Atomistry » Calcium » PDB 3ecj-3eqd » 3ecq
Atomistry »
  Calcium »
    PDB 3ecj-3eqd »
      3ecq »

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: Sat Jul 13 09:22:19 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy