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Sodium in PDB 7x9i: Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 Mm MN2+

Enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 Mm MN2+

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 Mm MN2+:
3.6.1.55;

Protein crystallography data

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 Mm MN2+, PDB code: 7x9i 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) 32.14 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.239, 56.004, 59.34, 90, 90, 90
R / Rfree (%) 14.4 / 19

Other elements in 7x9i:

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 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 12 Hr Using 5 Mm MN2+ (pdb code 7x9i). 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 12 Hr Using 5 Mm MN2+, PDB code: 7x9i:

Sodium binding site 1 out of 1 in 7x9i

Go back to Sodium Binding Sites List in 7x9i
Sodium binding site 1 out of 1 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 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 12 Hr Using 5 Mm MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:30.9
occ:0.70
 MN A:MN206 0.2 30.4 0.3
O A:HOH408 2.2 16.4 0.7
OE1 A:GLU53 2.5 9.0 1.0
O2B A:8DG202 2.5 15.9 0.3
O A:HOH311 2.6 15.8 1.0
OE2 A:GLU57 2.9 14.0 1.0
O A:HOH307 3.0 17.9 1.0
MN A:MN205 3.0 21.0 0.3
O A:HOH355 3.0 21.2 0.7
O1B A:8DG202 3.2 10.1 0.3
PB A:8DG202 3.3 9.3 0.3
CD A:GLU53 3.4 9.5 1.0
OE2 A:GLU53 3.5 13.8 1.0
MN A:MN204 3.5 12.5 0.8
O1G A:8DG202 3.5 26.1 0.3
CD A:GLU57 3.7 13.5 1.0
O A:GLY37 3.9 5.8 1.0
O A:HOH323 3.9 20.3 1.0
CG A:GLU57 3.9 8.1 1.0
O3G A:8DG202 4.0 16.9 0.3
OE1 A:GLU56 4.1 15.6 1.0
O A:HOH351 4.1 36.4 1.0
PG A:8DG202 4.2 22.3 0.3
O3B A:8DG202 4.2 17.8 0.3
O A:HOH431 4.2 12.0 0.7
CA A:GLY38 4.4 6.0 1.0
O A:HOH402 4.6 16.2 1.0
OP1 A:8OG203 4.6 19.5 0.7
O3A A:8DG202 4.7 10.4 0.3
C A:GLY37 4.7 11.4 1.0
OE2 A:GLU98 4.7 14.1 1.0
CG A:GLU53 4.8 4.7 1.0
O A:HOH447 4.9 35.6 0.7
OE1 A:GLU57 4.9 9.8 1.0
OE1 A:GLU98 4.9 16.0 1.0
O A:HOH302 4.9 20.5 0.3
N A:GLY38 5.0 6.1 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: Wed Oct 9 09:38:33 2024

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