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Zinc in PDB 3bvw: Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside

Enzymatic activity of Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside

All present enzymatic activity of Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside:
3.2.1.114;

Protein crystallography data

The structure of Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside, PDB code: 3bvw 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) 10.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.744, 109.457, 138.358, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 17

Zinc Binding Sites:

The binding sites of Zinc atom in the Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside (pdb code 3bvw). 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 Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside, PDB code: 3bvw:

Zinc binding site 1 out of 1 in 3bvw

Go back to Zinc Binding Sites List in 3bvw
Zinc binding site 1 out of 1 in the Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Golgi Mannosidase II D204A Catalytic Nucleophile Mutant Complex with Methyl (2-Deoxy-2-Acetamido-Beta-D- Glucopyranosyl)-(1->2)-Alpha-D-Mannopyranosyl- (1->3)- [Alpha-D-Mannopyranosyl-(1->6)-6-Thio-Alpha-D- Mannopyranosyl- (1->6)]-Beta-D-Mannopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1046

b:10.1
occ:1.00
 OD1 A:ASP92 2.0 10.2 1.0
O31 A:WZ41047 2.0 10.7 1.0
NE2 A:HIS90 2.0 9.2 1.0
NE2 A:HIS471 2.0 8.9 1.0
O21 A:WZ41047 2.3 11.8 1.0
CG A:ASP92 2.8 9.8 1.0
C21 A:WZ41047 3.0 12.3 1.0
OD2 A:ASP92 3.0 12.7 1.0
CD2 A:HIS90 3.0 9.7 1.0
CE1 A:HIS471 3.0 9.0 1.0
C31 A:WZ41047 3.0 12.3 1.0
CE1 A:HIS90 3.0 9.2 1.0
CD2 A:HIS471 3.1 8.4 1.0
OD2 A:ASP472 3.8 9.7 1.0
CB A:ALA204 3.8 10.7 1.0
C41 A:WZ41047 4.1 10.6 1.0
ND1 A:HIS471 4.2 8.7 1.0
CG A:HIS90 4.2 9.2 1.0
ND1 A:HIS90 4.2 9.1 1.0
CE1 A:HIS470 4.2 7.2 1.0
CG A:HIS471 4.2 8.1 1.0
CB A:ASP92 4.2 9.5 1.0
O A:HOH1624 4.4 11.5 1.0
C11 A:WZ41047 4.4 15.5 1.0
OH A:TYR269 4.5 11.5 1.0
NE2 A:HIS470 4.7 10.7 1.0
CA A:ASP92 4.8 8.9 1.0
CG A:ASP472 4.9 8.5 1.0
O41 A:WZ41047 4.9 9.9 1.0
O01 A:WZ41047 5.0 13.8 1.0

Reference:

W.Zhong, D.A.Kuntz, B.Ember, H.Singh, K.W.Moremen, D.R.Rose, G.J.Boons. Probing the Substrate Specificity of Golgi Alpha-Mannosidase II By Use of Synthetic Oligosaccharides and A Catalytic Nucleophile Mutant. J.Am.Chem.Soc. V. 130 8975 2008.
ISSN: ISSN 0002-7863
PubMed: 18558690
DOI: 10.1021/JA711248Y
Page generated: Wed Aug 20 08:05:27 2025

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