Manganese in PDB 7me2: Yfea Oligomer Crystal 2, Form 2
Protein crystallography data
The structure of Yfea Oligomer Crystal 2, Form 2, PDB code: 7me2
was solved by
C.D.Radka,
S.G.Aller,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.51 /
1.85
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.31,
76.43,
107.36,
90,
90,
90
|
R / Rfree (%)
|
15.2 /
18.4
|
Other elements in 7me2:
The structure of Yfea Oligomer Crystal 2, Form 2 also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Yfea Oligomer Crystal 2, Form 2
(pdb code 7me2). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the
Yfea Oligomer Crystal 2, Form 2, PDB code: 7me2:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
Manganese binding site 1 out
of 7 in 7me2
Go back to
Manganese Binding Sites List in 7me2
Manganese binding site 1 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_01.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn403
b:3.5
occ:0.46
|
FE
|
A:FE401
|
0.5
|
4.1
|
0.3
|
ZN
|
A:ZN402
|
0.6
|
4.4
|
0.3
|
NE2
|
A:HIS76
|
1.8
|
10.0
|
1.0
|
NE2
|
A:HIS141
|
2.1
|
10.6
|
1.0
|
OD2
|
A:ASP282
|
2.2
|
17.9
|
1.0
|
OE1
|
A:GLU207
|
2.3
|
10.9
|
1.0
|
CE1
|
A:HIS76
|
2.7
|
11.4
|
1.0
|
OD1
|
A:ASP282
|
2.7
|
11.7
|
1.0
|
OE2
|
A:GLU207
|
2.7
|
10.1
|
1.0
|
CG
|
A:ASP282
|
2.8
|
13.7
|
1.0
|
CD
|
A:GLU207
|
2.8
|
11.2
|
1.0
|
CD2
|
A:HIS76
|
3.0
|
8.4
|
1.0
|
CE1
|
A:HIS141
|
3.0
|
8.0
|
1.0
|
CD2
|
A:HIS141
|
3.1
|
8.1
|
1.0
|
ND1
|
A:HIS76
|
3.8
|
10.2
|
1.0
|
CG
|
A:HIS76
|
4.0
|
8.7
|
1.0
|
ND2
|
A:ASN228
|
4.0
|
18.2
|
1.0
|
ND1
|
A:HIS141
|
4.2
|
7.6
|
1.0
|
CG
|
A:HIS141
|
4.2
|
8.6
|
1.0
|
CB
|
A:ASP282
|
4.3
|
10.0
|
1.0
|
CG
|
A:ASN228
|
4.3
|
16.2
|
1.0
|
CG
|
A:GLU207
|
4.4
|
8.3
|
1.0
|
CB
|
A:ALA209
|
4.5
|
8.1
|
1.0
|
O
|
A:HOH681
|
4.6
|
23.1
|
1.0
|
O
|
A:HOH555
|
4.6
|
12.2
|
1.0
|
OD1
|
A:ASN228
|
4.7
|
15.1
|
1.0
|
CB
|
A:ASN228
|
4.8
|
10.6
|
1.0
|
CD1
|
A:LEU101
|
4.9
|
13.1
|
1.0
|
|
Manganese binding site 2 out
of 7 in 7me2
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Manganese Binding Sites List in 7me2
Manganese binding site 2 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_02.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn404
b:36.9
occ:0.45
|
O
|
A:HOH718
|
1.9
|
44.1
|
1.0
|
O
|
A:HOH730
|
2.1
|
39.6
|
1.0
|
O
|
A:HOH556
|
2.3
|
38.0
|
1.0
|
OE2
|
A:GLU287
|
2.6
|
79.6
|
1.0
|
CD
|
A:GLU287
|
3.4
|
82.4
|
1.0
|
CG
|
A:GLU287
|
3.6
|
58.4
|
1.0
|
O
|
A:HOH676
|
3.9
|
41.3
|
1.0
|
O
|
A:HOH777
|
4.2
|
42.4
|
1.0
|
OD1
|
A:ASP53
|
4.3
|
18.4
|
1.0
|
OE1
|
A:GLN52
|
4.4
|
17.1
|
1.0
|
O
|
A:HOH797
|
4.5
|
39.7
|
1.0
|
OE1
|
A:GLU287
|
4.5
|
72.9
|
1.0
|
O
|
A:HOH587
|
4.6
|
35.8
|
1.0
|
O
|
A:PRO292
|
4.6
|
15.6
|
1.0
|
NE2
|
A:GLN52
|
4.7
|
22.8
|
1.0
|
CD
|
A:GLN52
|
5.0
|
21.3
|
1.0
|
|
Manganese binding site 3 out
of 7 in 7me2
Go back to
Manganese Binding Sites List in 7me2
Manganese binding site 3 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_03.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn403
b:5.3
occ:0.30
|
FE
|
B:FE401
|
0.4
|
6.0
|
0.3
|
ZN
|
B:ZN402
|
0.6
|
6.3
|
0.4
|
NE2
|
B:HIS76
|
1.9
|
10.2
|
1.0
|
NE2
|
B:HIS141
|
2.0
|
8.8
|
1.0
|
OD2
|
B:ASP282
|
2.1
|
15.3
|
1.0
|
OE1
|
B:GLU207
|
2.4
|
9.7
|
1.0
|
OD1
|
B:ASP282
|
2.6
|
12.5
|
1.0
|
CG
|
B:ASP282
|
2.7
|
14.9
|
1.0
|
CE1
|
B:HIS76
|
2.8
|
11.8
|
1.0
|
OE2
|
B:GLU207
|
2.9
|
9.5
|
1.0
|
CD2
|
B:HIS141
|
3.0
|
8.1
|
1.0
|
CD2
|
B:HIS76
|
3.0
|
10.0
|
1.0
|
CE1
|
B:HIS141
|
3.0
|
8.6
|
1.0
|
CD
|
B:GLU207
|
3.0
|
9.3
|
1.0
|
ND1
|
B:HIS76
|
4.0
|
8.9
|
1.0
|
CG
|
B:HIS76
|
4.1
|
9.1
|
1.0
|
ND1
|
B:HIS141
|
4.1
|
8.5
|
1.0
|
ND2
|
B:ASN228
|
4.1
|
18.2
|
1.0
|
CG
|
B:HIS141
|
4.1
|
9.2
|
1.0
|
CB
|
B:ASP282
|
4.2
|
10.0
|
1.0
|
CB
|
B:ALA209
|
4.5
|
9.6
|
1.0
|
O
|
B:HOH533
|
4.5
|
13.9
|
1.0
|
CG
|
B:ASN228
|
4.5
|
21.4
|
1.0
|
CG
|
B:GLU207
|
4.5
|
11.4
|
1.0
|
CD1
|
B:LEU101
|
4.7
|
13.9
|
1.0
|
O
|
B:HOH647
|
4.7
|
23.2
|
1.0
|
CB
|
B:ASN228
|
5.0
|
15.2
|
1.0
|
CD1
|
B:ILE75
|
5.0
|
10.3
|
1.0
|
OD1
|
B:ASN228
|
5.0
|
17.6
|
1.0
|
|
Manganese binding site 4 out
of 7 in 7me2
Go back to
Manganese Binding Sites List in 7me2
Manganese binding site 4 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_04.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn404
b:98.8
occ:0.91
|
OE2
|
B:GLU287
|
2.9
|
75.2
|
1.0
|
O
|
B:HOH664
|
3.6
|
30.0
|
1.0
|
CG
|
B:GLU287
|
3.7
|
57.6
|
1.0
|
CD
|
B:GLU287
|
3.7
|
79.8
|
1.0
|
OE1
|
B:GLN52
|
3.8
|
18.9
|
1.0
|
NE2
|
B:GLN52
|
4.1
|
18.9
|
1.0
|
OD1
|
B:ASP53
|
4.3
|
18.6
|
1.0
|
CD
|
B:GLN52
|
4.4
|
23.1
|
1.0
|
O
|
B:PRO292
