Atomistry » Manganese » PDB 5a58-5b49 » 5ava
Atomistry »
  Manganese »
    PDB 5a58-5b49 »
      5ava »

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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Go back to Manganese Binding Sites List in 5ava
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy