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Zinc in PDB 4ac1: The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution

Enzymatic activity of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution

All present enzymatic activity of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution:
3.2.1.96;

Protein crystallography data

The structure of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution, PDB code: 4ac1 was solved by I.Stals, S.Karkehabadi, B.Devreese, S.Kim, M.Ward, M.Sandgren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.438, 63.874, 59.360, 90.00, 100.97, 90.00
R / Rfree (%) 18.4 / 20.2

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution (pdb code 4ac1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution, PDB code: 4ac1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4ac1

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Zinc binding site 1 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1291

b:9.1
occ:0.75
 ZN X:ZN1294 1.8 7.0 0.2
O X:HOH2248 1.9 7.1 0.5
OE2 X:GLU131 2.1 9.3 1.0
OXT X:ACT1288 2.1 9.0 1.0
O X:HOH2242 2.1 16.2 1.0
O X:HOH2393 2.2 14.1 1.0
O X:HOH2251 2.2 9.4 0.8
O X:HOH2249 2.7 11.4 0.5
C X:ACT1288 3.0 9.2 1.0
CD X:GLU131 3.0 9.6 1.0
O X:HOH2250 3.1 3.6 0.2
O X:ACT1288 3.1 10.0 1.0
OE1 X:GLU131 3.4 9.8 1.0
O X:HOH2109 4.0 25.9 1.0
OD2 X:ASP129 4.0 7.8 1.0
O X:HOH2394 4.0 25.7 1.0
OE1 X:GLN193 4.1 7.5 1.0
CG X:GLU131 4.4 9.3 1.0
CH3 X:ACT1288 4.4 10.1 1.0
O X:HOH2027 4.5 18.6 1.0
N X:ALA89 4.5 10.5 1.0
CA X:GLY88 4.6 8.9 1.0
NE2 X:GLN193 4.6 6.4 1.0
O X:HOH2316 4.6 2.0 0.2
O X:HOH2309 4.7 19.7 0.8
OD1 X:ASP129 4.7 5.6 1.0
CD X:GLN193 4.7 5.4 1.0
CG X:ASP129 4.8 5.5 1.0
C X:GLY88 4.8 9.2 1.0

Zinc binding site 2 out of 8 in 4ac1

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Zinc binding site 2 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1292

b:13.6
occ:0.75
 O X:HOH2414 2.0 22.2 1.0
OE2 X:GLU274 2.1 12.7 1.0
OE1 X:GLU271 2.1 14.1 1.0
O X:HOH2415 2.1 21.6 1.0
O X:HOH2421 2.1 20.1 1.0
O X:HOH2413 2.2 18.5 1.0
CD X:GLU271 3.0 13.4 1.0
CD X:GLU274 3.0 10.9 1.0
OE1 X:GLU274 3.3 12.3 1.0
OE2 X:GLU271 3.3 15.1 1.0
O X:HOH2405 4.2 14.3 1.0
O X:HOH2402 4.2 30.3 1.0
CG X:GLU271 4.3 10.2 1.0
O X:HOH2417 4.3 16.9 1.0
CG X:GLU274 4.4 8.8 1.0
CB X:GLU271 4.5 8.3 1.0

Zinc binding site 3 out of 8 in 4ac1

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Zinc binding site 3 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1293

b:9.6
occ:0.50
 O X:HOH2345 1.9 27.5 1.0
O X:HOH2284 2.0 22.3 1.0
O X:HOH2285 2.1 20.1 1.0
OD1 X:ASN213 2.1 9.9 1.0
OD2 X:ASP167 2.1 14.3 1.0
O X:HOH2286 2.2 22.4 1.0
CG X:ASP167 3.0 12.2 1.0
CG X:ASN213 3.1 8.7 1.0
OD1 X:ASP167 3.1 12.3 1.0
ND2 X:ASN213 3.5 7.3 1.0
O X:HOH2343 4.0 19.8 1.0
O X:HOH2340 4.1 18.8 1.0
O X:HOH2279 4.2 16.7 1.0
O X:HOH2341 4.2 28.3 1.0
CB X:ASP167 4.4 11.5 1.0
CB X:ASN213 4.4 9.3 1.0
CA X:ASN213 4.8 9.8 1.0

Zinc binding site 4 out of 8 in 4ac1

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Zinc binding site 4 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1294

b:7.0
occ:0.25
 O X:HOH2251 1.2 9.4 0.8
ZN X:ZN1291 1.8 9.1 0.8
OXT X:ACT1288 1.9 9.0 1.0
O X:HOH2250 2.1 3.6 0.2
OE1 X:GLN193 2.4 7.5 1.0
OE2 X:GLU131 2.5 9.3 1.0
C X:ACT1288 2.6 9.2 1.0
O X:ACT1288 2.7 10.0 1.0
O X:HOH2393 3.0 14.1 1.0
CD X:GLN193 3.1 5.4 1.0
NE2 X:GLN193 3.1 6.4 1.0
O X:HOH2248 3.3 7.1 0.5
CD X:GLU131 3.4 9.6 1.0
O X:HOH2309 3.6 19.7 0.8
O X:HOH2249 3.6 11.4 0.5
O X:HOH2242 3.7 16.2 1.0
CH3 X:ACT1288 3.9 10.1 1.0
OE1 X:GLU131 3.9 9.8 1.0
O X:HOH2316 4.0 2.0 0.2
O X:HOH2109 4.0 25.9 1.0
OD2 X:ASP129 4.2 7.8 1.0
OD1 X:ASP129 4.3 5.6 1.0
CG X:GLU131 4.3 9.3 1.0
CG X:GLN193 4.5 6.2 1.0
CE1 X:TYR195 4.5 5.3 1.0
OH X:TYR195 4.6 6.4 1.0
CG X:ASP129 4.7 5.5 1.0

Zinc binding site 5 out of 8 in 4ac1

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Zinc binding site 5 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1295

b:8.6
occ:0.50
 OD2 X:ASP186 1.9 13.2 1.0
O X:HOH2306 2.0 29.4 1.0
O X:HOH2301 2.2 15.0 1.0
O X:HOH2305 2.3 14.7 1.0
O X:HOH2302 2.4 25.1 1.0
CG X:ASP186 2.6 10.9 1.0
OD1 X:ASP186 2.6 11.9 1.0
O X:HOH2303 2.7 18.0 1.0
OD1 X:ASN185 3.9 12.1 1.0
CB X:ASP186 4.0 8.8 1.0
ND2 X:ASN185 4.1 16.1 1.0
O X:HOH2153 4.2 28.0 1.0
O X:HOH2262 4.4 10.1 1.0
CG X:ASN185 4.4 11.0 1.0
O X:HOH2304 4.5 24.2 1.0
O X:THR182 4.7 7.5 1.0
CG X:GLN183 4.7 9.6 1.0
CG X:ARG147 4.8 6.5 0.5
CG X:ARG147 4.9 8.9 0.5
CA X:GLN183 5.0 7.1 1.0
O X:HOH2267 5.0 13.8 1.0
NE2 X:GLN183 5.0 11.5 1.0
N X:ASP186 5.0 8.3 1.0

Zinc binding site 6 out of 8 in 4ac1

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Zinc binding site 6 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1296

b:11.1
occ:0.50
 ZN X:ZN1298 1.0 16.1 0.5
O X:HOH2120 1.9 18.5 1.0
O X:HOH2119 2.0 29.8 1.0
NE2 X:HIS54 2.1 10.2 1.0
O X:HOH2434 2.2 24.4 1.0
CE1 X:HIS54 3.0 10.9 1.0
CD2 X:HIS54 3.1 10.1 1.0
ND1 X:HIS54 4.1 9.7 1.0
CD X:PRO59 4.1 9.9 1.0
CG X:HIS54 4.2 8.8 1.0
O X:HOH2054 4.3 33.6 1.0
O X:ASP57 4.4 11.9 1.0
O X:HOH2053 4.5 30.6 1.0
CG X:PRO59 4.6 10.2 1.0
O X:HOH2111 4.7 18.3 1.0

Zinc binding site 7 out of 8 in 4ac1

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Zinc binding site 7 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1297

b:7.6
occ:0.75
 OXT X:ACT1289 1.9 16.4 1.0
O X:HOH2274 2.2 15.3 1.0
OD2 X:ASP153 2.3 14.1 1.0
OD1 X:ASP153 2.3 17.3 1.0
CG X:ASP153 2.6 11.0 1.0
C X:ACT1289 2.7 15.8 1.0
O X:ACT1289 2.8 15.9 1.0
O X:HOH2433 4.0 28.7 1.0
CB X:ASP153 4.1 8.7 1.0
CH3 X:ACT1289 4.1 16.1 1.0
CA X:ASP153 4.9 7.8 1.0
CG X:PRO152 4.9 7.4 1.0

Zinc binding site 8 out of 8 in 4ac1

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Zinc binding site 8 out of 8 in the The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of A Fungal Endo-Beta-N-Acetylglucosaminidase From Glycosyl Hydrolase Family 18, at 1.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn1298

b:16.1
occ:0.50
 ZN X:ZN1296 1.0 11.1 0.5
O X:HOH2434 2.0 24.4 1.0
O X:HOH2120 2.2 18.5 1.0
NE2 X:HIS54 2.4 10.2 1.0
O X:HOH2119 2.9 29.8 1.0
CD2 X:HIS54 3.2 10.1 1.0
CE1 X:HIS54 3.4 10.9 1.0
O X:ASP57 4.1 11.9 1.0
CG X:HIS54 4.4 8.8 1.0
ND1 X:HIS54 4.4 9.7 1.0
O X:HOH2123 4.7 25.8 1.0
CD X:PRO59 4.9 9.9 1.0
C X:ASP57 5.0 11.2 1.0

Reference:

I.Stals, S.Karkehabadi, S.Kim, M.Ward, A.Van Landschoot, B.Devreese, M.Sandgren. High Resolution Crystal Structure of the Endo-N-Acetyl-Beta- D-Glucosaminidase Responsible For the Deglycosylation of Hypocrea Jecorina Cellulases. Plos One V. 7 40854 2012.
ISSN: ESSN 1932-6203
PubMed: 22859955
DOI: 10.1371/JOURNAL.PONE.0040854
Page generated: Sat Oct 26 19:11:10 2024

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