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Manganese in PDB 5ava: Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan

Protein crystallography data

The structure of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan, PDB code: 5ava was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.210, 122.838, 97.664, 90.00, 90.66, 90.00
R / Rfree (%) 22.9 / 27.4

Other elements in 5ava:

The structure of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan (pdb code 5ava). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan, PDB code: 5ava:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5ava

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Manganese binding site 1 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2001

b:33.4
occ:1.00
 O A:HOH2102 1.9 31.8 1.0
NE2 A:HIS160 1.9 32.6 1.0
OE2 A:GLU145 1.9 30.6 1.0
O A:HOH2101 1.9 31.1 1.0
OD1 A:ASP155 1.9 35.3 1.0
OD2 A:ASP147 1.9 33.9 1.0
CE1 A:HIS160 2.9 33.0 1.0
CG A:ASP147 2.9 32.2 1.0
CD2 A:HIS160 3.0 32.6 1.0
CG A:ASP155 3.0 36.6 1.0
CD A:GLU145 3.1 29.1 1.0
CB A:ASP147 3.2 30.9 1.0
OD2 A:ASP155 3.5 35.9 1.0
OE1 A:GLU145 3.7 29.1 1.0
O A:HOH2104 3.8 31.7 1.0
ND1 A:HIS160 4.0 32.8 1.0
CA A:CA2002 4.0 34.1 1.0
CG A:HIS160 4.1 32.7 1.0
OD1 A:ASP147 4.1 33.3 1.0
CB A:ASP155 4.3 37.9 1.0
CG A:GLU145 4.3 28.1 1.0
NE1 A:TRP154 4.5 51.5 1.0
OG A:SER170 4.5 32.1 1.0
CA A:ASP147 4.7 29.1 1.0
CD1 A:TRP154 4.7 49.3 1.0
O A:ILE168 4.7 35.2 1.0
CA A:ASP155 4.8 40.0 1.0
CD A:PRO156 4.9 38.5 1.0

Manganese binding site 2 out of 8 in 5ava

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Manganese binding site 2 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:34.8
occ:1.00
 O B:HOH2101 1.9 33.2 1.0
O B:HOH2103 1.9 30.0 1.0
NE2 B:HIS160 1.9 35.3 1.0
OD1 B:ASP155 1.9 36.8 1.0
OE2 B:GLU145 1.9 32.8 1.0
OD2 B:ASP147 2.0 33.3 1.0
CE1 B:HIS160 2.8 35.7 1.0
CG B:ASP147 3.0 30.9 1.0
CG B:ASP155 3.0 36.9 1.0
CD B:GLU145 3.1 31.3 1.0
CD2 B:HIS160 3.1 35.2 1.0
CB B:ASP147 3.4 30.3 1.0
OE1 B:GLU145 3.5 32.1 1.0
O B:HOH2104 3.6 33.5 1.0
OD2 B:ASP155 3.7 36.1 1.0
CA B:CA2002 3.9 35.4 1.0
ND1 B:HIS160 3.9 35.5 1.0
CG B:HIS160 4.1 35.2 1.0
OD1 B:ASP147 4.1 31.8 1.0
CB B:ASP155 4.2 37.5 1.0
CG B:GLU145 4.3 30.1 1.0
NE1 B:TRP154 4.4 38.2 1.0
OG B:SER170 4.5 28.7 1.0
CD1 B:TRP154 4.6 38.1 1.0
CA B:ASP155 4.7 38.2 1.0
O B:ILE168 4.7 29.7 1.0
CA B:ASP147 4.9 29.2 1.0
CD B:PRO156 4.9 37.5 1.0

Manganese binding site 3 out of 8 in 5ava

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Manganese binding site 3 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2001

b:41.2
occ:1.00
 OE2 C:GLU145 1.9 39.5 1.0
O C:HOH2101 1.9 37.1 1.0
NE2 C:HIS160 1.9 39.3 1.0
O C:HOH2102 1.9 38.6 1.0
OD1 C:ASP155 1.9 46.2 1.0
OD2 C:ASP147 1.9 41.5 1.0
CE1 C:HIS160 2.8 39.6 1.0
CG C:ASP147 2.9 40.6 1.0
CG C:ASP155 3.0 46.0 1.0
CD C:GLU145 3.0 38.1 1.0
CD2 C:HIS160 3.1 39.0 1.0
CB C:ASP147 3.2 40.1 1.0
OD2 C:ASP155 3.5 45.3 1.0
OE1 C:GLU145 3.5 38.4 1.0
O C:HOH2104 3.8 40.2 1.0
ND1 C:HIS160 3.9 39.5 1.0
CA C:CA2002 4.0 42.1 1.0
OD1 C:ASP147 4.1 41.4 1.0
CG C:HIS160 4.1 39.1 1.0
CG C:GLU145 4.2 36.4 1.0
CB C:ASP155 4.2 45.0 1.0
NE1 C:TRP154 4.5 41.7 1.0
OG C:SER170 4.5 31.0 1.0
CA C:ASP147 4.7 40.3 1.0
O C:ILE168 4.7 34.7 1.0
CD1 C:TRP154 4.8 42.4 1.0
CA C:ASP155 4.8 45.4 1.0
CD C:PRO156 4.9 47.3 1.0

