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Sodium 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:

Bromine (Br) 4 atoms
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with A Primer Single Stranded Dna, PDB code: 1kdh:

Sodium binding site 1 out of 1 in 1kdh

Go back to Sodium Binding Sites List in 1kdh
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
A:Na2

b:61.2
occ:1.00
 O A:VAL258 2.3 44.7 1.0
O A:THR253 2.4 41.9 1.0
OP1 D:BRU2 2.4 81.8 1.0
O A:VAL255 3.1 41.5 1.0
P D:BRU2 3.4 80.8 1.0
C A:VAL258 3.4 46.7 1.0
OP2 D:BRU2 3.5 81.1 1.0
C A:THR253 3.6 41.8 1.0
N A:VAL258 3.8 46.2 1.0
CA A:VAL258 4.0 45.7 1.0
C A:VAL255 4.0 41.7 1.0
O5' D:BRU2 4.2 81.9 1.0
CA A:THR253 4.2 41.7 1.0
CB A:VAL258 4.4 45.5 1.0
N A:GLY257 4.4 47.2 1.0
N A:VAL255 4.4 41.6 1.0
N A:GLY259 4.5 47.5 1.0
OG1 A:THR253 4.5 41.5 1.0
N A:SER254 4.6 40.9 1.0
CA A:PHE256 4.7 45.5 1.0
N A:PHE256 4.7 43.3 1.0
O3' D:BRU1 4.7 81.7 1.0
C A:SER254 4.7 41.2 1.0
CB A:THR253 4.8 41.5 1.0
C A:GLY257 4.8 48.2 1.0
CA A:GLY259 4.8 48.4 1.0
CA A:VAL255 4.9 41.5 1.0
CG2 A:THR253 4.9 41.2 1.0
CA A:SER254 4.9 39.9 1.0
C A:PHE256 4.9 46.4 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: Sun Oct 6 19:35:26 2024

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