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Bromine in PDB 4e10: Protelomerase Tela Y201A Covalently Complexed with Substrate Dna

Protein crystallography data

The structure of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna, PDB code: 4e10 was solved by K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.05 / 2.51
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.340, 119.660, 56.630, 90.00, 111.30, 90.00
R / Rfree (%) 18.3 / 27

Bromine Binding Sites:

The binding sites of Bromine atom in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna (pdb code 4e10). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna, PDB code: 4e10:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 4e10

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Bromine binding site 1 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br3

b:0.8
occ:1.00
 BR C:BRU3 0.0 0.8 1.0
C5 C:BRU3 1.9 0.4 1.0
C6 C:BRU3 2.8 0.7 1.0
C4 C:BRU3 3.0 0.3 1.0
O4 C:BRU3 3.3 0.3 1.0
C8 C:DA2 3.8 0.6 1.0
N9 C:DA2 3.9 0.6 1.0
C2' C:DA2 3.9 0.2 1.0
N1 C:BRU3 4.1 0.6 1.0
N7 C:DA2 4.2 0.6 1.0
C1' C:DA2 4.2 0.7 1.0
N3 C:BRU3 4.3 0.7 1.0
N6 C:DA4 4.3 0.9 1.0
C4 C:DA2 4.3 0.1 1.0
C5 C:DA2 4.5 0.3 1.0
C2 C:BRU3 4.7 0.6 1.0
C2' C:BRU3 4.8 0.7 1.0

Bromine binding site 2 out of 10 in 4e10

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Bromine binding site 2 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br6

b:0.9
occ:1.00
 BR C:BRU6 0.0 0.9 1.0
C5 C:BRU6 1.9 84.0 1.0
C4 C:BRU6 2.9 84.7 1.0
C6 C:BRU6 2.9 83.5 1.0
O4 C:BRU6 3.0 78.2 1.0
C8 C:DA5 3.6 0.0 1.0
N7 C:DA5 3.9 0.4 1.0
C2' C:DA5 4.0 84.2 1.0
N9 C:DA5 4.0 97.2 1.0
N3 C:BRU6 4.1 87.7 1.0
N1 C:BRU6 4.1 85.6 1.0
N6 C:DA7 4.2 72.3 1.0
C5 C:DA5 4.4 84.2 1.0
CD1 A:LEU340 4.5 75.4 1.0
C4 C:DA5 4.5 83.8 1.0
C1' C:DA5 4.6 92.6 1.0
C2 C:BRU6 4.6 87.7 1.0
O C:HOH114 4.7 74.4 1.0
CD2 A:LEU340 4.8 79.4 1.0
C6 C:DA7 5.0 72.4 1.0

Bromine binding site 3 out of 10 in 4e10

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Bromine binding site 3 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br12

b:97.1
occ:1.00
 BR C:BRU12 0.0 97.1 1.0
C5 C:BRU12 1.9 64.9 1.0
C6 C:BRU12 2.9 74.1 1.0
C4 C:BRU12 2.9 59.6 1.0
O4 C:BRU12 3.2 56.1 1.0
C2' C:DA11 3.7 60.4 1.0
O C:HOH103 3.8 46.9 1.0
C8 C:DA11 3.9 46.1 1.0
CB A:THR167 4.0 53.9 1.0
N9 C:DA11 4.0 45.6 1.0
O A:HOH725 4.1 40.4 1.0
CG2 A:THR167 4.1 53.9 1.0
O A:HOH656 4.1 33.1 1.0
N1 C:BRU12 4.1 44.4 1.0
N7 C:DA11 4.1 48.6 1.0
N3 C:BRU12 4.2 62.1 1.0
C4 C:DA11 4.4 44.9 1.0
C5 C:DA11 4.4 47.7 1.0
C1' C:DA11 4.5 61.0 1.0
C2 C:BRU12 4.6 69.5 1.0
OP2 C:BRU12 4.8 47.5 1.0
N6 C:DA13 4.8 46.9 1.0
OG1 A:THR167 4.9 61.2 1.0
CA A:THR167 4.9 54.1 1.0

