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Calcium in PDB 5a56: The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen

Enzymatic activity of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen

All present enzymatic activity of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen:
3.2.1.97;

Protein crystallography data

The structure of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen, PDB code: 5a56 was solved by K.J.Gregg, M.D.L.Suits, L.Deng, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 1.80
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.713, 121.764, 139.429, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.8

Other elements in 5a56:

The structure of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen (pdb code 5a56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen, PDB code: 5a56:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5a56

Go back to Calcium Binding Sites List in 5a56
Calcium binding site 1 out of 3 in the The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2427

b:15.6
occ:1.00
 OD1 A:ASP577 2.3 18.5 1.0
O A:ASN583 2.3 18.5 1.0
OD1 A:ASP581 2.3 18.2 1.0
O A:HOH3413 2.4 14.1 1.0
OD1 A:ASN579 2.4 14.8 1.0
OD1 A:ASP588 2.5 14.4 1.0
OD2 A:ASP588 2.5 12.2 1.0
CG A:ASP588 2.8 12.4 1.0
CG A:ASP581 3.2 18.7 1.0
CG A:ASN579 3.5 16.0 1.0
CG A:ASP577 3.5 17.1 1.0
C A:ASN583 3.5 19.5 1.0
OD2 A:ASP581 3.6 17.6 1.0
ND2 A:ASN579 3.9 14.5 1.0
N A:ASN583 4.1 21.2 1.0
N A:ALA578 4.2 16.0 1.0
N A:ASN579 4.3 16.8 1.0
OD2 A:ASP577 4.3 17.1 1.0
CA A:ASN583 4.3 21.3 1.0
CA A:ASP577 4.3 16.2 1.0
CB A:ASP588 4.3 12.3 1.0
CB A:ASP577 4.3 16.7 1.0
N A:ASP581 4.4 18.8 1.0
N A:VAL584 4.5 15.6 1.0
OD1 A:ASP585 4.5 15.2 1.0
CB A:ASP581 4.5 18.3 1.0
CA A:VAL584 4.5 14.9 1.0
CB A:ASN583 4.5 24.5 1.0
CB A:ASN579 4.7 15.8 1.0
C A:ASP577 4.8 16.5 1.0
N A:LYS582 4.8 19.5 1.0
CA A:ASP581 4.8 18.5 1.0
N A:ASP585 4.8 14.2 1.0
CA A:ASN579 4.8 16.9 1.0
C A:ASP581 4.9 18.2 1.0
N A:ASP588 4.9 12.0 1.0
C A:ASN579 5.0 18.0 1.0
N A:ALA580 5.0 18.7 1.0

Calcium binding site 2 out of 3 in 5a56

Go back to Calcium Binding Sites List in 5a56
Calcium binding site 2 out of 3 in the The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2429

b:12.5
occ:1.00
 O A:GLU1281 2.3 13.0 1.0
O A:TRP1284 2.4 11.2 1.0
OE2 A:GLU1235 2.4 13.2 1.0
O A:ASP1233 2.4 12.3 1.0
O A:HOH4332 2.4 11.9 1.0
OD2 A:ASP1411 2.5 11.8 1.0
OD1 A:ASP1411 2.6 11.1 1.0
CG A:ASP1411 2.9 11.8 1.0
C A:GLU1281 3.5 13.3 1.0
CD A:GLU1235 3.5 13.6 1.0
C A:TRP1284 3.6 11.9 1.0
C A:ASP1233 3.6 12.2 1.0
CG A:GLU1235 4.1 13.7 1.0
N A:TRP1284 4.2 11.9 1.0
CA A:ASP1233 4.3 12.5 1.0
OG A:SER1285 4.4 10.9 1.0
CA A:TRP1284 4.4 11.8 1.0
N A:GLU1281 4.4 13.2 1.0
CA A:GLU1281 4.4 14.2 1.0
N A:GLY1282 4.4 13.6 1.0
CB A:ASP1411 4.4 11.2 1.0
O A:HOH3712 4.4 24.8 1.0
CB A:ASP1233 4.4 13.8 1.0
CA A:GLY1282 4.5 13.0 1.0
OD1 A:ASN1412 4.5 15.8 1.0
OE1 A:GLU1235 4.6 13.5 1.0
N A:SER1285 4.6 11.9 1.0
N A:PHE1234 4.6 11.6 1.0
CB A:PHE1234 4.6 11.5 1.0
CB A:GLU1281 4.6 16.2 1.0
CA A:SER1285 4.7 11.5 1.0
CB A:TRP1284 4.8 11.5 1.0
C A:GLY1282 4.8 13.2 1.0
N A:ASN1283 4.9 12.5 1.0
CA A:PHE1234 4.9 11.6 1.0
C A:PHE1234 4.9 11.6 1.0
N A:GLU1235 4.9 11.5 1.0

Calcium binding site 3 out of 3 in 5a56

Go back to Calcium Binding Sites List in 5a56
Calcium binding site 3 out of 3 in the The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of GH101 From Streptococcus Pneumoniae TIGR4 in Complex with 1-O-Methyl-T-Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2430

b:13.1
occ:1.00
 O A:ASP1091 2.4 12.7 1.0
O A:HOH4098 2.4 13.2 1.0
OD1 A:ASN1090 2.4 13.2 1.0
O A:HOH4097 2.4 12.8 1.0
O A:GLY1063 2.4 10.7 1.0
OD2 A:ASP1207 2.4 12.9 1.0
OD1 A:ASP1207 2.6 12.1 1.0
CG A:ASP1207 2.8 12.1 1.0
C A:GLY1063 3.4 11.5 1.0
C A:ASP1091 3.5 13.9 1.0
CG A:ASN1090 3.6 13.8 1.0
CA A:GLY1063 3.9 11.3 1.0
N A:ASP1091 3.9 15.1 1.0
CA A:ASP1091 4.2 14.9 1.0
ND2 A:ASN1090 4.3 13.7 1.0
O A:HOH4145 4.3 16.3 1.0
CB A:ASP1207 4.4 11.6 1.0
C A:ASN1090 4.4 14.7 1.0
O A:HOH4100 4.5 17.6 1.0
N A:MET1092 4.6 13.8 1.0
N A:PHE1064 4.6 11.4 1.0
CB A:ASP1091 4.6 16.1 1.0
NE2 A:HIS1160 4.7 12.4 1.0
O A:HOH3520 4.7 21.7 1.0
OD1 A:ASN1065 4.7 12.4 1.0
CB A:ASN1090 4.8 13.5 1.0
O A:HOH3512 4.8 20.2 1.0
CA A:MET1092 4.9 13.5 1.0
CB A:PHE1064 4.9 12.6 1.0
CA A:ASN1090 4.9 14.2 1.0

Reference:

K.J.Gregg, M.D.Suits, L.Deng, D.J.Vocadlo, A.B.Boraston. Structural Analysis of A Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights Into Its Mechanism. J.Biol.Chem. V. 290 25657 2015.
ISSN: ESSN 1083-351X
PubMed: 26304114
DOI: 10.1074/JBC.M115.680470
Page generated: Sun Jul 14 16:18:55 2024

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