Manganese in PDB 7mxu: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)
Protein crystallography data
The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2), PDB code: 7mxu
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)
|
38.73 /
3.04
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.169,
73.169,
182.621,
90,
90,
90
|
R / Rfree (%)
|
23 /
26.9
|
Other elements in 7mxu:
The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)
(pdb code 7mxu). 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 Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2), PDB code: 7mxu:
Jump to Manganese binding site number:
1;
2;
3;
Manganese binding site 1 out
of 3 in 7mxu
Go back to
Manganese Binding Sites List in 7mxu
Manganese binding site 1 out
of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)
 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 (Wt) in Complex with 5' Flap Dna (CF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mn401
b:78.2
occ:1.00
|
O
|
B:HOH101
|
2.1
|
89.2
|
1.0
|
O
|
Z:HOH524
|
2.2
|
87.9
|
1.0
|
OP1
|
B:DC1
|
2.2
|
118.2
|
1.0
|
O
|
Z:HOH527
|
2.2
|
74.6
|
1.0
|
O
|
Z:HOH511
|
2.2
|
80.8
|
1.0
|
OD1
|
Z:ASP152
|
2.2
|
70.0
|
1.0
|
CG
|
Z:ASP152
|
3.1
|
70.7
|
1.0
|
OD2
|
Z:ASP152
|
3.3
|
72.0
|
1.0
|
P
|
B:DC1
|
3.4
|
119.1
|
1.0
|
OP3
|
B:DC1
|
3.6
|
122.0
|
1.0
|
MN
|
Z:MN402
|
3.6
|
65.9
|
1.0
|
OD2
|
Z:ASP30
|
4.1
|
74.2
|
1.0
|
OD2
|
Z:ASP171
|
4.1
|
77.0
|
1.0
|
O5'
|
B:DC1
|
4.2
|
123.4
|
1.0
|
OD1
|
Z:ASP78
|
4.2
|
75.6
|
1.0
|
OD2
|
Z:ASP78
|
4.3
|
77.4
|
1.0
|
N
|
Z:ASP152
|
4.5
|
69.3
|
1.0
|
CB
|
Z:ASP152
|
4.5
|
70.7
|
1.0
|
C5'
|
B:DC1
|
4.6
|
129.3
|
1.0
|
OP2
|
B:DC1
|
4.6
|
114.6
|
1.0
|
CG
|
Z:ASP78
|
4.7
|
77.1
|
1.0
|
OD1
|
Z:ASP30
|
4.8
|
75.4
|
1.0
|
N
|
Z:ALA151
|
4.8
|
74.0
|
1.0
|
CG
|
Z:ASP30
|
4.9
|
75.6
|
1.0
|
OE1
|
Z:GLU150
|
4.9
|
80.0
|
1.0
|
CA
|
Z:ASP152
|
5.0
|
69.5
|
1.0
|
|
Manganese binding site 2 out
of 3 in 7mxu
Go back to
Manganese Binding Sites List in 7mxu
Manganese binding site 2 out
of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)
 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 (Wt) in Complex with 5' Flap Dna (CF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mn402
b:65.9
occ:1.00
|
OP1
|
B:DC1
|
2.0
|
118.2
|
1.0
|
OD2
|
Z:ASP171
|
2.1
|
77.0