Bromine binding site 4 out of 10 in 4e10

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Bromine binding site 4 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br22

b:82.2
occ:1.00
 BR D:BRU22 0.0 82.2 1.0
C5 D:BRU22 2.0 67.2 1.0
C6 D:BRU22 2.8 61.9 1.0
C4 D:BRU22 3.0 65.2 1.0
O4 D:BRU22 3.3 55.7 1.0
O D:HOH103 3.5 46.1 1.0
O D:HOH102 3.6 61.7 1.0
C8 D:DA21 3.8 50.1 1.0
C2' D:DA21 3.8 41.9 1.0
N9 D:DA21 3.9 47.8 1.0
N1 D:BRU22 4.1 54.6 1.0
C1' D:DA21 4.2 43.0 1.0
O A:HOH613 4.2 46.8 1.0
N3 D:BRU22 4.3 63.8 1.0
N7 D:DA21 4.3 46.4 1.0
BR D:BRU23 4.3 74.7 1.0
C4 D:DA21 4.6 47.9 1.0
CG2 A:ILE331 4.6 47.7 1.0
C2 D:BRU22 4.7 54.7 1.0
O4 D:BRU23 4.7 56.9 1.0
C5 D:DA21 4.8 45.0 1.0

Bromine binding site 5 out of 10 in 4e10

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Bromine binding site 5 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br23

b:74.7
occ:1.00
 BR D:BRU23 0.0 74.7 1.0
C5 D:BRU23 1.9 49.7 1.0
C4 D:BRU23 2.9 60.4 1.0
C6 D:BRU23 2.9 53.2 1.0
O4 D:BRU23 3.0 56.9 1.0
NH2 A:ARG339 3.4 40.5 1.0
C6 D:BRU22 3.4 61.9 1.0
C5 D:BRU22 3.6 67.2 1.0
CG1 A:ILE331 3.6 51.8 1.0
N1 D:BRU22 3.7 54.6 1.0
C2' D:BRU22 3.8 47.8 1.0
OG A:SER335 3.8 54.5 1.0
O A:HOH613 3.8 46.8 1.0
CD1 A:ILE331 3.9 58.9 1.0
C4 D:BRU22 3.9 65.2 1.0
C2 D:BRU22 4.0 54.7 1.0
N3 D:BRU23 4.1 65.3 1.0
N3 D:BRU22 4.1 63.8 1.0
N1 D:BRU23 4.2 50.2 1.0
C3' D:BRU22 4.3 50.8 1.0
C1' D:BRU22 4.3 51.0 1.0
BR D:BRU22 4.3 82.2 1.0
CZ A:ARG339 4.4 48.4 1.0
O4 D:BRU22 4.6 55.7 1.0
C2 D:BRU23 4.7 59.0 1.0
O2 D:BRU22 4.8 50.1 1.0
O4' D:BRU22 4.8 50.9 1.0
OP2 D:BRU23 4.8 47.7 1.0
NE A:ARG339 4.8 49.0 1.0
O5' D:BRU23 4.9 46.5 1.0

Bromine binding site 6 out of 10 in 4e10

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Bromine binding site 6 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br25

b:72.2
occ:1.00
 BR D:BRU25 0.0 72.2 1.0
C5 D:BRU25 1.9 65.1 1.0
C6 D:BRU25 2.9 65.2 1.0
C4 D:BRU25 2.9 67.7 1.0
O4 D:BRU25 3.2 59.6 1.0
N9 D:DG24 3.5 52.1 1.0
C8 D:DG24 3.6 62.0 1.0
C4 D:DG24 3.7 52.9 1.0
C2' D:DG24 3.7 53.7 1.0
N7 D:DG24 3.8 66.2 1.0
C5 D:DG24 3.8 52.9 1.0
CG A:ARG339 3.9 42.3 1.0
CD A:ARG343 4.0 44.6 1.0
C1' D:DG24 4.1 70.8 1.0
N1 D:BRU25 4.2 62.8 1.0
N3 D:BRU25 4.2 64.0 1.0
N3 D:DG24 4.3 69.6 1.0
NE A:ARG343 4.5 55.1 1.0
CG A:LEU340 4.5 52.6 1.0
C6 D:DG24 4.6 61.5 1.0
C2 D:BRU25 4.7 63.7 1.0
CD A:ARG339 4.9 45.4 1.0
CB A:ARG339 4.9 55.4 1.0
C2 D:DG24 4.9 71.5 1.0

