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Bromine in PDB 1kdh: Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna

Enzymatic activity of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna

All present enzymatic activity of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna:
2.7.7.31;

Protein crystallography data

The structure of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna, PDB code: 1kdh was solved by M.Delarue, J.B.Boule, J.Lescar, N.Expert-Bezancon, N.Jourdan, N.Sukumar, F.Rougeon, C.Papanicolaou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.800, 85.000, 111.400, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 29.7

Other elements in 1kdh:

The structure of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna (pdb code 1kdh). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna, PDB code: 1kdh:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 1kdh

Go back to Bromine Binding Sites List in 1kdh
Bromine binding site 1 out of 4 in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br1

b:0.1
occ:1.00
 BR D:BRU1 0.0 0.1 1.0
C5 D:BRU1 2.0 99.5 1.0
C6 D:BRU1 2.9 97.6 1.0
C4 D:BRU1 3.0 98.5 1.0
O4 D:BRU1 3.3 98.5 1.0
BR D:BRU2 3.8 97.9 1.0
N3 D:BRU1 4.2 96.4 1.0
N1 D:BRU1 4.3 93.4 1.0
OP3 D:BRU1 4.5 76.6 1.0
C2 D:BRU1 4.8 94.3 1.0
O4 D:BRU2 4.9 92.0 1.0

Bromine binding site 2 out of 4 in 1kdh

Go back to Bromine Binding Sites List in 1kdh
Bromine binding site 2 out of 4 in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br2

b:97.9
occ:1.00
 BR D:BRU2 0.0 97.9 1.0
C5 D:BRU2 2.0 93.5 1.0
C6 D:BRU2 2.9 92.3 1.0
C4 D:BRU2 3.0 93.0 1.0
O4 D:BRU3 3.1 0.7 1.0
O4 D:BRU2 3.3 92.0 1.0
C6 D:BRU1 3.4 97.6 1.0
C5 D:BRU1 3.5 99.5 1.0
BR D:BRU3 3.8 0.5 1.0
BR D:BRU1 3.8 0.1 1.0
C4 D:BRU3 3.8 0.6 1.0
N1 D:BRU1 4.0 93.4 1.0
C4 D:BRU1 4.2 98.5 1.0
N1 D:BRU2 4.2 90.2 1.0
C5 D:BRU3 4.2 0.2 1.0
N3 D:BRU2 4.2 91.9 1.0
C2' D:BRU1 4.4 85.5 1.0
C1' D:BRU1 4.6 89.0 1.0
C2 D:BRU1 4.6 94.3 1.0
N3 D:BRU1 4.6 96.4 1.0
C2 D:BRU2 4.8 91.1 1.0
O4 D:BRU1 4.9 98.5 1.0
N3 D:BRU3 5.0 0.9 1.0

Bromine binding site 3 out of 4 in 1kdh

Go back to Bromine Binding Sites List in 1kdh
Bromine binding site 3 out of 4 in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br3

b:0.5
occ:1.00
 BR D:BRU3 0.0 0.5 1.0
C5 D:BRU3 2.0 0.2 1.0
C6 D:BRU3 2.9 0.1 1.0
C4 D:BRU3 3.0 0.6 1.0
O4 D:BRU3 3.3 0.7 1.0
C6 D:BRU2 3.5 92.3 1.0
C2' D:BRU2 3.7 87.1 1.0
BR D:BRU2 3.8 97.9 1.0
OP2 D:BRU3 3.9 84.7 1.0
C5 D:BRU2 4.0 93.5 1.0
N1 D:BRU3 4.2 98.4 1.0
NH2 A:ARG454 4.3 69.2 1.0
N3 D:BRU3 4.3 0.9 1.0
N1 D:BRU2 4.4 90.2 1.0
C1' D:BRU2 4.6 88.2 1.0
O5' D:BRU3 4.6 85.0 1.0
C2 D:BRU3 4.8 0.1 1.0
P D:BRU3 4.9 84.3 1.0
C3' D:BRU2 5.0 86.0 1.0

Bromine binding site 4 out of 4 in 1kdh

Go back to Bromine Binding Sites List in 1kdh
Bromine binding site 4 out of 4 in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br4

b:96.7
occ:1.00
 BR D:BRU4 0.0 96.7 1.0
C5 D:BRU4 2.0 95.7 1.0
C6 D:BRU4 2.9 94.6 1.0
C4 D:BRU4 3.0 95.4 1.0
O4 D:BRU4 3.2 95.2 1.0
CE2 A:TRP450 3.4 42.6 1.0
CZ2 A:TRP450 3.6 44.0 1.0
CD2 A:TRP450 3.8 41.3 1.0
NE1 A:TRP450 3.8 41.2 1.0
C1' D:BRU3 3.9 94.5 1.0
O A:GLY449 3.9 35.6 1.0
CH2 A:TRP450 4.0 43.1 1.0
O2 D:BRU3 4.1 99.8 1.0
OD1 A:ASN474 4.2 38.7 1.0
N1 D:BRU4 4.2 93.8 1.0
CE3 A:TRP450 4.2 41.6 1.0
N3 D:BRU4 4.2 95.1 1.0
CZ3 A:TRP450 4.3 42.9 1.0
CD1 A:TRP450 4.3 40.0 1.0
O4' D:BRU3 4.3 90.6 1.0
CG A:TRP450 4.3 39.9 1.0
O3' D:BRU3 4.4 89.4 1.0
C2' D:BRU3 4.5 92.6 1.0
O5' D:BRU4 4.7 87.3 1.0
C A:GLY449 4.7 35.2 1.0
C2 D:BRU4 4.8 95.1 1.0
CA A:TRP450 4.8 36.8 1.0
N1 D:BRU3 4.9 98.4 1.0
C2 D:BRU3 4.9 0.1 1.0
C3' D:BRU3 4.9 90.5 1.0
C4' D:BRU3 5.0 89.6 1.0

Reference:

M.Delarue, J.B.Boule, J.Lescar, N.Expert-Bezancon, N.Jourdan, N.Sukumar, F.Rougeon, C.Papanicolaou. Crystal Structures of A Template-Independent Dna Polymerase: Murine Terminal Deoxynucleotidyltransferase. Embo J. V. 21 427 2002.
ISSN: ISSN 0261-4189
PubMed: 11823435
DOI: 10.1093/EMBOJ/21.3.427
Page generated: Wed Jul 10 16:47:58 2024

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