Phosphorus in PDB 1a3q: Human Nf-Kappa-B P52 Bound to Dna

Protein crystallography data

The structure of Human Nf-Kappa-B P52 Bound to Dna, PDB code: 1a3q was solved by P.Cramer, C.J.Larson, G.L.Verdine, C.W.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.200, 121.000, 134.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 32

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Human Nf-Kappa-B P52 Bound to Dna (pdb code 1a3q). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the Human Nf-Kappa-B P52 Bound to Dna, PDB code: 1a3q:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1a3q

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Phosphorus binding site 1 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P506

b:56.6
occ:1.00
 P C:DG506 0.0 56.6 1.0
OP2 C:DG506 1.5 59.7 1.0
OP1 C:DG506 1.5 61.6 1.0
O5' C:DG506 1.6 46.6 1.0
O3' C:DG505 1.6 59.5 1.0
C5' C:DG506 2.6 52.4 1.0
C3' C:DG505 2.7 60.0 1.0
C2' C:DG505 3.3 56.6 1.0
C4' C:DG506 3.9 48.8 1.0
C1' C:DG505 4.0 56.2 1.0
C4' C:DG505 4.0 59.9 1.0
O C:HOH2596 4.1 46.2 1.0
C3' C:DG506 4.4 50.3 1.0
O4' C:DG506 4.4 52.7 1.0
O4' C:DG505 4.5 58.5 1.0
C2' C:DG506 4.7 52.8 1.0
O B:HOH2052 4.8 47.8 1.0

Phosphorus binding site 2 out of 20 in 1a3q

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Phosphorus binding site 2 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P507

b:52.9
occ:1.00
 P C:DG507 0.0 52.9 1.0
OP2 C:DG507 1.5 58.2 1.0
OP1 C:DG507 1.5 56.4 1.0
O5' C:DG507 1.6 54.2 1.0
O3' C:DG506 1.6 53.2 1.0
C3' C:DG506 2.6 50.3 1.0
C5' C:DG507 2.6 52.5 1.0
C2' C:DG506 3.6 52.8 1.0
C4' C:DG506 3.8 48.8 1.0
O C:HOH2630 3.9 55.8 1.0
C4' C:DG507 3.9 51.6 1.0
O4' C:DG507 4.2 50.0 1.0
NZ A:LYS283 4.3 48.1 1.0
C1' C:DG506 4.3 51.3 1.0
C3' C:DG507 4.4 50.5 1.0
C2' C:DG507 4.5 48.4 1.0
C8 C:DG507 4.6 37.9 1.0
O4' C:DG506 4.6 52.7 1.0
C5' C:DG506 4.8 52.4 1.0
C1' C:DG507 4.9 49.2 1.0

Phosphorus binding site 3 out of 20 in 1a3q

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Phosphorus binding site 3 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P508

b:53.7
occ:1.00
 P C:DG508 0.0 53.7 1.0
OP2 C:DG508 1.5 51.7 1.0
OP1 C:DG508 1.5 60.0 1.0
O5' C:DG508 1.6 55.8 1.0
O3' C:DG507 1.6 54.0 1.0
C5' C:DG508 2.6 43.2 1.0
C3' C:DG507 2.6 50.5 1.0
C2' C:DG507 3.4 48.4 1.0
O C:HOH2197 3.5 41.8 1.0
C4' C:DG508 3.8 35.5 1.0
C4' C:DG507 3.9 51.6 1.0
O C:HOH2202 4.0 50.5 1.0
O4' C:DG508 4.2 36.9 1.0
C1' C:DG507 4.3 49.2 1.0
C3' C:DG508 4.4 32.3 1.0
C2' C:DG508 4.5 28.4 1.0
O4' C:DG507 4.7 50.0 1.0
O A:HOH2271 4.7 66.2 1.0
O A:HOH2044 4.9 39.5 1.0
C5' C:DG507 5.0 52.5 1.0

Phosphorus binding site 4 out of 20 in 1a3q

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Phosphorus binding site 4 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P509

