Manganese in PDB 7ww7: Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1 Hr in 5 Mm MN2+

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1 Hr in 5 Mm MN2+:
3.6.1.55;

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1 Hr in 5 Mm MN2+, PDB code: 7ww7 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)	31.60 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.278, 55.968, 59.181, 90, 90, 90
R / Rfree (%)	15.9 / 19.8

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1 Hr in 5 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 1 Hr in 5 Mm MN2+ (pdb code 7ww7). 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 1 Hr in 5 Mm MN2+, PDB code: 7ww7:
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 1 Hr in 5 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 1 Hr in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:9.0 occ:1.00 O2B A:8DG201 2.1 12.5 1.0 O A:HOH331 2.2 8.9 1.0 OE2 A:GLU57 2.2 7.8 1.0 O1A A:8DG201 2.2 9.1 1.0 O A:GLY37 2.2 6.8 1.0 O A:HOH410 2.2 7.6 1.0 CD A:GLU57 3.1 8.5 1.0 MN A:MN205 3.2 8.7 0.3 PA A:8DG201 3.3 9.9 1.0 PB A:8DG201 3.4 11.3 1.0 C A:GLY37 3.4 5.9 1.0 OE1 A:GLU57 3.5 7.6 1.0 O3A A:8DG201 3.6 9.0 1.0 O A:HOH341 3.9 14.4 1.0 N2 A:8DG201 3.9 5.9 1.0 O A:HOH306 3.9 11.9 0.7 CA A:GLY38 4.0 5.7 1.0 O2A A:8DG201 4.1 10.8 1.0 N A:GLY38 4.2 5.1 1.0 O A:HOH337 4.2 14.2 1.0 NH1 A:ARG23 4.2 8.7 1.0 N A:GLY37 4.3 6.0 1.0 OE1 A:GLU53 4.3 10.0 1.0 O3B A:8DG201 4.4 16.2 1.0 CA A:GLY37 4.5 5.0 1.0 CG A:GLU57 4.5 6.8 1.0 O1B A:8DG201 4.5 10.1 1.0 O A:HOH338 4.5 25.7 1.0 OE1 A:GLU34 4.5 9.7 1.0 O5' A:8DG201 4.6 9.5 1.0 O3G A:8DG201 5.0 40.9 1.0 C5' A:8DG201 5.0 7.0 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1 Hr in 5 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 1 Hr in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:11.3 occ:0.30 NA A:NA204 0.1 11.3 0.7 O1B A:8DG201 2.2 10.1 1.0 O A:HOH308 2.3 12.0 1.0 O A:HOH316 2.4 27.7 1.0 O A:HOH334 2.4 12.3 1.0 OE2 A:GLU53 2.5 10.1 1.0 O A:HOH306 2.8 11.9 0.7 PB A:8DG201 3.3 11.3 1.0 O3G A:8DG201 3.4 40.9 1.0 CD A:GLU53 3.4 7.9 1.0 OE1 A:GLU53 3.7 10.0 1.0 MN A:MN205 3.8 8.7 0.3 O2B A:8DG201 3.8 12.5 1.0 O A:HOH305 3.9 35.7 1.0 O3B A:8DG201 4.0 16.2 1.0 N A:LYS39 4.0 7.1 1.0 PG A:8DG201 4.1 43.8 1.0 NH1 A:ARG52 4.1 10.5 1.0 O2G A:8DG201 4.1 39.0 1.0 O A:LYS39 4.4 8.6 1.0 O A:HOH310 4.4 17.1 1.0 OE2 A:GLU41 4.5 21.6 0.4 OE2 A:GLU41 4.5 23.1 0.6 OE1 A:GLU56 4.5 15.3 1.0 CA A:GLY38 4.6 5.7 1.0 O3A A:8DG201 4.6 9.0 1.0 CB A:LYS39 4.7 9.7 1.0 NH2 A:ARG52 4.7 7.2 1.0 C A:GLY38 4.7 4.8 1.0 CG A:GLU53 4.8 6.2 1.0 CA A:LYS39 4.8 6.6 1.0 CZ A:ARG52 4.9 8.9 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1 Hr in 5 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 1 Hr in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn205 b:8.7 occ:0.30 O A:HOH306 1.0 11.9 0.7 OE2 A:GLU57 2.1 7.8 1.0 O2B A:8DG201 2.3 12.5 1.0 O A:HOH341 2.4 14.4 1.0 OE1 A:GLU53 2.5 10.0 1.0 O A:HOH310 2.6 17.1 1.0 CD A:GLU57 3.0 8.5 1.0 MN A:MN202 3.2 9.0 1.0 O3G A:8DG201 3.2 40.9 1.0 CG A:GLU57 3.3 6.8 1.0 PB A:8DG201 3.5 11.3 1.0 CD A:GLU53 3.6 7.9 1.0 NA A:NA204 3.7 11.3 0.7 O A:GLY37 3.7 6.8 1.0 MN A:MN203 3.8 11.3 0.3 O1B A:8DG201 3.9 10.1 1.0 OE2 A:GLU53 3.9 10.1 1.0 O A:HOH410 4.1 7.6 1.0 OE1 A:GLU57 4.2 7.6 1.0 O3B A:8DG201 4.3 16.2 1.0 O A:HOH305 4.3 35.7 1.0 OE2 A:GLU98 4.3 14.0 1.0 OE1 A:GLU98 4.4 13.6 1.0 PG A:8DG201 4.4 43.8 1.0 OE1 A:GLU56 4.5 15.3 1.0 O A:HOH334 4.5 12.3 1.0 C A:GLY37 4.6 5.9 1.0 CA A:GLY38 4.6 5.7 1.0 CB A:GLU57 4.8 4.2 1.0 CD A:GLU98 4.8 11.8 1.0 O3A A:8DG201 4.8 9.0 1.0 CG A:GLU53 4.9 6.2 1.0 O A:HOH331 4.9 8.9 1.0 O1A A:8DG201 4.9 9.1 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