Manganese in PDB 7x9k: 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;

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

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:

Sodium

(Na)

1 atom

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 2 Hr Using 10 Mm MN2+, PDB code: 7x9k:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 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 Manganese with other atoms in the Mn 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:Mn204 b:16.6 occ:0.90 O1A A:8DG201 2.1 13.6 0.5 O A:HOH396 2.1 19.3 0.5 O2B A:8DG201 2.1 19.5 0.5 O A:GLY37 2.2 10.8 1.0 O A:HOH380 2.2 15.9 1.0 OE2 A:GLU57 2.2 17.9 1.0 OP2 A:8OG202 2.3 13.9 0.5 O A:HOH342 2.3 17.6 1.0 PA A:8DG201 3.2 18.4 0.5 CD A:GLU57 3.3 17.8 1.0 NA A:NA207 3.3 32.2 0.5 P A:8OG202 3.3 17.5 0.5 MN A:MN206 3.3 33.7 0.5 PB A:8DG201 3.4 16.4 0.5 C A:GLY37 3.4 12.2 1.0 OP1 A:8OG202 3.5 20.9 0.5 OE1 A:GLU57 3.6 11.4 1.0 O3A A:8DG201 3.7 20.1 0.5 N2 A:8OG202 3.8 9.2 0.5 N2 A:8DG201 3.9 9.2 0.5 O2A A:8DG201 3.9 15.7 0.5 CA A:GLY38 4.0 9.3 1.0 O A:HOH302 4.0 23.7 1.0 OP3 A:8OG202 4.1 16.9 0.5 N A:GLY38 4.2 9.8 1.0 O A:HOH305 4.3 31.6 1.0 O A:HOH335 4.3 22.8 1.0 NH1 A:ARG23 4.3 11.8 1.0 N A:GLY37 4.3 8.8 1.0 OE1 A:GLU53 4.4 16.5 1.0 O3B A:8DG201 4.4 26.1 0.5 O1B A:8DG201 4.5 12.5 0.5 CA A:GLY37 4.5 8.7 1.0 CG A:GLU57 4.6 10.2 1.0 O5' A:8DG201 4.6 17.0 0.5 OE1 A:GLU34 4.6 13.7 1.0 O5' A:8OG202 4.6 17.2 0.5 O3G A:8DG201 4.6 32.5 0.5 C5' A:8OG202 5.0 15.1 0.5 O A:HOH418 5.0 21.0 0.5

Manganese binding site 2 out of 3 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 Manganese with other atoms in the Mn binding site number 2 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:Mn205 b:26.7 occ:0.50 O A:HOH353 0.2 27.6 0.5 O1B A:8DG201 2.2 12.5 0.5 O A:HOH341 2.4 23.1 1.0 O A:HOH322 2.4 15.6 1.0 OE2 A:GLU53 2.7 16.4 1.0 O2G A:8DG201 2.8 33.6 0.5 O A:HOH418 2.9 21.0 0.5 PB A:8DG201 3.3 16.4 0.5 NA A:NA207 3.4 32.2 0.5 MN A:MN206 3.6 33.7 0.5 CD A:GLU53 3.6 14.9 1.0 O A:HOH396 3.8 19.3 0.5 PG A:8DG201 3.8 33.3 0.5 OE1 A:GLU53 3.8 16.5 1.0 O2B A:8DG201 3.8 19.5 0.5 O3B A:8DG201 3.9 26.1 0.5 O3G A:8DG201 4.0 32.5 0.5 N A:LYS39 4.1 10.7 0.4 N A:LYS39 4.1 10.6 0.6 NH1 A:ARG52 4.2 14.5 1.0 O A:HOH309 4.4 23.4 1.0 OE2 A:GLU41 4.5 28.6 0.6 OE1 A:GLU56 4.6 21.9 1.0 OP1 A:8OG202 4.6 20.9 0.5 O3A A:8DG201 4.6 20.1 0.5 O A:LYS39 4.6 11.9 0.6 O A:LYS39 4.6 11.9 0.4 CA A:GLY38 4.7 9.3 1.0 OE2 A:GLU41 4.7 23.9 0.4 O A:HOH425 4.8 35.1 0.5 CB A:LYS39 4.8 12.8 0.4 CB A:LYS39 4.8 12.8 0.6 C A:GLY38 4.8 9.7 1.0 CD A:LYS39 4.9 22.6 0.4 NH2 A:ARG52 4.9 11.2 1.0 CA A:LYS39 4.9 12.9 0.4 CA A:LYS39 4.9 12.9 0.6 CG A:LYS39 5.0 16.8 0.4

Manganese binding site 3 out of 3 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 Manganese with other atoms in the Mn binding site number 3 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:Mn206 b:33.7 occ:0.50 NA A:NA207 0.2 32.2 0.5 O A:HOH396 2.3 19.3 0.5 O2B A:8DG201 2.4 19.5 0.5 O A:HOH309 2.4 23.4 1.0 OE2 A:GLU57 2.5 17.9 1.0 O A:HOH302 2.6 23.7 1.0 OE1 A:GLU53 2.6 16.5 1.0 O3G A:8DG201 3.2 32.5 0.5 MN A:MN204 3.3 16.6 0.9 CD A:GLU57 3.3 17.8 1.0 PB A:8DG201 3.5 16.4 0.5 CG A:GLU57 3.5 10.2 1.0 O A:HOH353 3.5 27.6 0.5 MN A:MN205 3.6 26.7 0.5 CD A:GLU53 3.6 14.9 1.0 O1B A:8DG201 3.8 12.5 0.5 O A:GLY37 3.9 10.8 1.0 OE2 A:GLU53 3.9 16.4 1.0 O A:HOH380 4.2 15.9 1.0 O A:HOH341 4.2 23.1 1.0 PG A:8DG201 4.2 33.3 0.5 OE1 A:GLU56 4.3 21.9 1.0 O3B A:8DG201 4.3 26.1 0.5 OE2 A:GLU98 4.3 18.6 1.0 OE1 A:GLU98 4.5 19.9 1.0 OE1 A:GLU57 4.5 11.4 1.0 O2G A:8DG201 4.5 33.6 0.5 C A:GLY37 4.7 12.2 1.0 CA A:GLY38 4.7 9.3 1.0 OP1 A:8OG202 4.7 20.9 0.5 O A:HOH418 4.8 21.0 0.5 CD A:GLU98 4.8 18.4 1.0 O3A A:8DG201 4.9 20.1 0.5 O1A A:8DG201 4.9 13.6 0.5 CG A:GLU53 5.0 10.6 1.0

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