Atomistry » Bromine » PDB 1iha-1m9r » 1kdh
Atomistry »
  Bromine »
    PDB 1iha-1m9r »
      1kdh »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy