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Calcium in PDB 4bq5: Structural Analysis of An Exo-Beta-Agarase

Enzymatic activity of Structural Analysis of An Exo-Beta-Agarase

All present enzymatic activity of Structural Analysis of An Exo-Beta-Agarase:
3.2.1.81;

Protein crystallography data

The structure of Structural Analysis of An Exo-Beta-Agarase, PDB code: 4bq5 was solved by B.Pluvinage, J.H.Hehemann, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.030, 116.170, 207.970, 90.00, 90.00, 90.00
R / Rfree (%) 18.917 / 25.149

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Analysis of An Exo-Beta-Agarase (pdb code 4bq5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structural Analysis of An Exo-Beta-Agarase, PDB code: 4bq5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4bq5

Go back to Calcium Binding Sites List in 4bq5
Calcium binding site 1 out of 6 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1802

b:17.3
occ:1.00
 O A:ASP50 2.3 12.4 1.0
O A:LYS81 2.3 16.1 1.0
OD2 A:ASP228 2.4 12.5 1.0
O A:HOH2032 2.5 30.0 1.0
OD1 A:ASP228 2.5 12.3 1.0
OG A:SER80 2.6 20.9 1.0
OE2 A:GLU52 2.6 19.8 1.0
CG A:ASP228 2.8 13.0 1.0
C A:ASP50 3.4 13.5 1.0
C A:LYS81 3.4 18.5 1.0
CD A:GLU52 3.6 19.9 1.0
N A:LYS81 3.8 18.9 1.0
CB A:SER80 3.8 21.1 1.0
CG A:GLU52 3.9 17.9 1.0
OD1 A:ASN229 3.9 12.2 1.0
CA A:LYS81 4.0 19.0 1.0
CA A:ASP50 4.1 14.2 1.0
O A:HOH2031 4.2 17.6 1.0
CB A:ASP50 4.2 14.6 1.0
CB A:ASP228 4.3 13.1 1.0
CB A:LYS81 4.4 20.0 1.0
C A:SER80 4.4 20.1 1.0
O A:HOH2005 4.5 13.6 1.0
N A:PHE51 4.5 13.6 1.0
CA A:SER80 4.6 22.0 1.0
N A:GLY82 4.6 17.4 1.0
C A:PHE51 4.7 15.1 1.0
N A:GLU52 4.7 16.8 1.0
CB A:PHE51 4.7 14.0 1.0
CG A:ASN229 4.7 13.1 1.0
OE1 A:GLU52 4.8 20.8 1.0
CA A:PHE51 4.8 14.1 1.0
ND2 A:ASN229 4.9 12.6 1.0
CE1 A:TYR72 4.9 19.8 1.0
CA A:GLY82 4.9 16.8 1.0

Calcium binding site 2 out of 6 in 4bq5

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Calcium binding site 2 out of 6 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1803

b:16.4
occ:1.00
 O A:HOH2245 3.1 7.9 1.0
ND2 A:ASN336 3.2 11.7 1.0
N A:TYR754 3.4 15.0 1.0
CA A:ASN336 3.5 11.1 1.0
CB A:TYR754 3.6 15.2 1.0
CB A:ARG752 3.6 13.6 1.0
N A:ALA753 3.8 14.3 1.0
CB A:ASN336 3.9 11.5 1.0
CG A:ARG752 3.9 13.6 1.0
O A:SER335 3.9 10.1 1.0
O A:ASN336 4.0 11.8 1.0
CD A:ARG752 4.0 13.6 1.0
CG A:ASN336 4.0 11.5 1.0
C A:ASN336 4.0 11.2 1.0
CA A:TYR754 4.1 15.2 1.0
CB A:ALA753 4.2 14.6 1.0
C A:ARG752 4.2 13.9 1.0
CA A:ALA753 4.3 14.2 1.0
C A:ALA753 4.3 15.4 1.0
CA A:ARG752 4.4 13.5 1.0
N A:ASN336 4.5 10.9 1.0
O A:HOH2131 4.5 27.3 1.0
C A:SER335 4.6 10.8 1.0
O A:SER338 4.8 11.7 1.0
O A:ASP362 4.8 15.1 1.0
CG A:TYR754 4.8 15.7 1.0
NE A:ARG752 4.8 13.3 1.0
O A:ARG752 4.9 13.0 1.0

Calcium binding site 3 out of 6 in 4bq5

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Calcium binding site 3 out of 6 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1804

b:35.4
occ:1.00
 O A:HOH2281 2.3 21.9 1.0
OE2 A:GLU427 2.4 14.2 1.0
OD1 A:ASN400 2.6 26.0 1.0
O A:PRO397 2.6 26.1 1.0
OE1 A:GLU427 2.9 14.6 1.0
CD A:GLU427 3.0 14.6 1.0
CG A:ASN400 3.4 24.4 1.0
OE1 A:GLU432 3.6 41.3 1.0
CD A:GLU432 3.7 40.0 1.0
OE2 A:GLU432 3.7 42.5 1.0
ND2 A:ASN400 3.8 23.8 1.0
C A:PRO397 3.8 25.2 1.0
CG A:GLU427 4.5 14.2 1.0
CB A:ASN400 4.5 23.6 1.0
CA A:PRO397 4.6 27.3 1.0
CG A:GLU432 4.6 36.5 1.0
NE2 A:HIS401 4.7 20.0 1.0
CB A:GLU432 4.7 33.1 1.0
N A:LEU398 4.8 24.4 1.0
OH A:TYR438 4.8 15.4 1.0
CE1 A:TYR438 4.8 13.7 1.0
O A:HOH2291 4.9 26.2 1.0
CA A:LEU398 4.9 22.7 1.0
CB A:PRO397 5.0 27.3 1.0

Calcium binding site 4 out of 6 in 4bq5

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Calcium binding site 4 out of 6 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1805

b:19.4
occ:1.00
 O B:LYS81 2.2 14.7 1.0
O B:HOH2003 2.3 19.9 1.0
O B:ASP50 2.3 20.0 1.0
OD2 B:ASP228 2.4 12.5 1.0
OE2 B:GLU52 2.4 24.1 1.0
OD1 B:ASP228 2.6 12.0 1.0
OG B:SER80 2.8 14.3 1.0
CG B:ASP228 2.8 13.6 1.0
C B:LYS81 3.3 15.5 1.0
C B:ASP50 3.5 20.0 1.0
CD B:GLU52 3.6 25.6 1.0
N B:LYS81 3.6 17.0 1.0
CA B:LYS81 3.9 16.5 1.0
CB B:SER80 4.0 15.7 1.0
O B:HOH2026 4.1 18.4 1.0
CG B:GLU52 4.1 25.7 1.0
CA B:ASP50 4.2 20.1 1.0
OD1 B:ASN229 4.2 15.2 1.0
CB B:LYS81 4.3 17.8 1.0
C B:SER80 4.4 16.8 1.0
CB B:ASP228 4.4 14.4 1.0
N B:GLY82 4.4 15.5 1.0
CB B:ASP50 4.4 21.7 1.0
O B:HOH2006 4.4 24.2 1.0
N B:PHE51 4.5 20.4 1.0
O B:HOH2004 4.6 21.0 1.0
CB B:PHE51 4.6 20.4 1.0
OE1 B:GLU52 4.6 25.9 1.0
CA B:SER80 4.7 17.0 1.0
N B:GLU52 4.7 24.2 1.0
CA B:GLY82 4.8 15.7 1.0
CG B:ASN229 4.8 16.4 1.0
CA B:PHE51 4.9 21.1 1.0
C B:PHE51 4.9 22.1 1.0
ND2 B:ASN229 4.9 15.2 1.0

Calcium binding site 5 out of 6 in 4bq5

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Calcium binding site 5 out of 6 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1806

b:26.2
occ:1.00
 ND2 B:ASN400 2.4 21.6 1.0
O B:PRO397 2.5 20.7 1.0
O B:HOH2243 2.5 16.1 1.0
O B:HOH2242 2.5 22.2 1.0
OE1 B:GLU427 2.6 13.3 1.0
OE2 B:GLU427 2.7 15.1 1.0
CD B:GLU427 3.0 14.3 1.0
OE2 B:GLU432 3.1 30.6 1.0
CG B:ASN400 3.2 21.1 1.0
OD1 B:ASN400 3.5 21.2 1.0
C B:PRO397 3.6 21.6 1.0
CD B:GLU432 3.6 30.3 1.0
OE1 B:GLU432 3.8 31.7 1.0
CA B:PRO397 4.3 22.0 1.0
CG B:GLU427 4.4 14.5 1.0
CB B:ASN400 4.5 20.8 1.0
NE2 B:HIS401 4.5 18.8 1.0
N B:LEU398 4.6 21.1 1.0
CG B:GLU432 4.7 28.6 1.0
CA B:LEU398 4.7 21.9 1.0
CB B:PRO397 4.8 21.9 1.0
O B:HOH2252 4.8 24.9 1.0
CE2 B:TYR438 4.9 17.0 1.0
OH B:TYR438 4.9 18.4 1.0

Calcium binding site 6 out of 6 in 4bq5

Go back to Calcium Binding Sites List in 4bq5
Calcium binding site 6 out of 6 in the Structural Analysis of An Exo-Beta-Agarase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Analysis of An Exo-Beta-Agarase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1807

b:21.6
occ:1.00
 O B:HOH2209 3.1 37.7 1.0
O B:HOH2210 3.1 10.5 1.0
ND2 B:ASN336 3.2 14.5 1.0
N B:TYR754 3.4 16.1 1.0
CB B:TYR754 3.5 16.6 1.0
CB B:ARG752 3.6 13.5 1.0
CA B:ASN336 3.6 13.3 1.0
N B:ALA753 3.8 15.3 1.0
O B:ASN336 3.9 12.0 1.0
CB B:ASN336 3.9 14.1 1.0
O B:SER335 4.0 14.3 1.0
CG B:ARG752 4.0 12.3 1.0
C B:ASN336 4.0 12.6 1.0
CA B:TYR754 4.1 16.4 1.0
CG B:ASN336 4.1 14.3 1.0
C B:ARG752 4.1 14.8 1.0
CD B:ARG752 4.3 11.2 1.0
CA B:ARG752 4.3 14.5 1.0
C B:ALA753 4.4 15.7 1.0
CA B:ALA753 4.4 15.0 1.0
CB B:ALA753 4.5 14.3 1.0
N B:ASN336 4.7 13.5 1.0
O B:SER338 4.7 13.9 1.0
C B:SER335 4.7 14.1 1.0
O B:ARG752 4.7 15.1 1.0
CG B:TYR754 4.8 16.1 1.0
O B:ASP362 5.0 19.0 1.0
NE B:ARG752 5.0 10.7 1.0

Reference:

B.Pluvinage, J.H.Hehemann, A.B.Boraston. Substrate Recognition and Hydrolysis By A Family 50 Exo-Beta-Agarase AGA50D From the Marine Bacterium Saccharophagus Degradans J.Biol.Chem. V. 288 28078 2013.
ISSN: ISSN 0021-9258
PubMed: 23921382
DOI: 10.1074/JBC.M113.491068
Page generated: Tue Jul 8 19:00:13 2025

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