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Zinc in PDB 2f1b: Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol

Enzymatic activity of Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol

All present enzymatic activity of Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol:
3.2.1.114;

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol, PDB code: 2f1b was solved by D.A.Kuntz, D.R.Rose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.56 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.433, 110.578, 139.890, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol (pdb code 2f1b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol, PDB code: 2f1b:

Zinc binding site 1 out of 1 in 2f1b

Go back to Zinc Binding Sites List in 2f1b
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Golgi Alpha-Mannosidase II Complex with (2R,3R,4S,5R)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)-5-Methylpyrrolidine-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1804

b:9.7
occ:1.00
 OD2 A:ASP204 2.1 10.8 1.0
NE2 A:HIS471 2.1 8.2 1.0
NE2 A:HIS90 2.1 8.1 1.0
OD1 A:ASP92 2.2 10.6 1.0
O3 A:GB31803 2.2 11.8 1.0
O4 A:GB31803 2.3 12.3 1.0
CD2 A:HIS90 3.1 8.7 1.0
CE1 A:HIS471 3.1 7.1 1.0
CD2 A:HIS471 3.1 9.3 1.0
CG A:ASP92 3.1 11.2 1.0
CG A:ASP204 3.2 8.5 1.0
CE1 A:HIS90 3.2 8.5 1.0
C3 A:GB31803 3.2 11.7 1.0
C4 A:GB31803 3.2 13.7 1.0
OD2 A:ASP92 3.4 12.4 1.0
CB A:ASP204 3.6 9.1 1.0
C5 A:GB31803 3.9 11.8 1.0
N1 A:GB31803 4.0 12.7 1.0
OD2 A:ASP472 4.1 12.4 1.0
ND1 A:HIS471 4.2 8.4 1.0
C2 A:GB31803 4.2 12.1 1.0
CG A:HIS90 4.2 8.0 1.0
CG A:HIS471 4.3 8.5 1.0
OD1 A:ASP204 4.3 9.6 1.0
ND1 A:HIS90 4.3 9.7 1.0
CB A:ASP92 4.5 10.1 1.0
NE2 A:HIS470 4.5 11.8 1.0
C21 A:GB31803 4.7 13.3 1.0
O A:HOH2546 4.7 11.3 1.0
OH A:TYR269 4.9 11.0 1.0

Reference:

P.Englebienne, H.Fiaux, D.A.Kuntz, C.R.Corbeil, S.Gerber-Lemaire, D.R.Rose, N.Moitessier. Evaluation of Docking Programs For Predicting Binding of Golgi Alpha-Mannosidase II Inhibitors: A Comparison with Crystallography. Proteins V. 69 160 2007.
ISSN: ISSN 0887-3585
PubMed: 17557336
DOI: 10.1002/PROT.21479
Page generated: Wed Oct 16 23:36:52 2024

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