Manganese in PDB 7x9i: 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;

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

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:

Sodium

(Na)

1 atom

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 12 Hr Using 5 Mm MN2+, PDB code: 7x9i:
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 12 Hr Using 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 12 Hr Using 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:12.5 occ:0.80 O2B A:8DG202 2.1 15.9 0.3 O A:GLY37 2.2 5.8 1.0 O A:HOH408 2.2 16.4 0.7 O A:HOH339 2.2 13.4 1.0 O1A A:8DG202 2.2 10.0 0.3 OP2 A:8OG203 2.3 10.0 0.7 OE2 A:GLU57 2.3 14.0 1.0 O A:HOH402 2.3 16.2 1.0 CD A:GLU57 3.2 13.5 1.0 C A:GLY37 3.4 11.4 1.0 PA A:8DG202 3.4 12.5 0.3 P A:8OG203 3.4 13.7 0.7 PB A:8DG202 3.5 9.3 0.3 MN A:MN206 3.5 30.4 0.3 OE1 A:GLU57 3.5 9.8 1.0 NA A:NA207 3.5 30.9 0.7 OP1 A:8OG203 3.6 19.5 0.7 N2 A:8OG203 3.8 4.7 0.7 O3A A:8DG202 3.8 10.4 0.3 N2 A:8DG202 3.9 4.8 0.3 O A:HOH307 4.0 17.9 1.0 CA A:GLY38 4.0 6.0 1.0 O2A A:8DG202 4.1 11.1 0.3 N A:GLY38 4.2 6.1 1.0 OP3 A:8OG203 4.3 11.1 0.7 N A:GLY37 4.3 4.1 1.0 O A:HOH347 4.3 19.6 1.0 O1G A:8DG202 4.3 26.1 0.3 NH1 A:ARG23 4.4 7.1 1.0 O A:HOH325 4.4 29.9 1.0 OE1 A:GLU53 4.4 9.0 1.0 CA A:GLY37 4.5 4.9 1.0 O1B A:8DG202 4.5 10.1 0.3 OE1 A:GLU34 4.5 8.0 1.0 O3B A:8DG202 4.5 17.8 0.3 CG A:GLU57 4.6 8.1 1.0 O5' A:8OG203 4.6 13.2 0.7 O5' A:8DG202 4.7 12.4 0.3 O A:HOH431 4.9 12.0 0.7 C5' A:8OG203 4.9 7.3 0.7

Manganese binding site 2 out of 3 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 Manganese with other atoms in the Mn binding site number 2 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:Mn205 b:21.0 occ:0.30 O A:HOH355 0.2 21.2 0.7 O1B A:8DG202 2.0 10.1 0.3 O A:HOH323 2.4 20.3 1.0 O A:HOH301 2.5 11.1 1.0 O A:HOH302 2.6 20.5 0.3 OE2 A:GLU53 2.7 13.8 1.0 O A:HOH431 2.9 12.0 0.7 NA A:NA207 3.0 30.9 0.7 MN A:MN206 3.2 30.4 0.3 O3G A:8DG202 3.3 16.9 0.3 PB A:8DG202 3.3 9.3 0.3 CD A:GLU53 3.6 9.5 1.0 O A:HOH408 3.7 16.4 0.7 OE1 A:GLU53 3.8 9.0 1.0 O A:HOH351 3.9 36.4 1.0 O3B A:8DG202 3.9 17.8 0.3 O2B A:8DG202 4.0 15.9 0.3 NH1 A:ARG52 4.1 9.7 1.0 N A:LYS39 4.2 6.9 0.4 N A:LYS39 4.2 6.9 0.6 PG A:8DG202 4.2 22.3 0.3 O A:HOH311 4.4 15.8 1.0 OE1 A:GLU56 4.4 15.6 1.0 O3A A:8DG202 4.5 10.4 0.3 OE2 A:GLU41 4.6 18.2 0.5 O A:HOH447 4.6 35.6 0.7 OE2 A:GLU41 4.6 23.3 0.5 CA A:GLY38 4.6 6.0 1.0 O A:LYS39 4.7 7.0 0.6 O A:LYS39 4.7 7.0 0.4 O1G A:8DG202 4.7 26.1 0.3 OP1 A:8OG203 4.7 19.5 0.7 C A:GLY38 4.8 8.5 1.0 CB A:LYS39 4.9 11.7 0.4 NH2 A:ARG52 4.9 5.9 1.0 CB A:LYS39 4.9 11.7 0.6 CZ A:ARG52 5.0 8.8 1.0

Manganese binding site 3 out of 3 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 Manganese with other atoms in the Mn binding site number 3 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:Mn206 b:30.4 occ:0.30 NA A:NA207 0.2 30.9 0.7 O A:HOH408 2.3 16.4 0.7 O A:HOH311 2.5 15.8 1.0 OE1 A:GLU53 2.6 9.0 1.0 O2B A:8DG202 2.6 15.9 0.3 OE2 A:GLU57 2.7 14.0 1.0 O A:HOH307 2.8 17.9 1.0 O A:HOH355 3.2 21.2 0.7 MN A:MN205 3.2 21.0 0.3 PB A:8DG202 3.4 9.3 0.3 O1B A:8DG202 3.4 10.1 0.3 O1G A:8DG202 3.5 26.1 0.3 MN A:MN204 3.5 12.5 0.8 CD A:GLU53 3.5 9.5 1.0 CD A:GLU57 3.6 13.5 1.0 OE2 A:GLU53 3.7 13.8 1.0 CG A:GLU57 3.7 8.1 1.0 O A:GLY37 3.9 5.8 1.0 O A:HOH323 4.0 20.3 1.0 O3G A:8DG202 4.1 16.9 0.3 O A:HOH351 4.1 36.4 1.0 OE1 A:GLU56 4.1 15.6 1.0 PG A:8DG202 4.2 22.3 0.3 O3B A:8DG202 4.3 17.8 0.3 O A:HOH431 4.4 12.0 0.7 O A:HOH402 4.4 16.2 1.0 OE2 A:GLU98 4.5 14.1 1.0 CA A:GLY38 4.6 6.0 1.0 OE1 A:GLU98 4.7 16.0 1.0 OE1 A:GLU57 4.7 9.8 1.0 C A:GLY37 4.7 11.4 1.0 OP1 A:8OG203 4.7 19.5 0.7 O3A A:8DG202 4.8 10.4 0.3 O A:HOH447 4.9 35.6 0.7 CG A:GLU53 4.9 4.7 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