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Calcium in PDB 5kk7: Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex

Enzymatic activity of Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex

All present enzymatic activity of Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex:
3.2.1.113;

Protein crystallography data

The structure of Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex, PDB code: 5kk7 was solved by K.Karaveg, Y.Xiang, K.W.Moremen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.16 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.887, 56.302, 89.555, 105.68, 94.15, 114.25
R / Rfree (%) 17.6 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex (pdb code 5kk7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex, PDB code: 5kk7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5kk7

Go back to Calcium Binding Sites List in 5kk7
Calcium binding site 1 out of 2 in the Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:8.3
occ:1.00
O A:HOH932 2.3 5.4 1.0
O A:HOH853 2.4 5.4 1.0
O A:HOH901 2.4 6.6 1.0
O13 A:SMD700 2.4 10.4 1.0
O A:ALA688 2.4 13.8 1.0
O12 A:SMD700 2.6 11.4 1.0
O A:HOH935 2.6 6.8 1.0
C13 A:SMD700 3.4 2.8 1.0
C12 A:SMD700 3.5 11.4 1.0
C A:ALA688 3.5 13.8 1.0
CA A:ALA688 4.0 14.0 1.0
O A:HOH849 4.1 6.0 1.0
OE1 A:GLU663 4.1 13.5 1.0
C11 A:SMD700 4.1 17.1 1.0
CB A:ALA688 4.2 14.3 1.0
O A:HOH850 4.3 3.0 1.0
OE2 A:GLU663 4.3 13.7 1.0
OE2 A:GLU602 4.4 13.4 1.0
OE1 A:GLU599 4.4 15.4 1.0
OE2 A:GLU467 4.5 8.5 1.0
O A:HOH1044 4.6 6.4 1.0
OE1 A:GLU467 4.6 6.8 1.0
CD A:GLU663 4.6 13.6 1.0
N A:GLU689 4.7 13.9 1.0
C14 A:SMD700 4.7 9.7 1.0
C16 A:SMD700 4.7 8.7 1.0
OE1 A:GLU602 4.9 13.5 1.0
CD A:GLU467 5.0 7.6 1.0

Calcium binding site 2 out of 2 in 5kk7

Go back to Calcium Binding Sites List in 5kk7
Calcium binding site 2 out of 2 in the Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Class I Human Endoplasmic Reticulum 1,2- Alpha-Mannosidase T688A Mutant and Thio-Disaccharide Substrate Analog Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:8.5
occ:1.00
O B:HOH946 2.3 10.0 1.0
O B:ALA688 2.4 6.0 1.0
O B:HOH856 2.4 11.2 1.0
O13 B:SMD700 2.4 1.3 1.0
O B:HOH951 2.4 8.8 1.0
O12 B:SMD700 2.6 5.8 1.0
O B:HOH912 2.6 6.3 1.0
C13 B:SMD700 3.4 5.7 1.0
C B:ALA688 3.5 5.8 1.0
C12 B:SMD700 3.5 6.1 1.0
CA B:ALA688 3.9 5.5 1.0
O B:HOH853 4.0 6.7 1.0
OE1 B:GLU663 4.1 3.8 1.0
C11 B:SMD700 4.1 11.7 1.0
CB B:ALA688 4.2 4.8 1.0
O B:HOH911 4.3 10.5 1.0
OE2 B:GLU663 4.3 6.4 1.0
OE2 B:GLU602 4.5 4.9 1.0
OE1 B:GLU467 4.5 12.8 1.0
OE2 B:GLU599 4.5 3.9 1.0
OE2 B:GLU467 4.6 12.7 1.0
N B:GLU689 4.6 5.0 1.0
CD B:GLU663 4.6 5.8 1.0
C14 B:SMD700 4.6 10.5 1.0
C16 B:SMD700 4.6 15.6 1.0
O B:HOH1023 4.6 8.7 1.0
OE1 B:GLU602 4.9 4.8 1.0
C15 B:SMD700 5.0 12.7 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 Jul 15 06:53:44 2024

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