Manganese in PDB 1s8e: Crystal Structure of MRE11-3
Protein crystallography data
The structure of Crystal Structure of MRE11-3, PDB code: 1s8e
was solved by
K.P.Hopfner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
12.00 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.960,
88.570,
144.990,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.1 /
27.8
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of MRE11-3
(pdb code 1s8e). 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 MRE11-3, PDB code: 1s8e:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1s8e
Go back to
Manganese Binding Sites List in 1s8e
Manganese binding site 1 out
of 4 in the Crystal Structure of MRE11-3
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 MRE11-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:42.9
occ:1.00
|
OD1
|
A:ASN84
|
2.3
|
51.4
|
1.0
|
OD1
|
A:ASP49
|
2.3
|
31.5
|
1.0
|
O
|
A:HOH630
|
2.3
|
34.7
|
1.0
|
NE2
|
A:HIS173
|
2.4
|
45.5
|
1.0
|
ND1
|
A:HIS206
|
2.4
|
53.8
|
1.0
|
O
|
A:HOH602
|
2.7
|
41.6
|
1.0
|
CE1
|
A:HIS206
|
3.1
|
53.0
|
1.0
|
CG
|
A:ASP49
|
3.2
|
35.3
|
1.0
|
CG
|
A:ASN84
|
3.3
|
53.7
|
1.0
|
CE1
|
A:HIS173
|
3.3
|
47.5
|
1.0
|
MN
|
A:MN402
|
3.3
|
44.3
|
1.0
|
CD2
|
A:HIS173
|
3.4
|
43.1
|
1.0
|
OD2
|
A:ASP49
|
3.4
|
35.7
|
1.0
|
CG
|
A:HIS206
|
3.6
|
53.1
|
1.0
|
ND2
|
A:ASN84
|
3.7
|
52.6
|
1.0
|
OD1
|
A:ASP8
|
4.0
|
41.5
|
1.0
|
CA
|
A:HIS206
|
4.0
|
50.6
|
1.0
|
CB
|
A:HIS206
|
4.1
|
51.5
|
1.0
|
NE2
|
A:HIS206
|
4.4
|
55.7
|
1.0
|
O
|
A:HIS206
|
4.4
|
53.6
|
1.0
|
CB
|
A:ASP49
|
4.4
|
34.0
|
1.0
|
ND1
|
A:HIS173
|
4.4
|
46.5
|
1.0
|
N
|
A:ASN84
|
4.5
|
48.6
|
1.0
|
CG
|
A:HIS173
|
4.5
|
44.4
|
1.0
|
CD2
|
A:HIS206
|
4.6
|
53.5
|
1.0
|
CB
|
A:ASN84
|
4.6
|
51.0
|
1.0
|
C
|
A:HIS206
|
4.7
|
51.3
|
1.0
|
N
|
A:HIS206
|
5.0
|
46.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1s8e
Go back to
Manganese Binding Sites List in 1s8e
Manganese binding site 2 out
of 4 in the Crystal Structure of MRE11-3
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 MRE11-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:44.3
occ:1.00
|
OD1
|
A:ASP8
|
2.1
|
41.5
|
1.0
|
OD1
|
A:ASP49
|
2.2
|
31.5
|
1.0
|
NE2
|
A:HIS10
|
2.3
|
38.4
|
1.0
|
O
|
A:HOH630
|
2.3
|
34.7
|
1.0
|
NE2
|
A:HIS208
|
2.4
|
46.7
|
1.0
|
CE1
|
A:HIS10
|
2.9
|
38.4
|
1.0
|
O
|
A:HOH602
|
2.9
|
41.6
|
1.0
|
CG
|
A:ASP8
|
3.2
|
42.1
|
1.0
|
CG
|
A:ASP49
|
3.2
|
35.3
|
1.0
|
MN
|
A:MN401
|
3.3
|
42.9
|
1.0
|
CE1
|
A:HIS208
|
3.4
|
45.7
|
1.0
|
CD2
|
A:HIS208
|
3.4
|
47.8
|
1.0
|
CD2
|
A:HIS10
|
3.5
|
37.8
|
1.0
|
CB
|
A:ASP49
|
3.6
|
34.0
|
1.0
|
CB
|
A:ASP8
|
3.7
|
36.9
|
1.0
|
ND1
|
A:HIS10
|
4.1
|
41.0
|
1.0
|
OD2
|
A:ASP8
|
4.2
|
39.7
|
1.0
|
O
|
A:HIS206
|
4.2
|
53.6
|
1.0
|
CA
|
A:ASP8
|
4.3
|
37.5
|
1.0
|
OD2
|
A:ASP49
|
4.3
|
35.7
|
1.0
|
CE1
|
A:HIS173
|
4.5
|
47.5
|
1.0
|
CG
|
A:HIS10
|
4.5
|
39.1
|
1.0
|
ND1
|
A:HIS208
|
4.5
|
47.7
|
1.0
|
NE2
|
A:HIS173
|
4.5
|
45.5
|
1.0
|
CG
|
A:HIS208
|
4.6
|
