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Sodium in PDB 7x9k: Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+

Enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+:
3.6.1.55;

Protein crystallography data

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+, PDB code: 7x9k was solved by T.Nakamura, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.53 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.15, 55.984, 59.135, 90, 90, 90
R / Rfree (%) 15.6 / 18.2

Other elements in 7x9k:

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+ also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+ (pdb code 7x9k). 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 Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+, PDB code: 7x9k:

Sodium binding site 1 out of 1 in 7x9k

Go back to Sodium Binding Sites List in 7x9k
Sodium binding site 1 out of 1 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:32.2
occ:0.50
 MN A:MN206 0.2 33.7 0.5
O A:HOH396 2.2 19.3 0.5
O2B A:8DG201 2.3 19.5 0.5
OE1 A:GLU53 2.5 16.5 1.0
O A:HOH309 2.5 23.4 1.0
OE2 A:GLU57 2.6 17.9 1.0
O A:HOH302 2.7 23.7 1.0
O3G A:8DG201 3.2 32.5 0.5
MN A:MN204 3.3 16.6 0.9
PB A:8DG201 3.3 16.4 0.5
O A:HOH353 3.4 27.6 0.5
MN A:MN205 3.4 26.7 0.5
CD A:GLU57 3.5 17.8 1.0
CD A:GLU53 3.5 14.9 1.0
CG A:GLU57 3.6 10.2 1.0
O1B A:8DG201 3.6 12.5 0.5
OE2 A:GLU53 3.7 16.4 1.0
O A:GLY37 3.8 10.8 1.0
O A:HOH341 4.1 23.1 1.0
PG A:8DG201 4.1 33.3 0.5
O3B A:8DG201 4.2 26.1 0.5
O A:HOH380 4.2 15.9 1.0
OE1 A:GLU56 4.3 21.9 1.0
O2G A:8DG201 4.4 33.6 0.5
OE2 A:GLU98 4.5 18.6 1.0
CA A:GLY38 4.5 9.3 1.0
OP1 A:8OG202 4.6 20.9 0.5
O A:HOH418 4.6 21.0 0.5
OE1 A:GLU57 4.6 11.4 1.0
C A:GLY37 4.6 12.2 1.0
OE1 A:GLU98 4.7 19.9 1.0
O3A A:8DG201 4.7 20.1 0.5
O1A A:8DG201 4.8 13.6 0.5
CG A:GLU53 4.8 10.6 1.0
N A:GLY38 5.0 9.8 1.0

Reference:

T.Nakamura, Y.Yamagata. Visualization of Mutagenic Nucleotide Processing By Escherichia Coli Mutt, A Nudix Hydrolase. Proc.Natl.Acad.Sci.Usa V. 119 18119 2022.
ISSN: ESSN 1091-6490
PubMed: 35594391
DOI: 10.1073/PNAS.2203118119
Page generated: Mon Aug 18 12:32:23 2025

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