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Calcium in PDB 3ecq: Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure

Enzymatic activity of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure

All present enzymatic activity of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure:
3.2.1.97;

Protein crystallography data

The structure of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure, PDB code: 3ecq was solved by M.E.C.Caines, H.Zhu, M.Vuckovic, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.51 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 210.611, 158.209, 112.436, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.5

Other elements in 3ecq:

The structure of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure (pdb code 3ecq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure, PDB code: 3ecq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ecq

Go back to Calcium Binding Sites List in 3ecq
Calcium binding site 1 out of 4 in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2000

b:63.3
occ:1.00
 OD1 A:ASP581 2.1 65.5 1.0
OD1 A:ASN579 2.3 63.1 1.0
O A:LYS583 2.4 64.4 1.0
OD2 A:ASP588 2.5 60.4 1.0
OD1 A:ASP577 2.5 65.1 1.0
OD1 A:ASP588 2.6 59.6 1.0
CG A:ASP588 2.9 59.9 1.0
CG A:ASP581 3.0 65.6 1.0
OD2 A:ASP581 3.2 64.0 1.0
CG A:ASN579 3.3 60.9 1.0
C A:LYS583 3.6 65.4 1.0
CG A:ASP577 3.7 66.8 1.0
ND2 A:ASN579 3.7 59.0 1.0
OD2 A:ASP577 4.2 68.2 1.0
N A:LYS583 4.3 68.4 1.0
CB A:ASP581 4.4 67.0 1.0
CB A:ASP588 4.4 58.4 1.0
N A:VAL584 4.4 64.8 1.0
CG A:LYS583 4.4 67.1 1.0
CA A:VAL584 4.5 63.1 1.0
N A:ASP581 4.5 67.4 1.0
CA A:LYS583 4.5 67.7 1.0
N A:ASN579 4.5 61.4 1.0
OD1 A:ASP585 4.6 60.9 1.0
CB A:ASN579 4.6 60.5 1.0
N A:ASP585 4.7 60.4 1.0
N A:ALA578 4.7 61.8 1.0
CB A:ASP577 4.8 66.4 1.0
CA A:ASP577 4.8 64.5 1.0
CA A:ASP581 4.9 68.4 1.0
CG A:ASP585 4.9 60.9 1.0
N A:ASP588 4.9 56.2 1.0
CA A:ASN579 4.9 61.7 1.0

Calcium binding site 2 out of 4 in 3ecq

Go back to Calcium Binding Sites List in 3ecq
Calcium binding site 2 out of 4 in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:42.1
occ:1.00
 O A:HOH2004 2.1 34.9 1.0
O A:TRP1284 2.2 34.8 1.0
OE2 A:GLU1235 2.2 32.6 1.0
O A:GLU1281 2.3 37.2 1.0
OD2 A:ASP1411 2.4 31.3 1.0
O A:ASP1233 2.5 34.9 1.0
OD1 A:ASP1411 2.7 32.2 1.0
CG A:ASP1411 2.9 34.0 1.0
CD A:GLU1235 3.4 34.8 1.0
C A:TRP1284 3.4 33.9 1.0
C A:GLU1281 3.5 38.3 1.0
C A:ASP1233 3.6 34.8 1.0
O A:HOH2055 4.0 29.8 1.0
CG A:GLU1235 4.0 36.0 1.0
N A:TRP1284 4.0 35.6 1.0
OG A:SER1285 4.1 33.9 1.0
CA A:TRP1284 4.2 34.5 1.0
N A:GLY1282 4.4 39.5 1.0
OE1 A:GLU1235 4.4 34.4 1.0
CA A:GLU1281 4.4 39.0 1.0
CA A:ASP1233 4.4 36.0 1.0
N A:SER1285 4.4 32.4 1.0
N A:GLU1281 4.4 37.6 1.0
CA A:GLY1282 4.4 39.3 1.0
CB A:ASP1411 4.4 35.4 1.0
CB A:PHE1234 4.5 32.0 1.0
CB A:ASP1233 4.5 37.3 1.0
CB A:TRP1284 4.6 34.6 1.0
CA A:SER1285 4.6 31.9 1.0
OD1 A:ASN1412 4.6 38.9 1.0
CB A:GLU1281 4.6 40.3 1.0
N A:PHE1234 4.7 33.9 1.0
N A:ASN1283 4.8 38.2 1.0
C A:GLY1282 4.8 38.7 1.0
N A:GLU1235 4.8 34.7 1.0
CA A:PHE1234 4.9 33.1 1.0
C A:PHE1234 4.9 33.7 1.0

