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Manganese in PDB 2zxq: Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf)

Enzymatic activity of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf)

All present enzymatic activity of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf):
3.2.1.97;

Protein crystallography data

The structure of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf), PDB code: 2zxq was solved by R.Suzuki, T.Katayama, H.Ashida, K.Yamamoto, M.Kitaoka, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.49 / 2.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 192.267, 192.267, 123.017, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 19.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf) (pdb code 2zxq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf), PDB code: 2zxq:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2zxq

Go back to Manganese Binding Sites List in 2zxq
Manganese binding site 1 out of 4 in the Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:30.6
occ:1.00
 OD1 A:ASP601 2.3 24.8 1.0
O A:ALA607 2.4 26.4 1.0
OD2 A:ASP612 2.4 21.8 1.0
OD1 A:ASN603 2.4 24.2 1.0
OD1 A:ASP612 2.4 21.6 1.0
O A:HOH78 2.5 24.3 1.0
OD1 A:ASP605 2.5 25.1 1.0
CG A:ASP612 2.7 21.2 1.0
CG A:ASP605 3.4 27.0 1.0
CG A:ASN603 3.4 26.3 1.0
CG A:ASP601 3.5 27.2 1.0
C A:ALA607 3.5 27.1 1.0
OD2 A:ASP605 3.8 25.8 1.0
ND2 A:ASN603 3.9 23.9 1.0
N A:ASP605 4.2 29.1 1.0
CA A:ASP601 4.2 25.3 1.0
CB A:ASP612 4.3 21.1 1.0
N A:ALA607 4.3 27.7 1.0
OD2 A:ASP601 4.3 26.3 1.0
N A:ASN603 4.3 26.0 1.0
CB A:ASP601 4.3 25.1 1.0
CA A:VAL608 4.4 25.8 1.0
N A:VAL608 4.4 25.6 1.0
CA A:ALA607 4.5 27.1 1.0
CB A:ASP605 4.5 27.4 1.0
C A:ASP601 4.5 25.4 1.0
OD1 A:ASN609 4.5 24.1 1.0
N A:GLU604 4.6 28.6 1.0
N A:GLU602 4.6 25.4 1.0
CB A:ASN603 4.7 25.9 1.0
CA A:ASP605 4.7 28.3 1.0
C A:ASN603 4.8 27.8 1.0
CA A:ASN603 4.8 26.6 1.0
N A:ASN609 4.8 23.0 1.0
N A:GLY606 4.8 28.6 1.0
CB A:ALA607 4.9 26.8 1.0
C A:ASP605 5.0 28.5 1.0
N A:ASP612 5.0 21.1 1.0

Manganese binding site 2 out of 4 in 2zxq

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Manganese binding site 2 out of 4 in the Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:42.4
occ:1.00
 OE1 A:GLU727 2.1 27.4 1.0
OD2 A:ASP752 2.2 24.8 1.0
O A:HOH1708 2.2 23.6 1.0
NE2 A:HIS1299 2.3 22.3 1.0
O A:HOH223 2.3 20.6 1.0
O A:HOH272 2.3 23.0 1.0
CD A:GLU727 3.1 27.2 1.0
CG A:ASP752 3.1 27.2 1.0
CD2 A:HIS1299 3.2 24.3 1.0
CE1 A:HIS1299 3.3 23.0 1.0
OE2 A:GLU727 3.4 25.0 1.0
OD1 A:ASP752 3.5 26.8 1.0
O A:HOH128 4.1 22.5 1.0
O A:HOH298 4.2 25.8 1.0
O A:HOH276 4.2 23.6 1.0
CA A:SER1301 4.3 25.6 1.0
O A:LEU1300 4.3 25.0 1.0
ND1 A:HIS1299 4.4 24.0 1.0
CG A:HIS1299 4.4 23.4 1.0
CB A:ASP752 4.4 25.2 1.0
CG A:GLU727 4.4 25.6 1.0
O A:HOH248 4.4 23.0 1.0
CB A:GLU727 4.7 24.8 1.0
N A:GLU1302 4.8 25.9 1.0
OG A:SER683 4.8 20.9 1.0
CB A:LEU751 4.9 24.7 1.0
CB A:SER1301 4.9 25.6 1.0

Manganese binding site 3 out of 4 in 2zxq

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Manganese binding site 3 out of 4 in the Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3

b:33.2
occ:1.00
 ND2 A:ASN1135 2.3 20.5 1.0
O A:ALA1136 2.4 25.5 1.0
O A:GLY1108 2.4 26.1 1.0
OD2 A:ASP1248 2.4 24.8 1.0
O A:HOH1724 2.4 25.9 1.0
O A:HOH167 2.5 18.5 1.0
OD1 A:ASP1248 2.7 23.4 1.0
CG A:ASP1248 2.9 27.2 1.0
C A:GLY1108 3.4 24.8 1.0
C A:ALA1136 3.5 26.4 1.0
CG A:ASN1135 3.6 25.0 1.0
CA A:GLY1108 3.8 24.5 1.0
N A:ALA1136 3.9 25.0 1.0
C A:ASN1135 4.1 25.3 1.0
CA A:ALA1136 4.3 25.9 1.0
OD1 A:ASN1135 4.3 28.2 1.0
CB A:ASP1248 4.4 26.0 1.0
OD1 A:ASP1249 4.4 23.1 1.0
O A:ASN1135 4.5 24.9 1.0
NE2 A:HIS1203 4.5 24.9 1.0
N A:PHE1109 4.6 25.3 1.0
ND2 A:ASN1110 4.6 21.2 1.0
N A:MET1137 4.6 27.1 1.0
O A:HOH122 4.6 22.0 1.0
CA A:ASN1135 4.7 24.6 1.0
O A:HOH297 4.7 24.2 1.0
CB A:ASN1135 4.7 23.4 1.0
CA A:MET1137 4.8 27.5 1.0
CB A:ALA1136 4.9 25.6 1.0
OD1 A:ASN1110 4.9 25.8 1.0
CB A:PHE1109 4.9 25.2 1.0
CG A:ASP1249 5.0 27.3 1.0
OD2 A:ASP1249 5.0 29.8 1.0

Manganese binding site 4 out of 4 in 2zxq

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Manganese binding site 4 out of 4 in the Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Endo-Alpha-N-Acetylgalactosaminidase From Bifidobacterium Longum (Engbf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn4

b:37.6
occ:1.00
 O A:GLY1274 2.3 28.1 1.0
OE2 A:GLU1276 2.3 32.2 1.0
O A:ASP1322 2.3 32.4 1.0
O A:TRP1325 2.4 27.8 1.0
O A:HOH1930 2.4 30.8 1.0
OD2 A:ASP1442 2.5 28.2 1.0
OD1 A:ASP1442 2.6 28.4 1.0
CG A:ASP1442 2.9 28.3 1.0
C A:GLY1274 3.4 27.9 1.0
C A:ASP1322 3.5 32.6 1.0
CD A:GLU1276 3.5 31.3 1.0
C A:TRP1325 3.6 28.1 1.0
CA A:GLY1274 3.9 28.2 1.0
CG A:GLU1276 4.0 29.7 1.0
N A:TRP1325 4.2 27.9 1.0
CB A:ASP1322 4.2 35.6 1.0
CA A:ASP1322 4.3 34.4 1.0
CA A:TRP1325 4.4 28.0 1.0
OG A:SER1326 4.4 28.2 1.0
N A:GLY1323 4.4 31.2 1.0
CB A:ASP1442 4.4 30.6 1.0
O A:HOH2258 4.5 41.5 1.0
N A:ASP1322 4.5 33.4 1.0
OE1 A:GLU1276 4.5 30.2 1.0
CA A:GLY1323 4.5 30.3 1.0
N A:PHE1275 4.5 28.9 1.0
N A:SER1326 4.5 27.3 1.0
OD1 A:ASN1443 4.7 38.2 1.0
CA A:SER1326 4.7 26.9 1.0
N A:THR1324 4.8 29.8 1.0
CB A:TRP1325 4.8 28.2 1.0
CB A:PHE1275 4.8 28.8 1.0
C A:GLY1323 4.8 29.4 1.0
CA A:PHE1275 5.0 29.4 1.0
C A:PHE1275 5.0 30.0 1.0
N A:GLU1276 5.0 29.6 1.0

Reference:

R.Suzuki, T.Katayama, M.Kitaoka, H.Kumagai, T.Wakagi, H.Shoun, H.Ashida, K.Yamamoto, S.Fushinobu. Crystallographic and Mutational Analyses of Substrate Recognition of Endo-{Alpha}-N-Acetylgalactosaminidase From Bifidobacterium Longum. J.Biochem. 2009.
ISSN: ISSN 0021-924X
PubMed: 19502354
DOI: 10.1093/JB/MVP086
Page generated: Tue Dec 15 04:07:15 2020

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