Manganese in PDB 7mxx: Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)

Protein crystallography data

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4), PDB code: 7mxx 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) 32.45 / 2.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.885, 70.885, 182.462, 90, 90, 90
R / Rfree (%) 25.8 / 29.8

Other elements in 7mxx:

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4) (pdb code 7mxx). 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 (R92A) in Complex with 5' Flap Dna (UF4), PDB code: 7mxx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7mxx

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Manganese binding site 1 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn401

b:69.6
occ:1.00
OP1 B:DT1 2.0 169.2 1.0
OP2 B:DT1 2.1 170.0 1.0
OD1 Z:ASP173 2.2 75.8 1.0
OD1 Z:ASP152 2.2 66.2 1.0
OD2 Z:ASP171 2.2 77.2 1.0
P B:DT1 2.3 170.6 1.0
CG Z:ASP173 3.1 75.6 1.0
CG Z:ASP171 3.2 76.3 1.0
CG Z:ASP152 3.3 66.3 1.0
MN Z:MN403 3.3 98.3 1.0
OP3 B:DT1 3.3 170.7 1.0
CB Z:ASP173 3.4 74.7 1.0
MN Z:MN402 3.6 64.6 1.0
O5' B:DT1 3.6 174.2 1.0
OD1 Z:ASP171 3.6 76.9 1.0
OD2 Z:ASP152 3.8 66.0 1.0
C5' B:DT1 4.0 174.9 1.0
OE1 Z:GLU150 4.1 70.9 1.0
O B:HOH101 4.1 88.7 1.0
OD1 Z:ASP225 4.1 83.0 1.0
OD2 Z:ASP173 4.3 76.2 1.0
CB Z:ASP152 4.5 66.7 1.0
CB Z:ASP171 4.5 74.5 1.0
CD Z:GLU150 4.5 70.9 1.0
CG Z:ASP225 4.6 81.7 1.0
N Z:GLY2 4.7 90.2 1.0
O B:HOH104 4.8 82.8 1.0
O B:HOH103 4.8 96.8 1.0
CA Z:ASP173 4.8 73.7 1.0
OD2 Z:ASP225 4.8 80.2 1.0

Manganese binding site 2 out of 4 in 7mxx

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Manganese binding site 2 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn402

b:64.6
occ:1.00
OD2 Z:ASP152 2.1 66.0 1.0
O B:HOH101 2.2 88.7 1.0
O B:HOH103 2.2 96.8 1.0
O B:HOH104 2.2 82.8 1.0
O Z:HOH517 2.3 71.8 1.0
OP1 B:DT1 2.3 169.2 1.0
CG Z:ASP152 3.0 66.3 1.0
OD1 Z:ASP152 3.2 66.2 1.0
OP3 B:DT1 3.5 170.7 1.0
P B:DT1 3.5 170.6 1.0
MN Z:MN401 3.6 69.6 1.0
OD2 Z:ASP171 4.0 77.2 1.0
CG Z:GLU150 4.0 70.1 1.0
OD1 Z:ASP78 4.0 63.8 1.0
OD2 Z:ASP78 4.2 67.5 1.0
N Z:ASP152 4.4 66.8 1.0
CB Z:ASP152 4.4 66.7 1.0
OE1 Z:GLU150 4.5 70.9 1.0
O5' B:DT1 4.5 174.2 1.0
CG Z:ASP78 4.5 66.7 1.0
OP2 B:DT1 4.6 170.0 1.0
CD Z:GLU150 4.6 70.9 1.0
OD2 Z:ASP30 4.7 72.1 1.0
OD1 Z:ASP30 4.8 71.1 1.0
N Z:ALA151 4.8 66.9 1.0
CA Z:ASP152 4.9 66.2 1.0
CG Z:ASP171 4.9 76.3 1.0

Manganese binding site 3 out of 4 in 7mxx

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Manganese binding site 3 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn403

b:98.3
occ:1.00
OP2 B:DT1 2.0 170.0 1.0
OD2 Z:ASP225 2.1 80.2 1.0
OP2 B:DC2 2.2 177.1 1.0
OD1 Z:ASP173 2.2 75.8 1.0
OD1 Z:ASP225 2.2 83.0 1.0
N Z:GLY2 2.2 90.2 1.0
CG Z:ASP225 2.4 81.7 1.0
CG Z:ASP173 3.1 75.6 1.0
P B:DT1 3.2 170.6 1.0
MN Z:MN401 3.3 69.6 1.0
OD2 Z:ASP173 3.4 76.2 1.0
O5' B:DT1 3.4 174.2 1.0
P B:DC2 3.5 180.6 1.0
C5' B:DT1 3.5 174.9 1.0
CA Z:GLY2 3.6 89.7 1.0
OD1 Z:ASP171 3.8 76.9 1.0
CB Z:ASP225 3.9 82.0 1.0
OP1 B:DC2 4.0 181.1 1.0
OP1 B:DT1 4.1 169.2 1.0
O3' B:DT1 4.2 181.4 1.0
OD2 Z:ASP171 4.3 77.2 1.0
OP3 B:DT1 4.3 170.7 1.0
C3' B:DT1 4.4 181.2 1.0
C Z:GLY2 4.4 92.1 1.0
C4' B:DT1 4.4 178.8 1.0
CG Z:ASP171 4.5 76.3 1.0
CB Z:ASP173 4.5 74.7 1.0
O Z:GLY2 4.6 95.2 1.0
O5' B:DC2 4.6 184.6 1.0
N Z:ASP225 4.7 79.1 1.0
CA Z:ASP225 4.8 79.3 1.0

Manganese binding site 4 out of 4 in 7mxx

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Manganese binding site 4 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mn404

b:80.2
occ:1.00
SG Z:CYS80 2.3 70.0 1.0
CB Z:CYS80 3.2 71.4 1.0
CD1 Z:ILE325 3.9 74.5 1.0
O Z:PRO148 4.1 65.9 1.0
OH Z:TYR149 4.4 74.0 1.0
CZ Z:TYR149 4.5 72.2 1.0
CG1 Z:VAL317 4.6 79.8 1.0
CE1 Z:TYR149 4.6 71.8 1.0
CA Z:CYS80 4.7 73.2 1.0
CZ Z:PHE335 4.7 74.9 1.0
CE1 Z:PHE335 4.8 76.9 1.0
N Z:CYS80 5.0 69.7 1.0

Reference:

Y.Shi, H.W.Hellinga, L.S.Beese. Structures of Reaction Intermediates Reveal Transient MG2+-Binding Events That Dynamically Coordinate Human Exonuclease I Activities To Be Published.
Page generated: Fri Jul 28 02:04:12 2023

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