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Calcium in PDB 4b0a: The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation

Enzymatic activity of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation

All present enzymatic activity of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation:
2.3.1.48;

Protein crystallography data

The structure of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation, PDB code: 4b0a was solved by M.Anandapadamanaban, C.Andresen, M.Siponen, T.Kokubo, M.Ikura, M.Moche, M.Sunnerhagen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.54 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.894, 74.253, 99.667, 90.00, 90.00, 90.00
R / Rfree (%) 16.44 / 22.3

Other elements in 4b0a:

The structure of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation (pdb code 4b0a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation, PDB code: 4b0a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4b0a

Go back to Calcium Binding Sites List in 4b0a
Calcium binding site 1 out of 3 in the The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1067

b:41.6
occ:1.00
 O A:GLY37 2.1 23.5 1.0
O A:HOH2041 2.4 42.7 1.0
O A:HOH2042 2.5 45.1 1.0
O A:ASP39 2.6 43.1 0.5
O A:HOH2045 2.6 52.2 1.0
O A:HOH2081 2.6 60.0 1.0
O A:ASP39 3.0 46.4 0.5
C A:GLY37 3.3 25.4 1.0
C A:ASP39 3.7 43.5 0.5
C A:ASP39 3.7 46.6 0.5
CA A:GLY37 3.9 19.5 1.0
NH2 A:ARG205 4.1 26.0 1.0
N A:ASP39 4.1 37.1 0.5
N A:ASP39 4.2 34.5 0.5
OE1 A:GLU193 4.3 25.8 1.0
N A:GLU40 4.3 46.8 0.5
CA A:GLU40 4.3 48.4 0.5
N A:GLY38 4.4 24.9 1.0
C A:GLY38 4.4 37.2 1.0
N A:GLU40 4.5 44.8 0.5
CA A:ASP39 4.6 38.4 0.5
CA A:ASP39 4.6 34.6 0.5
O A:HOH2044 4.6 41.4 1.0
CA A:GLU40 4.6 47.0 0.5
CA A:GLY38 4.6 27.0 1.0
O A:GLY38 4.9 36.5 1.0
O A:ILE36 5.0 23.7 1.0

Calcium binding site 2 out of 3 in 4b0a

Go back to Calcium Binding Sites List in 4b0a
Calcium binding site 2 out of 3 in the The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1068

b:37.2
occ:1.00
 O A:HOH2046 2.0 28.1 1.0
OD1 A:ASP46 2.4 54.7 1.0
OD1 A:ASP39 2.4 24.2 0.5
O A:HOH2054 2.5 52.9 1.0
OD1 A:ASN195 2.5 36.1 1.0
O A:HOH2053 2.7 41.9 1.0
CG A:ASP46 3.4 52.3 1.0
CG A:ASP39 3.4 25.6 0.5
CG A:ASN195 3.5 40.3 1.0
O A:HOH2082 3.5 42.0 1.0
O A:TYR47 3.8 30.7 1.0
CB A:ASP39 3.9 39.7 0.5
ND2 A:ASN195 3.9 33.9 1.0
OD2 A:ASP46 3.9 48.1 1.0
C A:TYR47 4.0 32.1 1.0
N A:TYR47 4.0 36.8 1.0
OG1 A:THR48 4.1 21.1 1.0
OD2 A:ASP39 4.1 21.9 0.5
OD2 A:ASP39 4.2 47.6 0.5
CB A:ASP39 4.2 34.4 0.5
O A:TYR194 4.2 19.9 1.0
N A:THR48 4.2 25.7 1.0
CA A:ASP46 4.3 46.1 1.0
C A:ASP46 4.4 47.0 1.0
CB A:ASP46 4.4 47.2 1.0
CA A:TYR47 4.5 33.2 1.0
O A:HOH2024 4.5 70.8 1.0
CA A:THR48 4.5 24.0 1.0
CG A:ASP39 4.5 44.6 0.5
O A:HOH2043 4.7 52.3 1.0
CB A:ASN195 4.7 19.0 1.0
O A:HOH2121 4.8 60.0 1.0
CA A:ASP39 4.9 34.6 0.5
CA A:ASP39 4.9 38.4 0.5
C A:TYR194 4.9 20.4 1.0
CB A:THR48 5.0 22.4 1.0
O A:HOH2056 5.0 26.7 1.0

Calcium binding site 3 out of 3 in 4b0a

Go back to Calcium Binding Sites List in 4b0a
Calcium binding site 3 out of 3 in the The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The High-Resolution Structure of Ytbp-YTAF1 Identifies Conserved and Competing Interaction Surfaces in Transcriptional Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1244

b:40.1
occ:1.00
 O A:HOH2172 2.2 55.4 1.0
O A:HOH2163 2.3 27.4 1.0
O A:GLY280 2.3 25.4 1.0
O A:SER283 2.4 23.4 0.5
O A:HOH2167 2.4 44.3 1.0
O A:SER283 2.4 23.7 0.5
O A:HOH2166 2.5 48.7 1.0
O A:HOH2168 2.7 49.1 1.0
O A:HOH2173 2.8 65.3 1.0
C A:GLY280 3.5 27.4 1.0
C A:SER283 3.6 25.0 0.5
C A:SER283 3.7 25.0 0.5
CA A:GLY280 4.1 24.3 1.0
O A:HOH2176 4.3 39.3 1.0
N A:SER284 4.4 20.3 0.5
N A:SER284 4.5 20.3 0.5
CA A:SER284 4.5 19.0 0.5
N A:SER283 4.5 22.4 0.5
CA A:SER284 4.5 18.9 0.5
CA A:SER283 4.5 22.2 0.5
N A:THR281 4.5 24.1 1.0
OG A:SER284 4.6 27.6 0.5
N A:SER283 4.6 22.4 0.5
OG A:SER283 4.7 27.5 0.5
CA A:SER283 4.7 22.0 0.5
CA A:THR281 4.9 25.3 1.0
C A:THR281 4.9 31.8 1.0
CB A:SER283 5.0 24.7 0.5

Reference:

M.Anandapadamanaban, C.Andresen, M.Siponen, T.Kokubo, M.Ikura, M.Moche, M.Sunnerhagen. High-Resolution Structure of Tbp with TAF1 Reveals Anchoring Patterns in Transcriptional Regulation Nat.Struct.Mol.Biol. V. 20 1008 2013.
ISSN: ISSN 1545-9993
PubMed: 23851461
DOI: 10.1038/NSMB.2611
Page generated: Sat Jul 13 22:30:28 2024

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