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Zinc in PDB 2f18: Golgi Alpha-Mannosidase II Complex with (2R,3R,4S)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)Pyrrolidine-3,4-Diol

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

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

Protein crystallography data

The structure of Golgi Alpha-Mannosidase II Complex with (2R,3R,4S)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)Pyrrolidine-3,4-Diol, PDB code: 2f18 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) 29.85 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.965, 109.724, 138.911, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Alpha-Mannosidase II Complex with (2R,3R,4S)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)Pyrrolidine-3,4-Diol (pdb code 2f18). 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)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)Pyrrolidine-3,4-Diol, PDB code: 2f18:

Zinc binding site 1 out of 1 in 2f18

Go back to Zinc Binding Sites List in 2f18
Zinc binding site 1 out of 1 in the Golgi Alpha-Mannosidase II Complex with (2R,3R,4S)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)Pyrrolidine-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)-2-({[(1R)-2- Hydroxy-1-Phenylethyl]Amino}Methyl)Pyrrolidine-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1805

b:7.9
occ:1.00
 OD2 A:ASP204 2.1 7.7 1.0
NE2 A:HIS471 2.1 6.6 1.0
NE2 A:HIS90 2.1 6.6 1.0
OD1 A:ASP92 2.1 7.8 1.0
O3 A:GB11804 2.2 9.3 1.0
O4 A:GB11804 2.3 10.3 1.0
CD2 A:HIS471 3.1 6.2 1.0
CD2 A:HIS90 3.1 6.9 1.0
CE1 A:HIS90 3.1 7.3 1.0
CG A:ASP92 3.1 8.1 1.0
CG A:ASP204 3.1 7.8 1.0
C3 A:GB11804 3.1 10.1 1.0
CE1 A:HIS471 3.1 6.0 1.0
C4 A:GB11804 3.2 9.7 1.0
OD2 A:ASP92 3.4 9.3 1.0
CB A:ASP204 3.6 7.7 1.0
C5 A:GB11804 3.8 9.5 1.0
N1 A:GB11804 4.0 10.3 1.0
OD2 A:ASP472 4.0 7.9 1.0
OD1 A:ASP204 4.2 8.7 1.0
C2 A:GB11804 4.2 8.9 1.0
ND1 A:HIS90 4.2 7.1 1.0
CG A:HIS90 4.2 6.8 1.0
CG A:HIS471 4.2 5.2 1.0
ND1 A:HIS471 4.2 6.5 1.0
NE2 A:HIS470 4.4 10.0 1.0
CB A:ASP92 4.5 7.8 1.0
O A:HOH2661 4.6 9.9 1.0
OH A:TYR269 4.7 9.2 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 23:36:45 2024

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