|
1.0
|
OD2
|
Z:ASP152
|
2.2
|
72.0
|
1.0
|
OD1
|
Z:ASP173
|
2.2
|
78.5
|
1.0
|
OP2
|
B:DC1
|
2.5
|
114.6
|
1.0
|
P
|
B:DC1
|
2.6
|
119.1
|
1.0
|
CG
|
Z:ASP173
|
3.1
|
78.5
|
1.0
|
MN
|
Z:MN403
|
3.2
|
94.2
|
1.0
|
CG
|
Z:ASP171
|
3.3
|
77.7
|
1.0
|
CG
|
Z:ASP152
|
3.3
|
70.7
|
1.0
|
CB
|
Z:ASP173
|
3.4
|
76.1
|
1.0
|
MN
|
Z:MN401
|
3.6
|
78.2
|
1.0
|
O5'
|
B:DC1
|
3.7
|
123.4
|
1.0
|
O
|
Z:HOH511
|
3.7
|
80.8
|
1.0
|
O
|
Z:HOH529
|
3.7
|
85.5
|
1.0
|
OP3
|
B:DC1
|
3.8
|
122.0
|
1.0
|
OD1
|
Z:ASP152
|
3.8
|
70.0
|
1.0
|
OD1
|
Z:ASP171
|
3.8
|
79.8
|
1.0
|
OD1
|
Z:ASP225
|
4.0
|
89.2
|
1.0
|
OD2
|
Z:ASP173
|
4.2
|
81.0
|
1.0
|
OE1
|
Z:GLU150
|
4.4
|
80.0
|
1.0
|
CB
|
Z:ASP171
|
4.5
|
76.6
|
1.0
|
CB
|
Z:ASP152
|
4.5
|
70.7
|
1.0
|
N
|
Z:GLY2
|
4.6
|
87.7
|
1.0
|
CA
|
Z:ASP173
|
4.8
|
76.5
|
1.0
|
O
|
B:HOH101
|
4.9
|
89.2
|
1.0
|
C5'
|
B:DC1
|
4.9
|
129.3
|
1.0
|
O
|
Z:HOH524
|
5.0
|
87.9
|
1.0
|
|
Manganese binding site 3 out
of 3 in 7mxu
Go back to
Manganese Binding Sites List in 7mxu
Manganese binding site 3 out
of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)
 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 (Wt) in Complex with 5' Flap Dna (CF2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mn403
b:94.2
occ:1.00
|
OP2
|
B:DC1
|
2.0
|
114.6
|
1.0
|
N
|
Z:GLY2
|
2.2
|
87.7
|
1.0
|
OD1
|
Z:ASP173
|
2.2
|
78.5
|
1.0
|
OD1
|
Z:ASP225
|
2.3
|
89.2
|
1.0
|
CA
|
Z:GLY2
|
2.6
|
89.8
|
1.0
|
MN
|
Z:MN402
|
3.2
|
65.9
|
1.0
|
P
|
B:DC1
|
3.2
|
119.1
|
1.0
|
CG
|
Z:ASP173
|
3.2
|
78.5
|
1.0
|
CG
|
Z:ASP225
|
3.4
|
90.9
|
1.0
|
OD1
|
Z:ASP171
|
3.5
|
79.8
|
1.0
|
O5'
|
B:DC1
|
3.5
|
123.4
|
1.0
|
OD2
|
Z:ASP173
|
3.6
|
81.0
|
1.0
|
OD2
|
Z:ASP171
|
3.7
|
77.0
|
1.0
|
OD2
|
Z:ASP225
|
3.8
|
92.2
|
1.0
|
CG
|
Z:ASP171
|
3.9
|
77.7
|
1.0
|
OP1
|
B:DC1
|
4.0
|
118.2
|
1.0
|
C
|
Z:GLY2
|
4.1
|
93.4
|
1.0
|
OP3
|
B:DC1
|
4.4
|
122.0
|
1.0
|
OP2
|
B:DG2
|
4.4
|
122.0
|
1.0
|
O
|
Z:HOH528
|
4.5
|
81.8
|
1.0
|
CB
|
Z:ASP173
|
4.6
|
76.1
|
1.0
|
CB
|
Z:ASP225
|
4.7
|
91.9
|
1.0
|
OP1
|
B:DG2
|
4.7
|
125.0
|
1.0
|
C3'
|
B:DC1
|
4.8
|
129.4
|
1.0
|
C5'
|
B:DC1
|
4.8
|
129.3
|
1.0
|
O
|
Z:GLY2
|
4.8
|
97.9
|
1.0
|
O
|
Z:HOH529
|
4.8
|
85.5
|
1.0
|
N
|
Z:ILE3
|
4.8
|
87.2
|
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: Sun Oct 6 10:13:09 2024
|