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Calcium in PDB 2nxp: Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid

Protein crystallography data

The structure of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid, PDB code: 2nxp was solved by S.Bhattacharya, S.Takada, R.H.Jacobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.42 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.620, 61.829, 133.357, 90.00, 105.16, 90.00
R / Rfree (%) 21.3 / 26.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid (pdb code 2nxp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid, PDB code: 2nxp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2nxp

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Calcium binding site 1 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:38.4
occ:1.00
 OD2 B:ASP230 2.2 34.6 1.0
O A:HOH644 2.2 37.4 1.0
O A:TYR274 2.3 31.5 1.0
O A:HOH658 2.3 36.6 1.0
OD1 A:ASP278 2.3 40.9 1.0
OD2 A:ASP277 2.5 45.1 1.0
CG B:ASP230 2.9 34.4 1.0
OD1 B:ASP230 3.0 35.1 1.0
CG A:ASP277 3.2 45.3 1.0
OD1 A:ASP277 3.3 50.2 1.0
CG A:ASP278 3.5 39.9 1.0
C A:TYR274 3.5 30.8 1.0
OD2 A:ASP278 4.0 43.5 1.0
CA A:TYR275 4.2 29.3 1.0
N A:TYR275 4.3 30.7 1.0
CB B:ASP230 4.4 33.8 1.0
CA A:TYR274 4.5 28.9 1.0
N A:ASP278 4.5 40.4 1.0
O B:HOH606 4.6 29.5 1.0
CB A:ASP277 4.6 43.5 1.0
CB A:ASP278 4.7 39.3 1.0
CB A:TYR274 4.7 30.7 1.0
C A:TYR275 4.8 29.5 1.0
CD2 A:TYR275 4.9 27.9 1.0

Calcium binding site 2 out of 8 in 2nxp

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Calcium binding site 2 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:33.0
occ:1.00
 OD1 B:ASP278 2.2 41.9 1.0
OD2 A:ASP230 2.3 28.0 1.0
O B:TYR274 2.3 33.2 1.0
O A:HOH660 2.4 45.9 1.0
O A:HOH652 2.4 38.2 1.0
OD1 B:ASP277 2.5 42.3 1.0
OD1 A:ASP230 2.9 29.1 1.0
OD2 B:ASP277 2.9 39.1 1.0
CG A:ASP230 2.9 29.2 1.0
CG B:ASP277 3.1 41.0 1.0
CG B:ASP278 3.3 39.2 1.0
C B:TYR274 3.5 30.4 1.0
OD2 B:ASP278 3.8 44.2 1.0
CA B:TYR275 4.2 31.0 1.0
N B:TYR275 4.3 28.4 1.0
CB A:ASP230 4.4 28.4 1.0
CA B:TYR274 4.5 28.1 1.0
CB B:ASP277 4.5 40.6 1.0
N B:ASP278 4.6 38.2 1.0
O A:HOH608 4.6 34.9 1.0
CB B:ASP278 4.6 39.7 1.0
O A:HOH629 4.6 38.2 1.0
C B:TYR275 4.7 30.7 1.0
CB B:TYR274 4.8 28.5 1.0
O C:HOH701 4.8 50.8 1.0
N B:ASP277 5.0 37.8 1.0

Calcium binding site 3 out of 8 in 2nxp

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Calcium binding site 3 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:27.7
occ:1.00
 O C:TYR274 2.3 28.6 1.0
O C:HOH683 2.3 33.9 1.0
O C:HOH684 2.4 42.9 1.0
OD1 C:ASP278 2.4 34.5 1.0
OD2 D:ASP230 2.4 26.4 1.0
OD1 C:ASP277 2.5 24.0 1.0
OD1 D:ASP230 2.7 27.3 1.0
CG D:ASP230 2.9 25.9 1.0
CG C:ASP277 3.2 28.9 1.0
OD2 C:ASP277 3.2 32.1 1.0
CG C:ASP278 3.5 29.9 1.0
C C:TYR274 3.5 24.4 1.0
OD2 C:ASP278 3.8 29.8 1.0
CA C:TYR275 4.2 24.7 1.0
N C:TYR275 4.3 23.6 1.0
O D:HOH609 4.4 27.6 1.0
CB D:ASP230 4.4 26.2 1.0
CA C:TYR274 4.6 24.1 1.0
N C:ASP278 4.6 24.4 1.0
CB C:ASP277 4.7 27.4 1.0
C C:TYR275 4.7 22.5 1.0
O D:HOH629 4.7 31.1 1.0
O C:HOH671 4.7 31.0 1.0
CB C:ASP278 4.7 28.6 1.0
CB C:TYR274 4.8 25.5 1.0
O D:HOH606 4.8 24.6 1.0
CD2 C:TYR275 5.0 26.0 1.0