b:31.1
occ:1.00
 P C:DA509 0.0 31.1 1.0
OP1 C:DA509 1.5 41.5 1.0
OP2 C:DA509 1.5 34.2 1.0
O3' C:DG508 1.6 33.4 1.0
O5' C:DA509 1.6 45.0 1.0
C3' C:DG508 2.6 32.3 1.0
C5' C:DA509 2.6 35.4 1.0
C2' C:DG508 3.5 28.4 1.0
NE2 A:GLN284 3.7 42.7 1.0
C4' C:DG508 3.8 35.5 1.0
C4' C:DA509 3.8 38.6 1.0
CB A:PRO223 3.9 34.9 1.0
CG A:PRO223 4.0 26.9 1.0
O C:HOH2018 4.0 31.2 1.0
C1' C:DG508 4.2 34.7 1.0
O4' C:DA509 4.2 36.6 1.0
C3' C:DA509 4.4 38.0 1.0
C8 C:DA509 4.5 39.4 1.0
C2' C:DA509 4.6 37.2 1.0
CD A:GLN284 4.6 38.0 1.0
O4' C:DG508 4.6 36.9 1.0
OE1 A:GLN284 4.6 32.0 1.0
C5' C:DG508 4.8 43.2 1.0
C1' C:DA509 4.9 37.6 1.0

Phosphorus binding site 5 out of 20 in 1a3q

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Phosphorus binding site 5 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P510

b:33.4
occ:1.00
 P C:DA510 0.0 33.4 1.0
OP2 C:DA510 1.5 34.8 1.0
OP1 C:DA510 1.5 36.2 1.0
O5' C:DA510 1.6 42.2 1.0
O3' C:DA509 1.6 37.5 1.0
C5' C:DA510 2.6 35.6 1.0
C3' C:DA509 2.6 38.0 1.0
C2' C:DA509 3.2 37.2 1.0
O A:HOH2416 3.9 36.9 1.0
C4' C:DA510 3.9 31.8 1.0
C4' C:DA509 3.9 38.6 1.0
C1' C:DA509 4.1 37.6 1.0
O C:HOH2738 4.1 56.8 1.0
O A:HOH2073 4.3 38.5 1.0
O4' C:DA510 4.4 33.4 1.0
C3' C:DA510 4.4 30.4 1.0
O C:HOH2552 4.6 41.8 1.0
O4' C:DA509 4.6 36.6 1.0
C2' C:DA510 4.7 30.3 1.0
O A:HOH2002 4.8 40.5 1.0
C8 C:DA510 4.8 35.7 1.0
CD A:PRO223 4.8 31.9 1.0

Phosphorus binding site 6 out of 20 in 1a3q

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Phosphorus binding site 6 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P511

b:33.6
occ:1.00
 P C:DT511 0.0 33.6 1.0
OP1 C:DT511 1.5 37.5 1.0
OP2 C:DT511 1.5 34.7 1.0
O5' C:DT511 1.6 27.3 1.0
O3' C:DA510 1.6 34.8 1.0
C5' C:DT511 2.5 35.3 1.0
C3' C:DA510 2.7 30.4 1.0
C2' C:DA510 3.3 30.3 1.0
OH A:TYR55 3.6 38.5 1.0
C4' C:DT511 3.9 35.6 1.0
C4' C:DA510 3.9 31.8 1.0
N A:LYS143 4.0 42.6 1.0
O A:HOH2019 4.1 34.6 1.0
CE1 A:TYR55 4.1 32.0 1.0
CA A:THR142 4.1 38.2 1.0
C1' C:DA510 4.2 29.5 1.0
CZ A:TYR55 4.2 32.2 1.0
O4' C:DT511 4.3 39.4 1.0
CB A:THR142 4.4 35.9 1.0
C3' C:DT511 4.5 39.0 1.0
CE A:LYS143 4.5 51.0 1.0
C A:THR142 4.6 38.9 1.0
O A:HOH2073 4.6 38.5 1.0
O4' C:DA510 4.7 33.4 1.0
CB A:LYS143 4.7 45.6 1.0
CG A:LYS143 4.8 44.9 1.0
CG2 A:THR142 5.0 26.8 1.0
CA A:LYS143 5.0 46.7 1.0

Phosphorus binding site 7 out of 20 in 1a3q

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Phosphorus binding site 7 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P512

b:35.5
occ:1.00
 P C:DC512 0.0 35.5 1.0
OP2 C:DC512 1.5 32.6 1.0
OP1 C:DC512 1.5 40.4 1.0
O5' C:DC512 1.6 32.6 1.0
O3' C:DT511 1.6 34.6 1.0
C5' C:DC512 2.6 35.1 1.0
C3' C:DT511 2.7 39.0 1.0
C2' C:DT511 3.2 40.4 1.0
O C:HOH2709 3.5 68.4 1.0
O C:HOH2108 3.8 56.6 1.0
C4' C:DC512 3.9 39.1 1.0
C4' C:DT511 3.9 35.6 1.0
O C:HOH2064 4.0 41.4 1.0
SG A:CYS57 4.0 41.0 1.0
C1' C:DT511 4.3 42.1 1.0
C3' C:DC512 4.4 40.2 1.0
CG2 A:THR142 4.4 26.8 1.0
O4' C:DC512 4.4 34.4 1.0
CB A:CYS57 4.7 37.8 1.0
O D:HOH2010 4.7 35.5 1.0
O4' C:DT511 4.8 39.4 1.0
CD1 A:TYR55 4.9 28.4 1.0
C2' C:DC512 5.0 41.6 1.0
CB A:TYR55 5.0 27.9 1.0
C5' C:DT511 5.0 35.3 1.0

