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Manganese in PDB 5kxe: Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2

Protein crystallography data

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2, PDB code: 5kxe was solved by S.V.Evans, O.Haji-Ghassemi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.584, 97.943, 149.158, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5kxe:

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 (pdb code 5kxe). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2, PDB code: 5kxe:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5kxe

Go back to Manganese Binding Sites List in 5kxe
Manganese binding site 1 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn307

b:26.5
occ:1.00
OD2 A:ASP157 2.1 17.4 1.0
OE1 A:GLU155 2.2 19.1 1.0
O A:HOH436 2.2 21.6 1.0
OD1 A:ASP164 2.2 20.1 1.0
O A:HOH404 2.2 17.9 1.0
NE2 A:HIS169 2.3 19.6 1.0
CG A:ASP157 3.1 17.8 1.0
CG A:ASP164 3.1 20.8 1.0
CD A:GLU155 3.2 19.8 1.0
CE1 A:HIS169 3.2 19.4 1.0
CD2 A:HIS169 3.4 18.4 1.0
OE2 A:GLU155 3.5 22.5 1.0
CB A:ASP157 3.6 17.9 1.0
OD2 A:ASP164 3.6 21.1 1.0
O A:HOH458 3.9 14.4 1.0
OG A:SER179 4.2 19.7 1.0
CA A:CA308 4.2 19.5 1.0
OD1 A:ASP157 4.2 17.3 1.0
CB A:ASP164 4.3 22.2 1.0
ND1 A:HIS169 4.3 19.3 1.0
O A:HOH515 4.4 20.0 1.0
CG A:HIS169 4.5 19.2 1.0
O A:ILE177 4.5 20.7 1.0
CG A:GLU155 4.5 18.9 1.0
NE1 A:TRP163 4.5 26.5 1.0
CD A:PRO165 4.7 25.6 1.0
CD1 A:TRP163 4.7 26.8 1.0
CA A:ASP164 4.8 22.2 1.0

Manganese binding site 2 out of 4 in 5kxe

Go back to Manganese Binding Sites List in 5kxe
Manganese binding site 2 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn309

b:27.7
occ:1.00
OD2 B:ASP157 2.1 19.1 1.0
O B:HOH462 2.2 20.0 1.0
OE1 B:GLU155 2.2 20.4 1.0
OD1 B:ASP164 2.2 20.8 1.0
O B:HOH410 2.2 24.5 1.0
NE2 B:HIS169 2.3 21.8 1.0
CG B:ASP164 3.2 22.6 1.0
CD B:GLU155 3.2 20.6 1.0
CG B:ASP157 3.2 19.8 1.0
CE1 B:HIS169 3.2 20.6 1.0
CD2 B:HIS169 3.3 20.4 1.0
OE2 B:GLU155 3.5 21.5 1.0
CB B:ASP157 3.6 20.4 1.0
OD2 B:ASP164 3.7 21.0 1.0
O B:HOH474 3.8 19.8 1.0
OG B:SER179 4.1 20.6 1.0
CA B:CA310 4.2 21.6 1.0
OD1 B:ASP157 4.3 18.3 1.0
CB B:ASP164 4.3 23.2 1.0
ND1 B:HIS169 4.3 21.7 1.0
CG B:HIS169 4.4 21.1 1.0
O B:HOH486 4.5 19.4 1.0
O B:ILE177 4.5 21.7 1.0
CG B:GLU155 4.5 19.9 1.0
NE1 B:TRP163 4.6 26.9 1.0
CD B:PRO165 4.7 26.3 1.0
CD1 B:TRP163 4.7 27.6 1.0
CA B:ASP164 4.8 23.5 1.0

Manganese binding site 3 out of 4 in 5kxe

Go back to Manganese Binding Sites List in 5kxe
Manganese binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn304

b:25.4
occ:1.00
O C:HOH436 2.1 20.4 1.0
OD2 C:ASP157 2.1 18.0 1.0
O C:HOH432 2.1 14.5 1.0
OD1 C:ASP164 2.2 18.0 1.0
OE1 C:GLU155 2.2 16.3 1.0
NE2 C:HIS169 2.4 18.1 1.0
CG C:ASP157 3.1 17.4 1.0
CG C:ASP164 3.2 20.1 1.0
CD C:GLU155 3.2 18.2 1.0
CE1 C:HIS169 3.2 18.2 1.0
CD2 C:HIS169 3.4 17.7 1.0
OE2 C:GLU155 3.5 18.7 1.0
CB C:ASP157 3.6 17.7 1.0
OD2 C:ASP164 3.6 18.7 1.0
O C:HOH444 3.9 15.4 1.0
OG C:SER179 4.2 17.1 1.0
CA C:CA305 4.2 18.1 1.0
OD1 C:ASP157 4.2 17.8 1.0
CB C:ASP164 4.3 20.7 1.0
ND1 C:HIS169 4.4 18.4 1.0
O C:ILE177 4.4 22.2 1.0
O C:HOH517 4.4 19.2 1.0
CG C:HIS169 4.5 17.5 1.0
NE1 C:TRP163 4.5 20.9 1.0
CG C:GLU155 4.5 18.1 1.0
CD1 C:TRP163 4.7 20.7 1.0
CD C:PRO165 4.8 23.5 1.0
CA C:ASP164 4.8 20.9 1.0

Manganese binding site 4 out of 4 in 5kxe

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Manganese binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 4.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn304

b:30.2
occ:1.00
O D:HOH426 2.1 20.4 1.0
OE1 D:GLU155 2.1 24.0 1.0
OD2 D:ASP157 2.2 21.4 1.0
O D:HOH412 2.2 19.4 1.0
OD1 D:ASP164 2.2 27.9 1.0
NE2 D:HIS169 2.4 27.1 1.0
CD D:GLU155 3.1 24.2 1.0
CG D:ASP164 3.2 27.7 1.0
CG D:ASP157 3.2 22.4 1.0
CE1 D:HIS169 3.3 25.6 1.0
CD2 D:HIS169 3.4 25.9 1.0
OE2 D:GLU155 3.4 25.1 1.0
CB D:ASP157 3.6 22.4 1.0
OD2 D:ASP164 3.7 25.8 1.0
O D:HOH472 3.9 24.5 1.0
OG D:SER179 4.1 25.0 1.0
CA D:CA305 4.3 24.9 1.0
OD1 D:ASP157 4.3 22.7 1.0
CB D:ASP164 4.3 30.3 1.0
O D:HOH471 4.3 26.1 1.0
O D:ILE177 4.4 22.7 1.0
ND1 D:HIS169 4.4 25.6 1.0
CG D:GLU155 4.5 23.0 1.0
CG D:HIS169 4.5 25.6 1.0
NE1 D:TRP163 4.5 34.4 1.0
CD1 D:TRP163 4.7 34.9 1.0
CD D:PRO165 4.7 32.5 1.0
CA D:ASP164 4.8 30.0 1.0

Reference:

O.Haji-Ghassemi, M.Gilbert, J.Spence, M.J.Schur, M.J.Parker, M.L.Jenkins, J.E.Burke, H.Van Faassen, N.M.Young, S.V.Evans. Molecular Basis For Recognition of the Cancer Glycobiomarker, Lacdinac (Galnac[ Beta 14]Glcnac), By Wisteria Floribunda Agglutinin. J.Biol.Chem. V. 291 24085 2016.
ISSN: ESSN 1083-351X
PubMed: 27601469
DOI: 10.1074/JBC.M116.750463
Page generated: Tue Dec 15 04:43:25 2020

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