Calcium binding site 4 out of 8 in 2nxp

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Calcium binding site 4 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca603

b:24.7
occ:1.00
 O D:TYR274 2.2 22.1 1.0
OD2 C:ASP230 2.3 31.1 1.0
OD1 D:ASP278 2.3 25.2 1.0
O C:HOH606 2.4 24.8 1.0
OD1 D:ASP277 2.4 27.6 1.0
O C:HOH626 2.5 27.8 1.0
OD2 D:ASP277 2.8 32.7 1.0
CG D:ASP277 2.9 28.1 1.0
CG C:ASP230 3.2 31.5 1.0
CG D:ASP278 3.4 28.2 1.0
C D:TYR274 3.4 20.8 1.0
OD1 C:ASP230 3.4 30.4 1.0
OD2 D:ASP278 3.8 29.5 1.0
O C:HOH674 3.9 32.0 1.0
CA D:TYR275 4.2 23.0 1.0
N D:TYR275 4.3 21.4 1.0
CA D:TYR274 4.4 21.7 1.0
CB D:ASP277 4.4 27.1 1.0
N D:ASP278 4.5 20.0 1.0
O C:HOH607 4.6 21.8 1.0
CB C:ASP230 4.6 28.9 1.0
O D:HOH625 4.6 37.4 1.0
CB D:ASP278 4.7 25.5 1.0
O D:HOH651 4.7 45.9 1.0
CB D:TYR274 4.7 22.0 1.0
C D:TYR275 4.7 23.9 1.0
N D:ASP277 5.0 22.2 1.0

Calcium binding site 5 out of 8 in 2nxp

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Calcium binding site 5 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca604

b:26.5
occ:1.00
 O E:TYR274 2.3 21.6 1.0
OD2 F:ASP230 2.3 28.2 1.0
O E:HOH621 2.3 24.5 1.0
O E:HOH678 2.3 38.9 1.0
OD1 E:ASP278 2.4 30.8 1.0
OD1 E:ASP277 2.5 22.6 1.0
OD1 F:ASP230 2.6 26.6 1.0
CG F:ASP230 2.8 27.9 1.0
OD2 E:ASP277 3.2 27.9 1.0
CG E:ASP277 3.2 24.0 1.0
CG E:ASP278 3.5 29.4 1.0
C E:TYR274 3.5 19.5 1.0
OD2 E:ASP278 3.8 32.8 1.0
CA E:TYR275 4.2 22.4 1.0
N E:TYR275 4.3 19.6 1.0
CB F:ASP230 4.3 29.2 1.0
O F:HOH609 4.4 22.9 1.0
CA E:TYR274 4.5 19.2 1.0
N E:ASP278 4.6 21.9 1.0
C E:TYR275 4.7 20.8 1.0
CB E:ASP277 4.7 21.8 1.0
O F:HOH630 4.7 24.6 1.0
CB E:TYR274 4.7 23.3 1.0
O E:HOH647 4.8 31.1 1.0
CB E:ASP278 4.8 27.3 1.0
O F:HOH608 4.9 24.1 1.0
CD2 E:TYR275 4.9 23.6 1.0