Phosphorus binding site 8 out of 20 in 1a3q

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Phosphorus binding site 8 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P513

b:41.5
occ:1.00
 P C:DC513 0.0 41.5 1.0
OP1 C:DC513 1.5 45.6 1.0
OP2 C:DC513 1.5 34.8 1.0
O5' C:DC513 1.6 43.9 1.0
O3' C:DC512 1.6 49.3 1.0
C5' C:DC513 2.6 40.6 1.0
C3' C:DC512 2.7 40.2 1.0
C2' C:DC512 3.4 41.6 1.0
O A:HOH2020 3.8 29.8 1.0
C4' C:DC513 3.9 35.2 1.0
C4' C:DC512 3.9 39.1 1.0
O4' C:DC513 4.3 31.6 1.0
C3' C:DC513 4.4 36.3 1.0
C1' C:DC512 4.5 38.8 1.0
CE B:LYS144 4.6 78.4 1.0
NZ B:LYS144 4.7 82.5 1.0
O B:HOH2100 4.7 39.8 1.0
O C:HOH2023 4.8 23.7 1.0
C2' C:DC513 4.8 32.5 1.0
O4' C:DC512 4.8 34.4 1.0
C5' C:DC512 4.9 35.1 1.0
CB A:CYS57 5.0 37.8 1.0

Phosphorus binding site 9 out of 20 in 1a3q

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Phosphorus binding site 9 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P514

b:39.5
occ:1.00
 P C:DC514 0.0 39.5 1.0
OP2 C:DC514 1.5 38.4 1.0
OP1 C:DC514 1.5 43.7 1.0
O3' C:DC513 1.6 37.9 1.0
O5' C:DC514 1.6 42.1 1.0
C3' C:DC513 2.6 36.3 1.0
C5' C:DC514 2.6 35.9 1.0
C2' C:DC513 3.4 32.5 1.0
C4' C:DC513 3.9 35.2 1.0
C4' C:DC514 3.9 36.3 1.0
C1' C:DC513 4.3 34.1 1.0
O C:HOH2593 4.3 54.7 1.0
C3' C:DC514 4.3 38.2 1.0
O C:HOH2754 4.4 64.3 1.0
O4' C:DC514 4.6 41.5 1.0
O4' C:DC513 4.7 31.6 1.0
C2' C:DC514 4.8 41.4 1.0
C5' C:DC513 4.9 40.6 1.0

Phosphorus binding site 10 out of 20 in 1a3q

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Phosphorus binding site 10 out of 20 in the Human Nf-Kappa-B P52 Bound to Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Human Nf-Kappa-B P52 Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P515

b:56.5
occ:1.00
 P C:DC515 0.0 56.5 1.0
OP1 C:DC515 1.5 56.5 1.0
OP2 C:DC515 1.5 56.6 1.0
O5' C:DC515 1.6 58.7 1.0
O3' C:DC514 1.6 54.1 1.0
C3' C:DC514 2.6 38.2 1.0
C5' C:DC515 2.7 59.8 1.0
C2' C:DC514 3.6 41.4 1.0
C4' C:DC514 3.8 36.3 1.0
C4' C:DC515 3.9 58.8 1.0
O4' C:DC515 4.2 60.5 1.0
C6 C:DC515 4.4 47.7 1.0
C1' C:DC514 4.4 41.5 1.0
C3' C:DC515 4.6 59.7 1.0
C2' C:DC515 4.6 55.5 1.0
O4' C:DC514 4.7 41.5 1.0
C5' C:DC514 4.8 35.9 1.0
C1' C:DC515 4.8 54.4 1.0
O5' C:DC514 5.0 42.1 1.0

Reference:

P.Cramer, C.J.Larson, G.L.Verdine, C.W.Muller. Structure of the Human Nf-Kappab P52 Homodimer-Dna Complex at 2.1 A Resolution. Embo J. V. 16 7078 1997.
ISSN: ISSN 0261-4189
PubMed: 9384586
DOI: 10.1093/EMBOJ/16.23.7078
Page generated: Fri Sep 25 12:09:05 2020

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