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Manganese in PDB 5v0a: Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)

Protein crystallography data

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii), PDB code: 5v0a 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) 38.37 / 2.38
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.739, 73.739, 179.714, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.7

Other elements in 5v0a:

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii) (pdb code 5v0a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii), PDB code: 5v0a:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5v0a

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Manganese binding site 1 out of 6 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)


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 (Rviii) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn401

b:50.1
occ:1.00
 OD2 Z:ASP152 2.1 45.2 1.0
OP1 B:DC1 2.1 61.9 1.0
OD2 Z:ASP173 2.1 52.4 1.0
OD2 Z:ASP171 2.2 52.5 1.0
O Z:HOH533 2.2 57.2 1.0
OP3 B:DC1 2.5 59.8 1.0
P B:DC1 2.8 61.4 1.0
CG Z:ASP173 3.0 53.9 1.0
CB Z:ASP173 3.1 49.9 1.0
CG Z:ASP171 3.2 51.5 1.0
CG Z:ASP152 3.3 44.5 1.0
OD1 Z:ASP171 3.5 48.2 1.0
O5' B:DC1 3.6 74.3 1.0
MN Z:MN402 3.9 48.3 1.0
OD1 Z:ASP152 3.9 51.6 1.0
O Z:HOH513 3.9 48.3 1.0
N Z:GLY2 4.0 64.4 1.0
OP2 B:DC1 4.1 63.7 1.0
OE1 Z:GLU150 4.2 60.8 1.0
OD1 Z:ASP173 4.2 58.3 1.0
O Z:HOH564 4.2 56.4 1.0
C5' B:DC1 4.3 76.9 1.0
CB Z:ASP152 4.4 42.9 1.0
CB Z:ASP171 4.5 48.3 1.0
CA Z:ASP173 4.6 50.7 1.0
CA Z:GLY2 4.6 57.9 1.0
NZ Z:LYS85 4.8 66.2 1.0
O Z:HOH550 4.8 61.5 1.0
O Z:HOH512 5.0 56.0 1.0
CE2 Z:PHE177 5.0 46.3 1.0

Manganese binding site 2 out of 6 in 5v0a

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Manganese binding site 2 out of 6 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)


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 (Rviii) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn402

b:48.3
occ:1.00
 OP3 B:DC1 2.1 59.8 1.0
O Z:HOH521 2.2 51.3 1.0
O3' B:DA102 2.2 85.8 1.0
O Z:HOH513 2.2 48.3 1.0
OD1 Z:ASP152 2.2 51.6 1.0
O Z:HOH512 2.2 56.0 1.0
CG Z:ASP152 3.1 44.5 1.0
C3' B:DA102 3.3 84.5 1.0
OD2 Z:ASP152 3.3 45.2 1.0
P B:DC1 3.5 61.4 1.0
OD2 Z:ASP171 3.8 52.5 1.0
MN Z:MN401 3.9 50.1 1.0
OD1 Z:ASP78 3.9 48.7 1.0
O5' B:DC1 3.9 74.3 1.0
OE1 Z:GLU150 4.1 60.8 1.0
NZ Z:LYS85 4.1 66.2 1.0
OP2 B:DC1 4.2 63.7 1.0
C4' B:DA102 4.2 97.5 1.0
OD2 Z:ASP30 4.2 49.7 1.0
OD2 Z:ASP78 4.3 54.4 1.0
C2' B:DA102 4.4 80.0 1.0
N Z:ASP152 4.5 42.8 1.0
OD1 Z:ASP30 4.5 54.4 1.0
OP1 B:DC1 4.5 61.9 1.0
CB Z:ASP152 4.5 42.9 1.0
CG Z:ASP78 4.6 52.1 1.0
CG Z:ASP30 4.8 49.9 1.0
O Z:HOH533 4.8 57.2 1.0
CA Z:ASP152 5.0 45.4 1.0
CG Z:ASP171 5.0 51.5 1.0

Manganese binding site 3 out of 6 in 5v0a

Go back to Manganese Binding Sites List in 5v0a
Manganese binding site 3 out of 6 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)


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 (Rviii) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn403

b:76.6
occ:1.00
 O Z:HOH577 2.2 60.4 1.0
SG Z:CYS80 2.5 64.6 1.0
CD1 Z:ILE325 3.3 51.4 1.0
CB Z:CYS80 3.8 61.1 1.0
CZ Z:PHE335 3.9 54.9 1.0
CE1 Z:PHE335 4.0 57.9 1.0
CG1 Z:VAL317 4.5 58.9 1.0
CG2 Z:VAL317 4.6 58.3 1.0
O Z:PRO148 4.7 52.6 1.0
OH Z:TYR149 4.7 55.2 1.0
CG1 Z:ILE325 4.8 56.3 1.0

Manganese binding site 4 out of 6 in 5v0a

Go back to Manganese Binding Sites List in 5v0a
Manganese binding site 4 out of 6 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)


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 (Rviii) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn404

b:0.7
occ:1.00
 OD2 Z:ASP303 2.2 89.7 1.0
CG Z:ASP303 3.3 90.1 1.0
OE2 Z:GLU302 3.4 93.5 1.0
CD Z:GLU302 4.0 93.2 1.0
N Z:ASP303 4.1 84.5 1.0
OD1 Z:ASP303 4.2 90.2 1.0
CB Z:ASP303 4.2 91.3 1.0
OE1 Z:GLU302 4.4 98.2 1.0
CB Z:GLU302 4.6 87.6 1.0
CA Z:ASP303 4.8 88.2 1.0
CA Z:GLU302 4.9 83.5 1.0
CG Z:GLU302 4.9 88.0 1.0
O Z:HOH511 5.0 68.7 1.0
C Z:GLU302 5.0 87.0 1.0

Manganese binding site 5 out of 6 in 5v0a

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Manganese binding site 5 out of 6 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)


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 (Rviii) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn101

b:98.7
occ:1.00
 O2 A:DC11 2.4 91.3 1.0
C2 A:DC11 3.4 89.3 1.0
OE1 Z:GLU44 3.5 98.1 1.0
N3 A:DC11 3.6 93.1 1.0
O Z:ALA41 3.7 74.8 1.0
O Z:ILE40 4.2 69.7 1.0
C Z:ALA41 4.3 72.9 1.0
CA Z:ALA41 4.4 70.8 1.0
CD Z:GLU44 4.5 94.3 1.0
N1 A:DC11 4.6 85.6 1.0
OE2 Z:GLU44 4.7 94.7 1.0
O4' A:DA12 4.9 92.9 1.0
C4 A:DC11 5.0 93.0 1.0

Manganese binding site 6 out of 6 in 5v0a

Go back to Manganese Binding Sites List in 5v0a
Manganese binding site 6 out of 6 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rviii) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn101

b:0.5
occ:1.00
 O6 B:DG7 2.4 97.8 1.0
C6 B:DG7 3.6 97.0 1.0
N4 A:DC3 3.9 0.1 1.0
O6 A:DG2 4.0 0.3 1.0
N7 B:DG7 4.1 0.4 1.0
O A:HOH207 4.2 98.4 1.0
C5 B:DG7 4.2 0.3 1.0
N7 B:DA6 4.2 0.4 1.0
N1 B:DG7 4.7 93.1 1.0
C8 B:DA6 4.9 0.1 1.0
N6 B:DA6 4.9 93.9 1.0
C6 A:DG2 5.0 0.5 1.0

Reference:

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
Page generated: Sun Oct 6 03:07:14 2024

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