Calcium binding site 3 out of 4 in 3ecq

Go back to Calcium Binding Sites List in 3ecq
Calcium binding site 3 out of 4 in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2000

b:54.4
occ:1.00
 O B:LYS583 2.2 67.4 1.0
OD1 B:ASN579 2.3 62.6 1.0
OD1 B:ASP588 2.4 59.2 1.0
OD1 B:ASP581 2.5 71.4 1.0
O B:HOH2009 2.5 20.5 1.0
OD2 B:ASP588 2.5 60.7 1.0
OD1 B:ASP577 2.6 68.2 1.0
CG B:ASP588 2.8 59.6 1.0
CG B:ASP577 3.3 69.4 1.0
CG B:ASP581 3.4 71.3 1.0
C B:LYS583 3.5 69.0 1.0
CG B:ASN579 3.5 62.3 1.0
OD2 B:ASP581 3.8 71.1 1.0
CA B:ASP577 3.9 64.9 1.0
N B:ALA578 4.0 61.8 1.0
OD2 B:ASP577 4.0 71.9 1.0
CB B:ASP577 4.0 67.9 1.0
N B:ASN579 4.0 62.3 1.0
N B:LYS583 4.1 73.6 1.0
ND2 B:ASN579 4.2 60.7 1.0
CB B:ASP588 4.3 57.5 1.0
N B:ASP581 4.3 72.5 1.0
N B:VAL584 4.3 67.9 1.0
CA B:VAL584 4.4 64.8 1.0
CA B:LYS583 4.4 72.7 1.0
C B:ASP577 4.4 63.4 1.0
OD1 B:ASP585 4.5 63.3 1.0
N B:ALA580 4.5 67.9 1.0
CB B:ASN579 4.6 62.0 1.0
CA B:ASN579 4.6 63.2 1.0
CB B:ASP581 4.7 73.3 1.0
C B:ASN579 4.7 66.5 1.0
N B:LYS582 4.8 75.8 1.0
CG B:LYS583 4.8 73.0 1.0
CA B:ASP581 4.9 74.6 1.0
N B:ASP585 5.0 61.9 1.0
C B:ASP581 5.0 76.2 1.0

Calcium binding site 4 out of 4 in 3ecq

Go back to Calcium Binding Sites List in 3ecq
Calcium binding site 4 out of 4 in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2001

b:36.7
occ:1.00
 OE2 B:GLU1235 2.3 38.5 1.0
O B:GLU1281 2.4 42.1 1.0
O B:ASP1233 2.4 39.1 1.0
OD2 B:ASP1411 2.4 38.8 1.0
OD1 B:ASP1411 2.5 39.2 1.0
O B:TRP1284 2.5 40.2 1.0
CG B:ASP1411 2.8 40.3 1.0
O B:HOH2014 2.9 29.6 1.0
CD B:GLU1235 3.4 39.8 1.0
C B:GLU1281 3.5 43.0 1.0
C B:ASP1233 3.5 38.8 1.0
C B:TRP1284 3.7 39.8 1.0
CG B:GLU1235 3.9 39.5 1.0
OD1 B:ASN1412 4.0 44.2 1.0
CA B:ASP1233 4.1 39.7 1.0
CB B:ASP1233 4.2 40.8 1.0
CA B:GLU1281 4.3 44.1 1.0
CB B:ASP1411 4.3 41.6 1.0
OG B:SER1285 4.4 41.2 1.0
N B:GLY1282 4.4 43.8 1.0
N B:TRP1284 4.4 40.9 1.0
CB B:GLU1281 4.4 44.9 1.0
N B:GLU1281 4.4 43.4 1.0
CA B:GLY1282 4.5 43.4 1.0
OE1 B:GLU1235 4.5 39.2 1.0
CA B:TRP1284 4.6 40.1 1.0
N B:PHE1234 4.6 37.9 1.0
CB B:PHE1234 4.6 37.1 1.0
N B:SER1285 4.7 38.8 1.0
CA B:SER1285 4.9 38.6 1.0
N B:GLU1235 4.9 38.2 1.0
CB B:TRP1284 4.9 39.8 1.0
CA B:PHE1234 4.9 37.4 1.0
CG B:ASN1412 5.0 43.4 1.0
CG B:ASP1233 5.0 41.0 1.0
C B:PHE1234 5.0 37.7 1.0

Reference:

M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, N.C.Strynadka. The Structural Basis For T-Antigen Hydrolysis By Streptococcus Pneumoniae: A Target For Structure-Based Vaccine Design. J.Biol.Chem. V. 283 31279 2008.
ISSN: ISSN 0021-9258
PubMed: 18784084
DOI: 10.1074/JBC.C800150200
Page generated: Tue Jul 8 11:51:08 2025

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