Phosphorus in PDB 192d: Recombination-Like Structure of D(Ccgcgg)

Protein crystallography data

The structure of Recombination-Like Structure of D(Ccgcgg), PDB code: 192d was solved by L.Malinina, L.Urpi, X.Salas, T.Huynh-Dinh, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 34.330, 44.040, 38.270, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Recombination-Like Structure of D(Ccgcgg) (pdb code 192d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 10 binding sites of Phosphorus where determined in the Recombination-Like Structure of D(Ccgcgg), PDB code: 192d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 10 in 192d

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Phosphorus binding site 1 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:21.1
occ:1.00
P A:DC2 0.0 21.1 1.0
OP1 A:DC2 1.5 19.2 1.0
OP2 A:DC2 1.5 20.1 1.0
O5' A:DC2 1.6 17.3 1.0
O3' A:DC1 1.7 18.2 1.0
C3' A:DC1 2.6 14.2 1.0
C5' A:DC2 2.7 13.1 1.0
H2 A:HOH18 3.4 15.4 1.0
C2' A:DC1 3.5 11.5 1.0
H1 A:HOH18 3.5 16.8 1.0
H1 A:HOH14 3.8 15.4 1.0
C4' A:DC2 3.9 9.7 1.0
C4' A:DC1 3.9 14.2 1.0
O A:HOH18 4.0 34.3 1.0
C6 A:DC2 4.0 8.1 1.0
C2' A:DC2 4.1 7.1 1.0
C3' A:DC2 4.2 9.2 1.0
O A:HOH14 4.2 9.0 1.0
O4' A:DC2 4.2 6.5 1.0
C5' A:DC1 4.4 15.4 1.0
C1' A:DC2 4.5 6.6 1.0
N1 A:DC2 4.6 7.6 1.0
C5 A:DC2 4.8 5.8 1.0
C1' A:DC1 4.8 8.7 1.0
O4' A:DC1 4.9 11.2 1.0

Phosphorus binding site 2 out of 10 in 192d

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Phosphorus binding site 2 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:12.8
occ:1.00
P A:DG3 0.0 12.8 1.0
OP1 A:DG3 1.5 15.5 1.0
OP2 A:DG3 1.5 15.3 1.0
O3' A:DC2 1.6 13.0 1.0
O5' A:DG3 1.6 13.5 1.0
C5' A:DG3 2.6 11.1 1.0
C3' A:DC2 2.6 9.2 1.0
C4' A:DC2 3.4 9.7 1.0
C2' A:DC2 3.8 7.1 1.0
C4' A:DG3 3.8 10.8 1.0
O4' A:DG3 4.2 9.3 1.0
O4' A:DC2 4.3 6.5 1.0
C1' A:DC2 4.4 6.6 1.0
H1 A:HOH20 4.5 16.7 1.0
C5' A:DC2 4.5 13.1 1.0
O A:HOH20 4.6 19.8 1.0
H2 A:HOH20 4.7 10.9 1.0

Phosphorus binding site 3 out of 10 in 192d

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Phosphorus binding site 3 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:21.0
occ:1.00
P A:DC4 0.0 21.0 1.0
OP2 A:DC4 1.5 21.2 1.0
OP1 A:DC4 1.5 21.7 1.0
O3' A:DG3 1.6 16.0 1.0
O5' A:DC4 1.6 17.2 1.0
H2 A:HOH21 2.3 17.0 1.0
C3' A:DG3 2.6 11.8 1.0
C5' A:DC4 2.6 13.4 1.0
O A:HOH21 3.2 42.8 1.0
H1 A:HOH21 3.3 16.6 1.0
H2 A:HOH20 3.4 10.9 1.0
C2' A:DG3 3.6 9.4 1.0
C4' A:DG3 3.7 10.8 1.0
C4' A:DC4 3.7 11.8 1.0
C3' A:DC4 3.7 11.0 1.0
C2' A:DC4 4.1 11.0 1.0
C5' A:DG3 4.1 11.1 1.0
O A:HOH20 4.3 19.8 1.0
O4' A:DC4 4.4 10.2 1.0
O A:HOH48 4.5 30.4 1.0
H1 A:HOH20 4.6 16.7 1.0
H1 A:HOH48 4.7 17.2 1.0
O4' A:DG3 4.9 9.3 1.0
C1' A:DG3 4.9 8.3 1.0
C1' A:DC4 4.9 11.1 1.0
O A:HOH23 5.0 12.4 1.0
O3' A:DC4 5.0 12.1 1.0

Phosphorus binding site 4 out of 10 in 192d

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Phosphorus binding site 4 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:11.7
occ:1.00
P A:DG5 0.0 11.7 1.0
OP1 A:DG5 1.5 12.5 1.0
OP2 A:DG5 1.5 12.6 1.0
O5' A:DG5 1.6 11.0 1.0
O3' A:DC4 1.6 12.1 1.0
C5' A:DG5 2.6 7.7 1.0
C3' A:DC4 2.7 11.0 1.0
C4' A:DC4 3.4 11.8 1.0
C2' A:DC4 3.9 11.0 1.0
C4' A:DG5 3.9 8.2 1.0
H1 A:HOH48 4.4 17.2 1.0
O4' A:DG5 4.4 6.4 1.0
C5' A:DC4 4.4 13.4 1.0
O4' A:DC4 4.5 10.2 1.0
H2 A:HOH17 4.5 14.6 1.0
C1' A:DC4 4.5 11.1 1.0

Phosphorus binding site 5 out of 10 in 192d

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Phosphorus binding site 5 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:7.8
occ:1.00
P A:DG6 0.0 7.8 1.0
OP2 A:DG6 1.5 8.6 1.0
OP1 A:DG6 1.5 8.9 1.0
O3' A:DG5 1.6 9.5 1.0
O5' A:DG6 1.6 10.0 1.0
C3' A:DG5 2.7 7.9 1.0
C5' A:DG6 2.8 11.0 1.0
H2 A:HOH25 2.9 15.3 1.0
C4' A:DG5 3.4 8.2 1.0
C4' A:DG6 3.4 12.9 1.0
H1 A:HOH26 3.5 18.6 1.0
H2 A:HOH26 3.6 11.6 1.0
O4' A:DG6 3.7 11.8 1.0
O A:HOH25 3.9 39.1 1.0
C2' A:DG5 4.0 7.6 1.0
O A:HOH26 4.1 15.5 1.0
H1 A:HOH25 4.2 13.5 1.0
O4' A:DG5 4.4 6.4 1.0
C5' A:DG5 4.4 7.7 1.0
C1' A:DG5 4.6 6.9 1.0
C3' A:DG6 4.9 14.1 1.0

Phosphorus binding site 6 out of 10 in 192d

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Phosphorus binding site 6 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:27.5
occ:1.00
P B:DC8 0.0 27.5 1.0
OP2 B:DC8 1.5 28.1 1.0
OP1 B:DC8 1.5 27.6 1.0
O3' B:DC7 1.6 25.3 1.0
O5' B:DC8 1.6 24.7 1.0
C5' B:DC8 2.7 16.3 1.0
C3' B:DC7 2.7 20.6 1.0
H2 B:HOH29 2.9 14.3 1.0
C4' B:DC7 3.2 18.7 1.0
H2 B:HOH47 3.6 15.7 1.0
C5' B:DC7 3.7 17.9 1.0
C4' B:DC8 3.8 10.7 1.0
O B:HOH29 3.8 30.8 1.0
C2' B:DC7 3.8 17.1 1.0
C3' B:DC8 4.1 9.3 1.0
H1 B:HOH29 4.4 18.2 1.0
O B:HOH47 4.5 40.5 1.0
O4' B:DC7 4.5 16.8 1.0
O5' B:DC7 4.6 20.0 1.0
H1 B:HOH32 4.7 18.1 1.0
O B:HOH32 4.7 20.7 1.0
C1' B:DC7 4.8 14.2 1.0
OP1 B:DG9 4.9 12.6 1.0
C2' B:DC8 5.0 8.9 1.0
O4' B:DC8 5.0 11.2 1.0

Phosphorus binding site 7 out of 10 in 192d

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Phosphorus binding site 7 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:11.1
occ:1.00
P B:DG9 0.0 11.1 1.0
OP2 B:DG9 1.5 10.5 1.0
OP1 B:DG9 1.5 12.6 1.0
O5' B:DG9 1.6 8.6 1.0
O3' B:DC8 1.6 10.0 1.0
C5' B:DG9 2.6 6.2 1.0
C3' B:DC8 2.7 9.3 1.0
H2 B:HOH34 3.3 14.4 1.0
C4' B:DC8 3.5 10.7 1.0
O B:HOH34 3.8 19.1 1.0
C4' B:DG9 3.9 6.8 1.0
C2' B:DC8 3.9 8.9 1.0
O4' B:DG9 4.2 6.2 1.0
O4' B:DC8 4.4 11.2 1.0
C1' B:DC8 4.5 8.8 1.0
H1 B:HOH34 4.6 14.5 1.0
O5' B:DC8 4.7 24.7 1.0
C5' B:DC8 4.7 16.3 1.0
H1 B:HOH33 4.8 13.4 1.0
O B:HOH33 4.9 10.3 1.0

Phosphorus binding site 8 out of 10 in 192d

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Phosphorus binding site 8 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:6.7
occ:1.00
P B:DC10 0.0 6.7 1.0
OP2 B:DC10 1.5 8.8 1.0
OP1 B:DC10 1.5 6.1 1.0
O3' B:DG9 1.6 7.4 1.0
O5' B:DC10 1.6 7.5 1.0
C3' B:DG9 2.7 6.5 1.0
C5' B:DC10 2.7 5.4 1.0
H1 B:HOH41 3.2 15.4 1.0
H2 B:HOH33 3.3 14.3 1.0
H2 B:HOH41 3.5 14.9 1.0
C2' B:DG9 3.7 6.4 1.0
C4' B:DG9 3.7 6.8 1.0
C4' B:DC10 3.7 5.0 1.0
C3' B:DC10 3.8 7.6 1.0
H1 B:HOH33 3.8 13.4 1.0
O B:HOH41 3.8 30.9 1.0
O B:HOH33 4.0 10.3 1.0
C5' B:DG9 4.0 6.2 1.0
C2' B:DC10 4.1 6.9 1.0
O4' B:DC10 4.4 5.5 1.0
C1' B:DC10 4.8 6.9 1.0
H21 B:DG9 4.9 17.9 1.0
C6 B:DC10 4.9 4.8 1.0
H2 B:HOH39 4.9 17.0 1.0
O4' B:DG9 5.0 6.2 1.0
C1' B:DG9 5.0 6.2 1.0

Phosphorus binding site 9 out of 10 in 192d

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Phosphorus binding site 9 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:11.4
occ:1.00
P B:DG11 0.0 11.4 1.0
OP2 B:DG11 1.5 14.0 1.0
OP1 B:DG11 1.5 11.8 1.0
O5' B:DG11 1.6 12.2 1.0
O3' B:DC10 1.6 10.2 1.0
C3' B:DC10 2.6 7.6 1.0
C5' B:DG11 2.7 10.7 1.0
C4' B:DC10 3.4 5.0 1.0
C2' B:DC10 3.8 6.9 1.0
C4' B:DG11 3.9 9.6 1.0
H1 B:HOH41 3.9 15.4 1.0
H2 B:HOH45 4.1 16.3 1.0
C5' B:DC10 4.4 5.4 1.0
O4' B:DG11 4.4 8.5 1.0
O4' B:DC10 4.5 5.5 1.0
H1 B:HOH49 4.5 18.8 1.0
O B:HOH41 4.6 30.9 1.0
C1' B:DC10 4.6 6.9 1.0
H1 B:HOH45 4.9 17.3 1.0
O B:HOH49 4.9 45.2 1.0
O B:HOH45 5.0 32.6 1.0

Phosphorus binding site 10 out of 10 in 192d

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Phosphorus binding site 10 out of 10 in the Recombination-Like Structure of D(Ccgcgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Recombination-Like Structure of D(Ccgcgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:12.1
occ:1.00
P B:DG12 0.0 12.1 1.0
OP1 B:DG12 1.5 13.2 1.0
OP2 B:DG12 1.5 14.2 1.0
O3' B:DG11 1.6 12.2 1.0
O5' B:DG12 1.6 12.1 1.0
C5' B:DG12 2.6 11.5 1.0
C3' B:DG11 2.7 9.9 1.0
C2' B:DG11 3.6 7.8 1.0
C4' B:DG11 3.8 9.6 1.0
C4' B:DG12 3.9 10.4 1.0
O4' B:DG12 4.3 8.1 1.0
C8 B:DG12 4.4 7.1 1.0
C3' B:DG12 4.4 12.1 1.0
C1' B:DG11 4.5 8.3 1.0
O B:HOH40 4.5 28.7 1.0
O4' B:DG11 4.7 8.5 1.0
C5' B:DG11 4.8 10.7 1.0
H1 B:HOH40 4.9 14.4 1.0
N9 B:DG12 4.9 6.0 1.0

Reference:

L.Malinina, L.Urpi, X.Salas, T.Huynh-Dinh, J.A.Subirana. Recombination-Like Structure of D(Ccgcgg). J.Mol.Biol. V. 243 484 1994.
ISSN: ISSN 0022-2836
PubMed: 7966274
DOI: 10.1006/JMBI.1994.1674
Page generated: Fri Sep 25 11:49:54 2020

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