|
4.7
|
16.4
|
1.0
|
O
|
B:HOH553
|
4.9
|
30.7
|
1.0
|
OE1
|
B:GLU287
|
4.9
|
76.7
|
1.0
|
O
|
B:HOH721
|
5.0
|
41.9
|
1.0
|
|
Manganese binding site 5 out
of 7 in 7me2
Go back to
Manganese Binding Sites List in 7me2
Manganese binding site 5 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_05.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn405
b:21.5
occ:0.55
|
ZN
|
B:ZN406
|
0.4
|
21.7
|
0.5
|
ND1
|
B:HIS163
|
2.1
|
21.4
|
1.0
|
CE1
|
B:HIS163
|
3.0
|
28.2
|
1.0
|
CG
|
B:HIS163
|
3.2
|
23.3
|
1.0
|
CB
|
B:HIS163
|
3.6
|
20.7
|
1.0
|
CA
|
B:HIS163
|
3.8
|
19.3
|
1.0
|
NE2
|
B:HIS163
|
4.2
|
20.5
|
1.0
|
CD2
|
B:HIS163
|
4.3
|
20.4
|
1.0
|
CG
|
B:PRO116
|
4.3
|
26.4
|
1.0
|
O
|
B:HIS163
|
4.5
|
17.9
|
1.0
|
O
|
B:GLU162
|
4.7
|
24.8
|
1.0
|
C
|
B:HIS163
|
4.7
|
19.2
|
1.0
|
N
|
B:HIS163
|
4.8
|
14.6
|
1.0
|
CB
|
B:PRO116
|
4.9
|
21.3
|
1.0
|
|
Manganese binding site 6 out
of 7 in 7me2
Go back to
Manganese Binding Sites List in 7me2
Manganese binding site 6 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_06.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn407
b:103.2
occ:0.59
|
O
|
B:HOH653
|
2.8
|
42.2
|
1.0
|
OD2
|
B:ASP114
|
2.8
|
48.9
|
1.0
|
CG
|
B:ASP114
|
3.3
|
47.4
|
1.0
|
OD1
|
B:ASP114
|
3.4
|
48.0
|
1.0
|
O
|
B:HOH707
|
3.9
|
33.5
|
1.0
|
CB
|
B:ASP114
|
4.4
|
27.2
|
1.0
|
|
Manganese binding site 7 out
of 7 in 7me2
Go back to
Manganese Binding Sites List in 7me2
Manganese binding site 7 out
of 7 in the Yfea Oligomer Crystal 2, Form 2
![](/pictures/MN/pdb/me/7me2-MN-sphere_07.jpg) Mono view
![](/pictures/MN/pdb/me/7me2-MN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Yfea Oligomer Crystal 2, Form 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn408
b:112.3
occ:0.96
|
OD1
|
B:ASP92
|
2.8
|
25.7
|
1.0
|
O
|
B:HOH639
|
3.6
|
32.2
|
1.0
|
CG
|
B:ASP92
|
3.8
|
29.8
|
1.0
|
O
|
B:HOH620
|
4.1
|
37.0
|
1.0
|
OD2
|
B:ASP92
|
4.1
|
20.7
|
1.0
|
O
|
B:SER90
|
4.2
|
25.5
|
1.0
|
O
|
B:ALA91
|
4.6
|
14.6
|
1.0
|
O
|
B:HOH563
|
4.8
|
47.1
|
1.0
|
C
|
B:ALA91
|
4.9
|
17.5
|
1.0
|
C
|
B:SER90
|
5.0
|
21.1
|
1.0
|
|
Reference:
C.D.Radka,
S.G.Aller.
Yersinia Pestis Substrate-Binding Protein Yfea Site 2 Is A Dynamic and Polyspecific Surface Metal Binding Site To Be Published.
Page generated: Fri Sep 24 16:06:46 2021
|