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Sodium in PDB 4i2a: Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion

Enzymatic activity of Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion

All present enzymatic activity of Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion:
2.7.7.31;

Protein crystallography data

The structure of Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion, PDB code: 4i2a was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.65 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.935, 84.893, 114.687, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.9

Other elements in 4i2a:

The structure of Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion (pdb code 4i2a). 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 Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion, PDB code: 4i2a:

Sodium binding site 1 out of 1 in 4i2a

Go back to Sodium Binding Sites List in 4i2a
Sodium binding site 1 out of 1 in the Binary Complex of Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion


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 Mouse Tdt with Ssdna in Absence of Divalent Transition Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:32.1
occ:1.00
 O A:THR253 2.3 29.5 1.0
O C:HOH101 2.4 36.6 1.0
O A:VAL258 2.4 31.1 1.0
O A:HOH967 2.6 47.6 1.0
OP1 C:DA4 2.6 51.6 1.0
O A:VAL255 2.6 27.1 1.0
C A:THR253 3.3 29.6 1.0
C A:VAL258 3.5 31.9 1.0
P C:DA4 3.5 53.9 1.0
OP2 C:DA4 3.7 54.8 1.0
C A:VAL255 3.7 27.8 1.0
CA A:THR253 3.7 26.4 1.0
N A:VAL258 3.8 25.5 1.0
CA A:VAL258 4.1 25.8 1.0
CB A:THR253 4.1 34.0 1.0
N A:GLY257 4.2 26.1 1.0
N A:VAL255 4.4 25.0 1.0
CA A:PHE256 4.4 24.8 1.0
N A:PHE256 4.4 24.5 1.0
N A:SER254 4.5 27.1 1.0
CB A:VAL258 4.5 27.2 1.0
N A:GLY259 4.5 32.5 1.0
O3' C:BRU3 4.6 74.1 1.0
C A:SER254 4.7 30.1 1.0
C A:PHE256 4.7 29.0 1.0
CA A:VAL255 4.7 23.6 1.0
O5' C:DA4 4.7 56.0 1.0
C A:GLY257 4.8 29.7 1.0
CA A:GLY259 4.9 33.9 1.0
CA A:SER254 4.9 27.1 1.0
CG2 A:THR253 5.0 28.1 1.0
O A:PHE252 5.0 24.4 1.0

Reference:

J.Gouge, S.Rosario, F.Romain, P.Beguin, M.Delarue. Structures of Intermediates Along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism. J.Mol.Biol. V. 425 4334 2013.
ISSN: ISSN 0022-2836
PubMed: 23856622
DOI: 10.1016/J.JMB.2013.07.009
Page generated: Mon Oct 7 15:55:58 2024

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