46.5
|
1.0
|
CA
|
A:HIS206
|
4.7
|
50.6
|
1.0
|
C
|
A:HIS206
|
4.8
|
51.3
|
1.0
|
ND1
|
A:HIS206
|
5.0
|
53.8
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1s8e
Go back to
Manganese Binding Sites List in 1s8e
Manganese binding site 3 out
of 4 in the Crystal Structure of MRE11-3
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 MRE11-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn403
b:41.5
occ:1.00
|
OD2
|
B:ASP49
|
2.1
|
37.5
|
1.0
|
OD1
|
B:ASP8
|
2.2
|
39.1
|
1.0
|
NE2
|
B:HIS10
|
2.3
|
42.5
|
1.0
|
NE2
|
B:HIS208
|
2.3
|
35.5
|
1.0
|
O
|
B:HOH605
|
2.4
|
35.6
|
1.0
|
CE1
|
B:HIS10
|
3.0
|
37.7
|
1.0
|
CE1
|
B:HIS208
|
3.1
|
39.1
|
1.0
|
CG
|
B:ASP8
|
3.2
|
37.9
|
1.0
|
CG
|
B:ASP49
|
3.2
|
40.7
|
1.0
|
O
|
B:HOH601
|
3.3
|
37.8
|
1.0
|
MN
|
B:MN404
|
3.3
|
42.1
|
1.0
|
CD2
|
B:HIS208
|
3.4
|
38.7
|
1.0
|
CD2
|
B:HIS10
|
3.5
|
38.2
|
1.0
|
CB
|
B:ASP49
|
3.7
|
36.9
|
1.0
|
CB
|
B:ASP8
|
3.7
|
31.9
|
1.0
|
OD2
|
B:ASP8
|
4.2
|
36.0
|
1.0
|
ND1
|
B:HIS10
|
4.2
|
38.9
|
1.0
|
CA
|
B:ASP8
|
4.3
|
35.6
|
1.0
|
ND1
|
B:HIS208
|
4.3
|
38.4
|
1.0
|
OD1
|
B:ASP49
|
4.3
|
40.1
|
1.0
|
O
|
B:HIS206
|
4.4
|
41.2
|
1.0
|
CE1
|
B:HIS173
|
4.4
|
36.0
|
1.0
|
CG
|
B:HIS208
|
4.5
|
37.6
|
1.0
|
CG
|
B:HIS10
|
4.5
|
39.2
|
1.0
|
NE2
|
B:HIS173
|
4.5
|
36.2
|
1.0
|
CA
|
B:HIS206
|
4.8
|
43.6
|
1.0
|
C
|
B:HIS206
|
4.9
|
41.3
|
1.0
|
CD2
|
B:HIS206
|
5.0
|
50.7
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1s8e
Go back to
Manganese Binding Sites List in 1s8e
Manganese binding site 4 out
of 4 in the Crystal Structure of MRE11-3
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 MRE11-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn404
b:42.1
occ:1.00
|
O
|
B:HOH605
|
2.2
|
35.6
|
1.0
|
NE2
|
B:HIS173
|
2.3
|
36.2
|
1.0
|
OD1
|
B:ASN84
|
2.3
|
46.2
|
1.0
|
CD2
|
B:HIS206
|
2.4
|
50.7
|
1.0
|
OD2
|
B:ASP49
|
2.4
|
37.5
|
1.0
|
O
|
B:HOH601
|
2.5
|
37.8
|
1.0
|
NE2
|
B:HIS206
|
3.1
|
52.1
|
1.0
|
CE1
|
B:HIS173
|
3.1
|
36.0
|
1.0
|
CG
|
B:ASP49
|
3.1
|
40.7
|
1.0
|
CG
|
B:ASN84
|
3.2
|
45.8
|
1.0
|
OD1
|
B:ASP49
|
3.3
|
40.1
|
1.0
|
MN
|
B:MN403
|
3.3
|
41.5
|
1.0
|
CD2
|
B:HIS173
|
3.3
|
38.1
|
1.0
|
ND2
|
B:ASN84
|
3.4
|
40.6
|
1.0
|
CG
|
B:HIS206
|
3.5
|
51.0
|
1.0
|
OD1
|
B:ASP8
|
4.0
|
39.1
|
1.0
|
CA
|
B:HIS206
|
4.1
|
43.6
|
1.0
|
CB
|
B:HIS206
|
4.2
|
47.1
|
1.0
|
ND1
|
B:HIS173
|
4.3
|
37.3
|
1.0
|
CE1
|
B:HIS206
|
4.3
|
54.4
|
1.0
|
CG
|
B:HIS173
|
4.4
|
38.4
|
1.0
|
CB
|
B:ASP49
|
4.4
|
36.9
|
1.0
|
O
|
B:HIS206
|
4.5
|
41.2
|
1.0
|
ND1
|
B:HIS206
|
4.5
|
52.7
|
1.0
|
N
|
B:ASN84
|
4.6
|
46.4
|
1.0
|
CB
|
B:ASN84
|
4.6
|
46.0
|
1.0
|
C
|
B:HIS206
|
4.8
|
41.3
|
1.0
|
|
Reference:
L.M.Arthur,
K.Gustausson,
K.P.Hopfner,
C.T.Carson,
T.H.Stracker,
A.Karcher,
D.Felton,
M.D.Weitzman,
J.A.Tainer,
J.P.Carney.
Structural and Functional Analysis of MRE11-3 Nucleic Acids Res. V. 32 1886 2004.
ISSN: ISSN 0305-1048
PubMed: 15047855
DOI: 10.1093/NAR/GKH343
Page generated: Sat Oct 5 12:23:40 2024
|