Calcium binding site 6 out of 8 in 2nxp

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Calcium binding site 6 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca605

b:30.5
occ:1.00
 O E:HOH680 2.2 45.9 1.0
O F:TYR274 2.3 22.5 1.0
OD2 E:ASP230 2.3 22.7 1.0
OD1 F:ASP278 2.4 25.6 1.0
OD1 F:ASP277 2.5 30.0 1.0
O F:HOH665 2.7 45.9 1.0
OD2 F:ASP277 2.7 31.5 1.0
CG F:ASP277 2.9 29.2 1.0
CG E:ASP230 3.2 25.1 1.0
OD1 E:ASP230 3.3 27.7 1.0
CG F:ASP278 3.4 25.6 1.0
C F:TYR274 3.5 22.0 1.0
OD2 F:ASP278 3.8 29.2 1.0
O E:HOH606 4.0 33.7 1.0
CA F:TYR275 4.3 23.8 1.0
N F:TYR275 4.4 24.9 1.0
CB F:ASP277 4.4 26.3 1.0
CA F:TYR274 4.5 21.5 1.0
O E:HOH627 4.5 22.3 1.0
N F:ASP278 4.5 26.4 1.0
CB E:ASP230 4.6 21.6 1.0
CB F:ASP278 4.7 22.7 1.0
CB F:TYR274 4.7 23.6 1.0
C F:TYR275 4.8 23.4 1.0
N F:ASP277 5.0 19.3 1.0

Calcium binding site 7 out of 8 in 2nxp

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Calcium binding site 7 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca606

b:33.5
occ:1.00
 OD1 G:ASP278 2.2 34.9 1.0
O G:HOH628 2.3 35.1 1.0
O G:TYR274 2.3 33.6 1.0
O G:HOH649 2.4 50.9 1.0
OD1 G:ASP277 2.5 41.2 1.0
OD2 G:ASP277 2.8 46.1 1.0
CG G:ASP277 3.0 43.0 1.0
CG G:ASP278 3.3 31.4 1.0
C G:TYR274 3.5 26.0 1.0
OD2 G:ASP278 3.7 31.3 1.0
CA G:TYR275 4.3 26.0 1.0
N G:TYR275 4.4 27.7 1.0
N G:ASP278 4.5 30.9 1.0
CB G:ASP277 4.5 40.3 1.0
CA G:TYR274 4.5 26.2 1.0
CB G:ASP278 4.6 32.1 1.0
C G:TYR275 4.8 27.6 1.0
CB G:TYR274 4.8 27.3 1.0

Calcium binding site 8 out of 8 in 2nxp

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Calcium binding site 8 out of 8 in the Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of NTD2 Domain of the Human TAF5 Subunit of Tfiid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca607

b:38.1
occ:1.00
 O H:TYR274 2.2 32.9 1.0
OD2 H:ASP277 2.4 45.2 1.0
OD1 H:ASP278 2.5 46.1 1.0
CG H:ASP277 3.1 43.5 1.0
OD1 H:ASP277 3.1 43.6 1.0
CG H:ASP278 3.4 43.4 1.0
C H:TYR274 3.4 29.2 1.0
OD2 H:ASP278 3.7 44.6 1.0
CA H:TYR275 4.1 32.5 1.0
N H:TYR275 4.2 33.5 1.0
O H:HOH628 4.3 49.3 1.0
CA H:TYR274 4.5 27.9 1.0
N H:ASP278 4.5 39.9 1.0
CB H:ASP277 4.6 43.2 1.0
C H:TYR275 4.7 31.8 1.0
CB H:ASP278 4.7 41.0 1.0
CB H:TYR274 4.7 29.3 1.0
CD2 H:TYR275 5.0 32.1 1.0
N H:ASP277 5.0 38.6 1.0

Reference:

S.Bhattacharya, S.Takada, R.H.Jacobson. Structural Analysis and Dimerization Potential of the Human TAF5 Subunit of Tfiid. Proc.Natl.Acad.Sci.Usa V. 104 1189 2007.
ISSN: ISSN 0027-8424
PubMed: 17227857
DOI: 10.1073/PNAS.0610297104
Page generated: Tue Jul 8 07:13:47 2025

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