11 3.0 0.0 1.0
H1 E:HOH61 3.2 0.0 1.0
H5 G:DC27 3.2 0.0 1.0
H5 E:DC19 3.2 0.0 1.0
H2'' C:DC10 3.4 0.0 1.0
C2' C:DC10 3.5 20.4 1.0
N4 G:DC27 3.6 16.7 1.0
H2' C:DC10 3.7 0.0 1.0
H1 C:HOH46 3.7 0.0 1.0
O E:HOH61 3.8 18.4 1.0
O C:HOH42 3.8 24.5 1.0
C4' C:DC10 3.9 21.9 1.0
H2 C:HOH42 3.9 0.0 1.0
H5' C:DC10 3.9 0.0 1.0
H3' C:DC11 4.0 0.0 1.0
C4' C:DC11 4.0 20.3 1.0
C5 E:DC19 4.0 14.5 1.0
O C:HOH46 4.0 23.1 1.0
H4' C:DC10 4.1 0.0 1.0
C5 G:DC27 4.1 18.5 1.0
H41 E:DC19 4.3 0.0 1.0
H42 G:DC27 4.3 0.0 1.0
C4 G:DC27 4.4 17.4 1.0
H5 E:DC18 4.4 0.0 1.0
O4' C:DC11 4.4 19.5 1.0
C5' C:DC10 4.4 23.0 1.0
C3' C:DC11 4.5 20.5 1.0
H2 E:HOH62 4.5 0.0 1.0
H6 E:DC19 4.6 0.0 1.0
H2 E:HOH61 4.6 0.0 1.0
C6 E:DC19 4.7 15.5 1.0
H5'' C:DC10 4.7 0.0 1.0
H6 C:DC11 4.8 0.0 1.0
C4 E:DC19 4.8 14.2 1.0
C5 E:DC18 4.8 18.3 1.0
H4' C:DC11 4.8 0.0 1.0
N4 E:DC19 4.9 13.8 1.0
C1' C:DC10 4.9 19.0 1.0
H6 E:DC18 4.9 0.0 1.0
H2 C:HOH46 5.0 0.0 1.0
O4' C:DC10 5.0 20.8 1.0
H2 E:HOH52 5.0 0.0 1.0

Phosphorus binding site 9 out of 24 in 190d

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Phosphorus binding site 9 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P12

b:21.8
occ:1.00
P C:DC12 0.0 21.8 1.0
OP1 C:DC12 1.5 23.5 1.0
OP2 C:DC12 1.5 22.1 1.0
O5' C:DC12 1.6 21.8 1.0
O3' C:DC11 1.6 21.5 1.0
C5' C:DC12 2.6 20.1 1.0
C3' C:DC11 2.7 20.5 1.0
H41 G:DC26 2.8 0.0 1.0
H5'' C:DC12 2.9 0.0 1.0
H5' C:DC12 2.9 0.0 1.0
H3' C:DC11 3.0 0.0 1.0
H2'' C:DC11 3.3 0.0 1.0
C2' C:DC11 3.4 19.2 1.0
H2' C:DC11 3.5 0.0 1.0
H5 G:DC26 3.6 0.0 1.0
H5 E:DC20 3.8 0.0 1.0
N4 G:DC26 3.8 15.5 1.0
H5 E:DC19 4.0 0.0 1.0
C4' C:DC12 4.0 18.2 1.0
C4' C:DC11 4.0 20.3 1.0
O E:HOH47 4.1 24.7 1.0
H4' C:DC11 4.2 0.0 1.0
H4' C:DC12 4.2 0.0 1.0
H5'' C:DC11 4.3 0.0 1.0
H6 E:DC19 4.3 0.0 1.0
O4' C:DC12 4.3 17.8 1.0
C5 E:DC19 4.4 14.5 1.0
H42 G:DC26 4.4 0.0 1.0
C5 G:DC26 4.4 18.2 1.0
H2' E:DC19 4.5 0.0 1.0
C6 E:DC19 4.6 15.5 1.0
H1 E:HOH47 4.6 0.0 1.0
C5 E:DC20 4.6 12.4 1.0
C4 G:DC26 4.6 17.3 1.0
C5' C:DC11 4.7 20.9 1.0
H41 E:DC20 4.8 0.0 1.0
C1' C:DC11 4.8 18.5 1.0
H2 E:HOH47 4.8 0.0 1.0
H2 A:HOH49 4.9 0.0 1.0
O A:HOH73 5.0 42.0 1.0
H3' C:DC12 5.0 0.0 1.0

Phosphorus binding site 10 out of 24 in 190d

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Phosphorus binding site 10 out of 24 in the Crystal Structure of A Four-Stranded Intercalated Dna: D(C4)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal Structure of A Four-Stranded Intercalated Dna: D(C4) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:P14

b:18.0
occ:1.00
P D:DC14 0.0 18.0 1.0
OP1 D:DC14 1.5 19.1 1.0
OP2 D:DC14 1.5 19.1 1.0
O5' D:DC14 1.6 18.2 1.0
O3' D:DC13 1.6 17.7 1.0
C5' D:DC14 2.6 17.4 1.0
H2 D:HOH50 2.7 0.0 1.0
C3' D:DC13 2.7 16.9 1.0
H5' D:DC14 2.9 0.0 1.0
H3' D:DC13 2.9 0.0 1.0
H5'' D:DC14 2.9 0.0 1.0
H1 D:HOH67 3.3 0.0 1.0
H1 D:HOH38 3.5 0.0 1.0
C2' D:DC13 3.5 15.9 1.0
O D:HOH50 3.6 37.2 1.0
H2' D:DC13 3.6 0.0 1.0
H1 D:HOH50 3.6 0.0 1.0
H1 D:HOH70 3.6 0.0 1.0
H2'' D:DC13 3.6 0.0 1.0
O D:HOH40 3.7 23.2 1.0
H1 D:HOH40 3.8 0.0 1.0
H6 D:DC14 3.8 0.0 1.0
H2 D:HOH67 3.8 0.0 1.0
O D:HOH38 3.9 21.3 1.0
C4' D:DC14 4.0 17.2 1.0
O D:HOH67 4.0 30.5 1.0
C4' D:DC13 4.0 16.8 1.0
H3' D:DC14 4.1 0.0 1.0
H5'' D:DC13 4.1 0.0 1.0
H4' D:DC13 4.1 0.0 1.0
O4' D:DC14 4.2 17.1 1.0
HO5' D:DC13 4.3 0.0 1.0
O D:HOH70 4.5 37.1 1.0
C5' D:DC13 4.6 17.3 1.0
C3' D:DC14 4.6 16.7 1.0
H2 D:HOH70 4.6 0.0 1.0
H2 D:HOH40 4.6 0.0 1.0
C6 D:DC14 4.7 13.2 1.0
H4' D:DC14 4.8 0.0 1.0
H2 D:HOH38 4.8 0.0 1.0
C1' D:DC13 4.9 15.8 1.0
H2 D:HOH54 4.9 0.0 1.0
O5' D:DC13 5.0 18.8 1.0
HO3' A:DC4 5.0 0.0 1.0

Reference:

L.Chen, L.Cai, X.Zhang, A.Rich. Crystal Structure of A Four-Stranded Intercalated Dna: D(C4). Biochemistry V. 33 13540 1994.
ISSN: ISSN 0006-2960
PubMed: 7947764
DOI: 10.1021/BI00250A005
Page generated: Fri Sep 25 11:49:10 2020

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