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Calcium in PDB 1x9d: Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue

Enzymatic activity of Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue

All present enzymatic activity of Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue:
3.2.1.113;

Protein crystallography data

The structure of Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue, PDB code: 1x9d was solved by K.Karaveg, W.Tempel, Z.J.Liu, A.Siriwardena, K.W.Moremen, B.C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 1.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.687, 53.878, 56.234, 89.49, 63.60, 62.61
R / Rfree (%) 14.4 / 16.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue (pdb code 1x9d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue, PDB code: 1x9d:

Calcium binding site 1 out of 1 in 1x9d

Go back to Calcium Binding Sites List in 1x9d
Calcium binding site 1 out of 1 in the Crystal Structure of Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue


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 Human Class I Alpha-1,2-Mannosidase in Complex with Thio-Disaccharide Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:4.0
occ:1.00
 O A:HOH1010 2.4 6.8 1.0
O12 A:SMD1003 2.4 5.0 1.0
O A:HOH1009 2.4 7.3 1.0
O A:THR688 2.4 3.6 1.0
OG1 A:THR688 2.5 3.3 1.0
O A:HOH1008 2.5 5.9 1.0
O13 A:SMD1003 2.5 5.3 1.0
O A:HOH1005 2.5 5.0 1.0
C13 A:SMD1003 3.4 5.0 1.0
C12 A:SMD1003 3.4 4.7 1.0
C A:THR688 3.4 3.8 1.0
CB A:THR688 3.6 3.5 1.0
CA A:THR688 3.8 3.1 1.0
C11 A:SMD1003 4.1 8.2 1.0
O A:HOH1186 4.1 7.5 1.0
OE2 A:GLU467 4.2 4.5 1.0
OE2 A:GLU663 4.2 6.7 1.0
CG2 A:THR688 4.2 4.3 1.0
O15 A:SMD1003 4.4 10.3 1.0
O A:HOH1021 4.4 6.8 1.0
O A:HOH1006 4.5 5.2 1.0
OE2 A:GLU602 4.5 8.4 1.0
OE1 A:GLU599 4.5 13.3 1.0
OE1 A:GLU663 4.5 7.8 1.0
OE1 A:GLU467 4.6 5.5 1.0
N A:GLU689 4.7 3.0 1.0
C14 A:SMD1003 4.7 5.6 1.0
CD A:GLU663 4.8 7.6 1.0
CD A:GLU467 4.8 4.4 1.0
OE1 A:GLU602 4.9 6.7 1.0
C15 A:SMD1003 5.0 9.0 1.0

Reference:

K.Karaveg, A.Siriwardena, W.Tempel, Z.J.Liu, J.Glushka, B.C.Wang, K.W.Moremen. Mechanism of Class 1 (Glycosylhydrolase Family 47) {Alpha}-Mannosidases Involved in N-Glycan Processing and Endoplasmic Reticulum Quality Control. J.Biol.Chem. V. 280 16197 2005.
ISSN: ISSN 0021-9258
PubMed: 15713668
DOI: 10.1074/JBC.M500119200
Page generated: Tue Jul 8 03:24:30 2025

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