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Lanthanum in PDB 5kkb: Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex

Enzymatic activity of Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex

All present enzymatic activity of Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex:
3.2.1.113;

Protein crystallography data

The structure of Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex, PDB code: 5kkb was solved by Y.Xiang, K.W.Moremen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 1.77
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.955, 131.487, 87.785, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.1

Lanthanum Binding Sites:

The binding sites of Lanthanum atom in the Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex (pdb code 5kkb). This binding sites where shown within 5.0 Angstroms radius around Lanthanum atom.
In total 2 binding sites of Lanthanum where determined in the Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex, PDB code: 5kkb:
Jump to Lanthanum binding site number: 1; 2;

Lanthanum binding site 1 out of 2 in 5kkb

Go back to Lanthanum Binding Sites List in 5kkb
Lanthanum binding site 1 out of 2 in the Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 1 of Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La711

b:11.4
occ:0.79
OG1 A:THR635 2.6 14.2 1.0
O A:HOH1003 2.6 17.9 1.0
O A:THR635 2.6 13.5 1.0
O3 A:MAN709 2.6 15.2 1.0
O A:HOH827 2.6 16.1 1.0
O2 A:MAN709 2.7 14.2 1.0
O A:HOH927 2.7 19.6 1.0
O A:HOH808 2.7 21.2 1.0
O A:HOH1029 2.7 34.3 1.0
C3 A:MAN709 3.5 10.8 1.0
C2 A:MAN709 3.6 14.0 1.0
C A:THR635 3.6 16.8 1.0
CB A:THR635 3.7 12.4 1.0
CA A:THR635 3.9 13.8 1.0
O A:HOH806 4.0 16.9 1.0
OE1 A:GLU611 4.2 18.0 1.0
CG2 A:THR635 4.2 13.0 1.0
OE1 A:GLU419 4.2 17.9 1.0
O A:HOH846 4.2 18.1 1.0
C1 A:MAN709 4.3 19.9 1.0
OE2 A:GLU611 4.4 20.5 1.0
O A:HOH860 4.4 40.6 1.0
O A:HOH953 4.4 16.0 1.0
OE1 A:GLU552 4.5 25.0 1.0
OE1 A:GLU549 4.6 21.5 1.0
CD A:GLU611 4.7 18.3 1.0
N A:GLU636 4.8 13.5 1.0
OE2 A:GLU419 4.8 23.1 1.0
C4 A:MAN709 4.9 14.7 1.0
CD A:GLU419 5.0 25.7 1.0

Lanthanum binding site 2 out of 2 in 5kkb

Go back to Lanthanum Binding Sites List in 5kkb
Lanthanum binding site 2 out of 2 in the Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 2 of Structure of Mouse Golgi Alpha-1,2-Mannosidase Ia and MAN9GLCNAC2-Pa Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La712

b:11.8
occ:0.80
O B:HOH1015 2.5 17.0 1.0
O B:THR635 2.6 14.1 1.0
OG1 B:THR635 2.6 15.0 1.0
O3 B:MAN709 2.6 16.7 1.0
O2 B:MAN709 2.6 15.1 1.0
O B:HOH835 2.6 15.9 1.0
O B:HOH805 2.6 19.9 1.0
O B:HOH898 2.7 17.8 1.0
O B:HOH1026 2.7 28.5 1.0
C3 B:MAN709 3.5 12.7 1.0
C B:THR635 3.6 14.9 1.0
C2 B:MAN709 3.6 16.6 1.0
CB B:THR635 3.7 13.4 1.0
CA B:THR635 3.9 12.9 1.0
O B:HOH814 4.0 17.9 1.0
OE1 B:GLU611 4.2 18.1 1.0
CG2 B:THR635 4.2 17.0 1.0
OE1 B:GLU419 4.2 18.3 1.0
O B:HOH832 4.3 19.6 1.0
O B:HOH808 4.3 44.6 1.0
C1 B:MAN709 4.3 17.1 1.0
OE2 B:GLU611 4.4 18.5 1.0
OE1 B:GLU552 4.4 23.7 1.0
O B:HOH966 4.4 16.5 1.0
OE2 B:GLU549 4.6 21.8 1.0
CD B:GLU611 4.7 20.4 1.0
OE2 B:GLU419 4.8 20.9 1.0
N B:GLU636 4.8 13.2 1.0
C4 B:MAN709 4.9 17.6 1.0
CD B:GLU419 5.0 24.0 1.0
OE2 B:GLU552 5.0 23.6 1.0

Reference:

Y.Xiang, K.Karaveg, K.W.Moremen. Substrate Recognition and Catalysis By GH47 Alpha-Mannosidases Involved in Asn-Linked Glycan Maturation in the Mammalian Secretory Pathway. Proc. Natl. Acad. Sci. V. 113 E7890 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27856750
DOI: 10.1073/PNAS.1611213113
Page generated: Mon Dec 14 03:12:52 2020

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