Manganese in PDB 5v07: Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv), PDB code: 5v07 was solved by Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.92 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.837, 73.837, 179.067, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv) (pdb code 5v07). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv), PDB code: 5v07:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv)


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 Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:45.9 occ:1.00 OP1 B:DC2 2.1 46.3 1.0 OD2 Z:ASP152 2.1 39.7 1.0 O Z:HOH563 2.2 46.9 1.0 OD2 Z:ASP171 2.2 55.2 1.0 O Z:HOH583 2.2 65.8 1.0 O Z:HOH524 2.3 38.3 1.0 CG Z:ASP171 3.2 47.7 1.0 CG Z:ASP152 3.2 41.9 1.0 P B:DC2 3.3 45.1 1.0 OD1 Z:ASP171 3.6 53.3 1.0 O5' B:DC2 3.6 54.6 1.0 O Z:HOH590 3.6 58.0 1.0 MN B:MN101 3.6 41.2 1.0 OD1 Z:ASP152 3.8 45.6 1.0 O Z:HOH505 3.9 40.6 1.0 OE1 Z:GLU150 4.1 54.6 1.0 OP2 B:DC2 4.2 47.0 1.0 C5' B:DC2 4.4 53.5 1.0 OD1 Z:ASP225 4.4 63.5 1.0 CB Z:ASP152 4.4 40.4 1.0 O3' B:DT1 4.5 44.7 1.0 CB Z:ASP171 4.5 37.5 1.0 O Z:HOH585 4.6 33.6 1.0 N Z:GLY2 4.7 60.9 1.0 O Z:HOH539 4.8 34.2 1.0 NZ Z:LYS85 4.9 52.0 1.0 CD Z:GLU150 4.9 53.3 1.0 CB Z:ALA173 4.9 56.2 1.0 CD1 Z:LEU174 4.9 47.5 1.0 OE2 Z:GLU150 5.0 51.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv)


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 Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:90.5 occ:1.00 SG Z:CYS80 2.4 64.0 1.0 CB Z:CYS80 3.5 51.9 1.0 CD1 Z:ILE325 3.7 59.2 1.0 CE1 Z:PHE335 4.0 65.2 1.0 CZ Z:PHE335 4.1 63.0 1.0 O Z:PRO148 4.4 46.1 1.0 OH Z:TYR149 4.6 60.6 1.0 CZ Z:TYR149 4.8 55.5 1.0 CG1 Z:VAL317 4.8 61.7 1.0 CA Z:CYS80 4.9 45.6 1.0 CE1 Z:TYR149 4.9 53.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv)


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 Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:41.2 occ:1.00 OD1 Z:ASP152 2.1 45.6 1.0 O Z:HOH534 2.2 38.7 1.0 OP1 B:DC2 2.2 46.3 1.0 O Z:HOH505 2.2 40.6 1.0 O Z:HOH539 2.3 34.2 1.0 O3' B:DT1 2.4 44.7 1.0 P B:DC2 2.8 45.1 1.0 CG Z:ASP152 3.0 41.9 1.0 OD2 Z:ASP152 3.2 39.7 1.0 MN Z:MN401 3.6 45.9 1.0 O5' B:DC2 3.7 54.6 1.0 C3' B:DT1 3.7 44.4 1.0 OD2 Z:ASP171 3.8 55.2 1.0 OE1 Z:GLU150 3.9 54.6 1.0 OP2 B:DC2 4.1 47.0 1.0 OD2 Z:ASP78 4.2 46.9 1.0 C4' B:DT1 4.2 49.9 1.0 OD2 Z:ASP30 4.2 51.4 1.0 OD1 Z:ASP78 4.2 50.1 1.0 CB Z:ASP152 4.4 40.4 1.0 C2' B:DT1 4.4 42.9 1.0 N Z:ASP152 4.4 38.5 1.0 OD1 Z:ASP30 4.5 50.8 1.0 O Z:HOH524 4.5 38.3 1.0 CG Z:ASP78 4.6 47.2 1.0 C5' B:DT1 4.7 50.2 1.0 NZ Z:LYS85 4.8 52.0 1.0 CG Z:ASP30 4.8 50.5 1.0 CD Z:GLU150 4.8 53.3 1.0 CG Z:ASP171 4.8 47.7 1.0 CA Z:ASP152 4.8 39.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rv) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:56.0 occ:1.00 O B:HOH212 2.1 46.0 1.0 O Z:HOH510 2.2 66.3 1.0 O B:HOH205 2.2 47.8 1.0 O B:HOH213 2.2 52.8 1.0 O Z:HOH601 2.2 59.2 1.0 OP1 B:DT1 2.4 57.6 1.0 P B:DT1 3.5 60.2 1.0 OP3 B:DT1 3.5 53.9 1.0 OE1 Z:GLU89 3.9 87.5 1.0 O B:HOH201 4.0 50.7 1.0 O B:HOH206 4.0 57.1 1.0 OP2 B:DT1 4.4 60.7 1.0 O Z:HOH559 4.6 54.3 1.0 O B:HOH208 4.6 67.1 1.0 O Z:HOH561 4.6 63.9 1.0 O5' B:DT1 4.6 50.5 1.0 CE2 Z:TYR32 4.7 55.8 1.0 C5' B:DT1 4.7 50.2 1.0 CD Z:GLU89 4.7 81.0 1.0 O Z:ILE125 4.7 51.2 1.0 OE2 Z:GLU89 4.8 83.8 1.0 O Z:HOH575 4.9 59.8 1.0

Y.Shi, H.W.Hellinga, L.S.Beese. Interplay of Catalysis, Fidelity, Threading, and Processivity in the Exo- and Endonucleolytic Reactions of Human Exonuclease I. Proc. Natl. Acad. Sci. V. 114 6010 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28533382
DOI: 10.1073/PNAS.1704845114