Manganese binding site 4 out of 8 in 5ava

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Manganese binding site 4 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2001

b:40.9
occ:1.00
 O D:HOH2101 1.9 40.0 1.0
O D:HOH2102 1.9 38.1 1.0
OE2 D:GLU145 1.9 38.0 1.0
NE2 D:HIS160 1.9 37.3 1.0
OD1 D:ASP155 1.9 46.9 1.0
OD2 D:ASP147 1.9 41.8 1.0
CE1 D:HIS160 2.9 36.9 1.0
CG D:ASP155 2.9 49.3 1.0
CD2 D:HIS160 2.9 36.4 1.0
CG D:ASP147 3.0 40.1 1.0
CD D:GLU145 3.1 37.0 1.0
CB D:ASP147 3.3 38.4 1.0
OD2 D:ASP155 3.4 48.0 1.0
OE1 D:GLU145 3.7 38.1 1.0
O D:HOH2104 3.9 42.7 1.0
CA D:CA2002 4.0 44.2 1.0
ND1 D:HIS160 4.0 36.5 1.0
CG D:HIS160 4.1 36.2 1.0
OD1 D:ASP147 4.1 41.7 1.0
CB D:ASP155 4.1 50.1 1.0
CG D:GLU145 4.3 35.5 1.0
OG D:SER170 4.3 47.1 1.0
NE1 D:TRP154 4.5 63.0 1.0
O D:ILE168 4.7 47.8 1.0
CD1 D:TRP154 4.8 62.3 1.0
CA D:ASP147 4.8 36.6 1.0
CA D:ASP155 4.8 52.5 1.0
CD D:PRO156 5.0 49.4 1.0

Manganese binding site 5 out of 8 in 5ava

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Manganese binding site 5 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn2001

b:40.6
occ:1.00
 O E:HOH2102 1.9 38.3 1.0
O E:HOH2101 1.9 36.4 1.0
OE2 E:GLU145 1.9 36.0 1.0
OD1 E:ASP155 1.9 44.2 1.0
NE2 E:HIS160 1.9 38.7 1.0
OD2 E:ASP147 1.9 38.4 1.0
CE1 E:HIS160 2.8 38.6 1.0
CG E:ASP147 2.9 37.2 1.0
CG E:ASP155 3.0 45.2 1.0
CD2 E:HIS160 3.0 38.9 1.0
CD E:GLU145 3.1 33.4 1.0
CB E:ASP147 3.3 36.1 1.0
OD2 E:ASP155 3.4 44.3 1.0
O E:HOH2103 3.5 37.4 1.0
OE1 E:GLU145 3.6 33.3 1.0
ND1 E:HIS160 4.0 38.8 1.0
CA E:CA2002 4.0 40.2 1.0
CG E:HIS160 4.1 39.1 1.0
OD1 E:ASP147 4.1 38.5 1.0
OG E:SER170 4.2 34.0 1.0
CB E:ASP155 4.2 45.8 1.0
NE1 E:TRP154 4.3 43.4 1.0
CG E:GLU145 4.3 32.2 1.0
CD1 E:TRP154 4.6 44.4 1.0
O E:ILE168 4.7 35.8 1.0
CA E:ASP147 4.7 34.4 1.0
CA E:ASP155 4.8 47.0 1.0

Manganese binding site 6 out of 8 in 5ava

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Manganese binding site 6 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn2001

b:43.8
occ:1.00
 O F:HOH2101 1.9 39.7 1.0
NE2 F:HIS160 1.9 43.2 1.0
O F:HOH2102 1.9 42.0 1.0
OD1 F:ASP155 1.9 47.7 1.0
OE2 F:GLU145 1.9 42.8 1.0
OD2 F:ASP147 1.9 41.9 1.0
CE1 F:HIS160 2.9 42.7 1.0
CG F:ASP147 2.9 40.2 1.0
CD2 F:HIS160 3.0 42.6 1.0
CG F:ASP155 3.0 48.9 1.0
CD F:GLU145 3.1 41.2 1.0
CB F:ASP147 3.3 39.5 1.0
OD2 F:ASP155 3.5 47.8 1.0
OE1 F:GLU145 3.6 42.9 1.0
O F:HOH2104 3.7 43.5 1.0
CA F:CA2002 4.0 44.8 1.0
ND1 F:HIS160 4.0 42.0 1.0
CG F:HIS160 4.1 42.0 1.0
OD1 F:ASP147 4.1 42.1 1.0
CB F:ASP155 4.2 49.7 1.0
CG F:GLU145 4.3 38.7 1.0
NE1 F:TRP154 4.4 49.0 1.0
OG F:SER170 4.5 39.7 1.0
O F:ILE168 4.7 39.1 1.0
CD1 F:TRP154 4.7 50.1 1.0
CA F:ASP147 4.7 39.3 1.0
CA F:ASP155 4.8 50.6 1.0
CD F:PRO156 4.9 51.3 1.0

Manganese binding site 7 out of 8 in 5ava

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Manganese binding site 7 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn2001

b:54.3
occ:1.00
 O G:HOH2102 1.9 49.3 1.0
O G:HOH2101 1.9 54.2 1.0
OE2 G:GLU145 1.9 51.1 1.0
OD2 G:ASP147 1.9 59.5 1.0
NE2 G:HIS160 1.9 49.8 1.0
OD1 G:ASP155 1.9 60.2 1.0
CE1 G:HIS160 2.9 49.0 1.0
CG G:ASP147 2.9 59.3 1.0
CD2 G:HIS160 2.9 49.0 1.0
CD G:GLU145 3.0 50.2 1.0
CG G:ASP155 3.1 59.4 1.0
CB G:ASP147 3.2 57.5 1.0
OE1 G:GLU145 3.5 51.4 1.0
OD2 G:ASP155 3.6 61.1 1.0
O G:HOH2104 3.8 60.2 1.0
CA G:CA2002 4.0 61.9 1.0
ND1 G:HIS160 4.0 48.9 1.0
OD1 G:ASP147 4.0 61.6 1.0
CG G:HIS160 4.1 48.6 1.0
CB G:ASP155 4.3 57.7 1.0
CG G:GLU145 4.3 48.5 1.0
OG G:SER170 4.5 46.4 1.0
NE1 G:TRP154 4.6 68.8 1.0
CA G:ASP147 4.7 56.4 1.0
O G:ILE168 4.8 49.9 1.0
CD1 G:TRP154 4.8 68.2 1.0
CA G:ASP155 4.9 57.9 1.0

Manganese binding site 8 out of 8 in 5ava

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Manganese binding site 8 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn2001

b:63.9
occ:1.00
 O H:HOH2102 1.9 61.6 1.0
O H:HOH2101 1.9 57.8 1.0
OD1 H:ASP155 1.9 71.6 1.0
OE2 H:GLU145 1.9 59.7 1.0
NE2 H:HIS160 1.9 58.2 1.0
OD2 H:ASP147 1.9 69.8 1.0
CE1 H:HIS160 2.8 57.5 1.0
CG H:ASP147 2.9 69.0 1.0
CD2 H:HIS160 3.0 57.5 1.0
CG H:ASP155 3.0 73.2 1.0
CD H:GLU145 3.1 57.0 1.0
CB H:ASP147 3.3 65.5 1.0
OD2 H:ASP155 3.6 73.3 1.0
OE1 H:GLU145 3.8 56.9 1.0
ND1 H:HIS160 3.9 57.4 1.0
CA H:CA2002 4.0 72.9 1.0
CG H:HIS160 4.0 57.6 1.0
OD1 H:ASP147 4.1 71.2 1.0
CB H:ASP155 4.1 72.7 1.0
O H:HOH2104 4.2 69.2 1.0
CG H:GLU145 4.3 54.9 1.0
OG H:SER170 4.6 56.6 1.0
CA H:ASP155 4.7 73.8 1.0
CA H:ASP147 4.8 60.9 1.0
O H:ILE168 4.8 55.5 1.0
NE1 H:TRP154 4.8 93.9 1.0
CD1 H:TRP154 5.0 93.0 1.0

Reference:

M.Nagae, M.Kanagawa, K.Morita-Matsumoto, S.Hanashima, Y.Kizuka, N.Taniguchi, Y.Yamaguchi. Atomic Visualization of A Flipped-Back Conformation of Bisected Glycans Bound to Specific Lectins Sci Rep V. 6 22973 2016.
ISSN: ESSN 2045-2322
PubMed: 26971576
DOI: 10.1038/SREP22973
Page generated: Sat Oct 5 23:25:51 2024

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