Bromine binding site 7 out of 10 in 4e10

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Bromine binding site 7 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br26

b:0.4
occ:1.00
 BR D:BRU26 0.0 0.4 1.0
C5 D:BRU26 2.0 75.0 1.0
C6 D:BRU26 2.9 75.3 1.0
C4 D:BRU26 2.9 72.9 1.0
O4 D:BRU26 3.1 73.8 1.0
NH1 A:ARG343 3.6 50.2 1.0
CD2 A:LEU340 3.8 79.4 1.0
C6 D:BRU25 3.9 65.2 1.0
N1 D:BRU25 3.9 62.8 1.0
C2' D:BRU25 3.9 62.0 1.0
CZ A:ARG343 4.1 56.3 1.0
C5 D:BRU25 4.2 65.1 1.0
N1 D:BRU26 4.2 75.6 1.0
N3 D:BRU26 4.2 71.7 1.0
C2 D:BRU25 4.2 63.7 1.0
NH2 A:ARG343 4.3 56.4 1.0
C1' D:BRU25 4.4 59.9 1.0
C4 D:BRU25 4.5 67.7 1.0
N3 D:BRU25 4.5 64.0 1.0
C2 D:BRU26 4.7 76.2 1.0
O2 D:BRU25 4.8 69.2 1.0
NE A:ARG343 4.8 55.1 1.0
CG A:LEU340 4.8 52.6 1.0

Bromine binding site 8 out of 10 in 4e10

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Bromine binding site 8 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br28

b:0.2
occ:1.00
 BR D:BRU28 0.0 0.2 1.0
C5 D:BRU28 1.9 0.3 1.0
C6 D:BRU28 2.9 98.7 1.0
C4 D:BRU28 2.9 0.1 1.0
O4 D:BRU28 3.2 93.2 1.0
C8 D:DA27 3.6 85.0 1.0
C2' D:DA27 3.8 83.3 1.0
N9 D:DA27 3.9 83.0 1.0
N7 D:DA27 3.9 79.3 1.0
N1 D:BRU28 4.1 0.1 1.0
N3 D:BRU28 4.2 0.6 1.0
C4 D:DA27 4.3 86.5 1.0
C5 D:DA27 4.3 86.6 1.0
C1' D:DA27 4.4 78.2 1.0
C2 D:BRU28 4.7 0.4 1.0
BR D:BRU29 4.8 0.3 1.0

Bromine binding site 9 out of 10 in 4e10

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Bromine binding site 9 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br29

b:0.3
occ:1.00
 BR D:BRU29 0.0 0.3 1.0
C5 D:BRU29 2.0 1.0 1.0
C6 D:BRU29 2.9 0.8 1.0
C4 D:BRU29 2.9 0.4 1.0
O4 D:BRU29 3.1 0.7 1.0
C6 D:BRU28 3.7 98.7 1.0
C2' D:BRU28 3.8 94.6 1.0
N1 D:BRU28 3.8 0.1 1.0
C5 D:BRU28 4.0 0.3 1.0
N1 D:BRU29 4.2 0.9 1.0
N3 D:BRU29 4.2 0.2 1.0
C1' D:BRU28 4.2 91.8 1.0
C2 D:BRU28 4.3 0.4 1.0
N6 D:DA30 4.3 0.8 1.0
C4 D:BRU28 4.4 0.1 1.0
N3 D:BRU28 4.5 0.6 1.0
C2 D:BRU29 4.7 0.8 1.0
BR D:BRU28 4.8 0.2 1.0
O2 D:BRU28 4.9 0.3 1.0

Bromine binding site 10 out of 10 in 4e10

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Bromine binding site 10 out of 10 in the Protelomerase Tela Y201A Covalently Complexed with Substrate Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Protelomerase Tela Y201A Covalently Complexed with Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br31

b:0.6
occ:1.00
 BR D:BRU31 0.0 0.6 1.0
C5 D:BRU31 2.0 0.2 1.0
C6 D:BRU31 2.9 0.8 1.0
C4 D:BRU31 3.0 0.1 1.0
O4 D:BRU31 3.2 0.9 1.0
O D:HOH115 3.3 51.5 1.0
C8 D:DA30 3.7 0.1 1.0
O D:HOH118 3.7 60.5 1.0
C2' D:DA30 3.8 0.9 1.0
N1 D:BRU31 4.2 0.9 1.0
N9 D:DA30 4.2 0.9 1.0
N7 D:DA30 4.2 0.6 1.0
N3 D:BRU31 4.2 0.6 1.0
O D:HOH117 4.4 67.4 1.0
O D:HOH104 4.4 66.7 1.0
C1' D:DA30 4.5 0.3 1.0
C2 D:BRU31 4.7 0.6 1.0
C5 D:DA30 4.9 0.3 1.0
C4 D:DA30 4.9 0.6 1.0

Reference:

K.Shi, W.M.Huang, H.Aihara. An Enzyme-Catalyzed Multistep Dna Refolding Mechanism in Hairpin Telomere Formation. Plos Biol. V. 11 01472 2013.
ISSN: ISSN 1544-9173
PubMed: 23382649
DOI: 10.1371/JOURNAL.PBIO.1001472
Page generated: Wed Jul 10 21:09:20 2024

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