Manganese in PDB 5v09: Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii), PDB code: 5v09 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)	46.59 / 2.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.904, 73.904, 180.081, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.4

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii) 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 (D225A) in Complex with 5' Recessed-End Dna (Rvii) (pdb code 5v09). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii), PDB code: 5v09:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)


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 (D225A) in Complex with 5' Recessed-End Dna (Rvii) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:60.0 occ:1.00 OP1 B:DC2 2.0 76.2 1.0 OD2 Z:ASP173 2.1 69.8 1.0 OD2 Z:ASP152 2.1 44.5 1.0 OD2 Z:ASP171 2.1 57.7 1.0 O Z:HOH510 2.3 62.1 1.0 CG Z:ASP173 2.9 64.1 1.0 CB Z:ASP173 3.0 56.1 1.0 CG Z:ASP171 3.2 55.6 1.0 P B:DC2 3.2 76.3 1.0 CG Z:ASP152 3.4 48.7 1.0 O5' B:DC2 3.5 83.8 1.0 OD1 Z:ASP171 3.6 55.9 1.0 MN B:MN101 4.0 54.5 1.0 O Z:HOH513 4.0 50.8 1.0 OD1 Z:ASP152 4.0 51.6 1.0 N Z:GLY2 4.0 66.1 1.0 OP2 B:DC2 4.1 76.8 1.0 OD1 Z:ASP173 4.1 68.7 1.0 OE2 Z:GLU150 4.3 70.2 1.0 C5' B:DC2 4.3 81.8 1.0 O3' B:DA1 4.4 76.9 1.0 CB Z:ASP152 4.4 36.5 1.0 CB Z:ASP171 4.5 48.2 1.0 CA Z:ASP173 4.5 54.2 1.0 CA Z:GLY2 4.8 68.5 1.0 NZ Z:LYS85 4.8 52.0 1.0 N Z:ASP173 4.9 59.3 1.0 O Z:HOH519 4.9 65.5 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)


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 (D225A) in Complex with 5' Recessed-End Dna (Rvii) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:88.2 occ:1.00 O Z:HOH578 2.4 67.1 1.0 SG Z:CYS80 2.7 64.6 1.0 CB Z:CYS80 3.7 65.3 1.0 CD1 Z:ILE325 4.0 56.7 1.0 CE1 Z:PHE335 4.2 67.4 1.0 CZ Z:PHE335 4.2 66.3 1.0 OH Z:TYR149 4.4 69.6 1.0 CG1 Z:VAL317 4.5 62.9 1.0 O Z:PRO148 4.5 58.9 1.0 CZ Z:TYR149 4.6 68.0 1.0 CE1 Z:TYR149 4.7 66.1 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)


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 (D225A) in Complex with 5' Recessed-End Dna (Rvii) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:0.2 occ:1.00 O2 A:DC11 2.3 0.9 1.0 C2 A:DC11 3.1 0.9 1.0 N3 A:DC11 3.3 0.6 1.0 O Z:ALA41 3.8 89.0 1.0 N1 A:DC11 4.4 0.8 1.0 O Z:ILE40 4.5 89.7 1.0 C Z:ALA41 4.6 87.3 1.0 CA Z:ALA41 4.6 80.6 1.0 C4 A:DC11 4.6 0.1 1.0 O4' A:DA12 4.8 0.6 1.0 OE1 Z:GLU44 4.8 0.7 1.0 C1' A:DC11 5.0 100.0 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)


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 (D225A) in Complex with 5' Recessed-End Dna (Rvii) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:54.5 occ:1.00 O Z:HOH532 2.1 58.7 1.0 O Z:HOH513 2.1 50.8 1.0 O Z:HOH519 2.2 65.5 1.0 OD1 Z:ASP152 2.2 51.6 1.0 O3' B:DA1 2.3 76.9 1.0 OP1 B:DC2 2.4 76.2 1.0 P B:DC2 3.0 76.3 1.0 CG Z:ASP152 3.1 48.7 1.0 OD2 Z:ASP152 3.2 44.5 1.0 C3' B:DA1 3.6 82.2 1.0 OD1 Z:ASP78 3.8 60.8 1.0 O5' B:DC2 3.9 83.8 1.0 C4' B:DA1 3.9 86.6 1.0 MN Z:MN401 4.0 60.0 1.0 OD2 Z:ASP30 4.1 49.3 1.0 OD2 Z:ASP78 4.1 68.9 1.0 OD2 Z:ASP171 4.1 57.7 1.0 OP2 B:DC2 4.2 76.8 1.0 OE2 Z:GLU150 4.2 70.2 1.0 C2' B:DA1 4.3 85.6 1.0 C5' B:DA1 4.4 86.4 1.0 N Z:ASP152 4.4 49.0 1.0 CG Z:ASP78 4.4 60.2 1.0 O Z:HOH534 4.4 78.0 1.0 NZ Z:LYS85 4.5 52.0 1.0 CB Z:ASP152 4.5 36.5 1.0 OD1 Z:ASP30 4.5 60.2 1.0 CG Z:ASP30 4.8 55.9 1.0 N Z:ALA151 4.8 45.3 1.0 CB Z:ALA151 4.8 40.9 1.0 CA Z:ASP152 4.9 46.1 1.0 O Z:HOH510 5.0 62.1 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:93.2 occ:1.00 OP1 B:DA1 2.2 0.4 1.0 P B:DA1 3.3 90.2 1.0 OP3 B:DA1 3.4 93.6 1.0 OE1 Z:GLU89 3.8 0.1 1.0 OE2 Z:GLU89 4.1 0.6 1.0 CD Z:GLU89 4.4 1.0 1.0 O5' B:DA1 4.4 86.2 1.0 OP2 B:DA1 4.4 86.8 1.0 O Z:HOH572 4.5 54.5 1.0 C5' B:DA1 4.6 86.4 1.0 O B:HOH206 4.8 76.4 1.0 O Z:HOH534 4.8 78.0 1.0 CE2 Z:TYR32 4.8 70.3 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