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Calcium in PDB 3fha: Structure of Endo-Beta-N-Acetylglucosaminidase A

Enzymatic activity of Structure of Endo-Beta-N-Acetylglucosaminidase A

All present enzymatic activity of Structure of Endo-Beta-N-Acetylglucosaminidase A:
3.2.1.96;

Protein crystallography data

The structure of Structure of Endo-Beta-N-Acetylglucosaminidase A, PDB code: 3fha was solved by J.Yin, L.Li, N.Shaw, Y.Li, J.K.Song, W.Zhang, C.Xia, R.Zhang, A.Joachimiak, H.C.Zhang, L.X.Wang, P.Wang, Z.J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.892, 78.972, 117.267, 84.23, 80.77, 64.01
R / Rfree (%) 20.3 / 25.1

Other elements in 3fha:

The structure of Structure of Endo-Beta-N-Acetylglucosaminidase A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Endo-Beta-N-Acetylglucosaminidase A (pdb code 3fha). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Endo-Beta-N-Acetylglucosaminidase A, PDB code: 3fha:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3fha

Go back to Calcium Binding Sites List in 3fha
Calcium binding site 1 out of 4 in the Structure of Endo-Beta-N-Acetylglucosaminidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Endo-Beta-N-Acetylglucosaminidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:29.9
occ:1.00
 O A:HOH1855 2.4 30.5 1.0
O A:ALA366 2.4 13.1 1.0
O A:GLU377 2.5 15.7 1.0
OE1 D:GLU309 2.5 17.3 1.0
O D:HOH655 3.0 20.6 1.0
O D:HOH982 3.0 31.7 1.0
OE1 A:GLU377 3.1 34.6 1.0
C A:ALA366 3.5 12.4 1.0
C A:GLU377 3.5 15.5 1.0
CD D:GLU309 3.6 16.9 1.0
OE2 D:GLU309 4.0 18.0 1.0
CA A:GLU377 4.2 15.8 1.0
CB A:ALA366 4.3 12.1 1.0
CB A:GLN367 4.3 14.1 1.0
CD A:GLU377 4.3 26.3 1.0
CB A:GLU377 4.4 17.3 1.0
CA A:ALA366 4.4 12.3 1.0
N A:GLN367 4.4 12.8 1.0
CA A:GLN367 4.5 13.4 1.0
N A:GLN378 4.6 16.4 1.0
C A:GLN378 4.8 15.3 1.0
CA A:GLN378 4.9 17.0 1.0
N A:GLU379 4.9 14.0 1.0
CG D:GLU309 4.9 15.1 1.0
CG A:GLU377 5.0 23.9 1.0

Calcium binding site 2 out of 4 in 3fha

Go back to Calcium Binding Sites List in 3fha
Calcium binding site 2 out of 4 in the Structure of Endo-Beta-N-Acetylglucosaminidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Endo-Beta-N-Acetylglucosaminidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:28.3
occ:1.00
 O B:GLU377 2.5 15.1 1.0
O B:ALA366 2.5 12.8 1.0
O B:HOH1868 2.5 33.8 1.0
OE1 C:GLU309 2.6 17.4 1.0
O C:HOH1890 2.6 29.8 1.0
O C:HOH667 3.0 16.2 1.0
OE1 B:GLU377 3.0 33.4 1.0
C B:GLU377 3.5 15.4 1.0
C B:ALA366 3.6 12.6 1.0
CD C:GLU309 3.7 16.8 1.0
OE2 C:GLU309 4.0 17.1 1.0
CA B:GLU377 4.1 15.5 1.0
O C:HOH817 4.2 27.4 1.0
CD B:GLU377 4.2 25.6 1.0
CB B:GLN367 4.3 15.3 1.0
CB B:GLU377 4.3 16.9 1.0
CB B:ALA366 4.4 12.2 1.0
N B:GLN367 4.5 13.2 1.0
CA B:ALA366 4.5 12.4 1.0
CA B:GLN367 4.5 14.4 1.0
N B:GLN378 4.6 16.5 1.0
O B:HOH1170 4.6 27.6 1.0
C B:GLN378 4.9 15.6 1.0
CA B:GLN378 4.9 17.2 1.0
CG B:GLU377 4.9 23.0 1.0
N B:GLU379 4.9 14.3 1.0
CG C:GLU309 5.0 14.5 1.0

Calcium binding site 3 out of 4 in 3fha

Go back to Calcium Binding Sites List in 3fha
Calcium binding site 3 out of 4 in the Structure of Endo-Beta-N-Acetylglucosaminidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Endo-Beta-N-Acetylglucosaminidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:32.0
occ:1.00
 O C:ALA366 2.5 13.9 1.0
O C:HOH802 2.6 22.8 1.0
O C:GLU377 2.6 15.3 1.0
OE1 B:GLU309 2.7 15.4 1.0
O B:HOH728 2.9 20.1 1.0
OE1 C:GLU377 3.0 33.2 1.0
C C:GLU377 3.6 15.6 1.0
C C:ALA366 3.6 13.2 1.0
CD B:GLU309 3.7 17.3 1.0
O C:HOH729 3.9 38.6 1.0
OE2 B:GLU309 4.1 17.0 1.0
CD C:GLU377 4.2 29.4 1.0
CA C:GLU377 4.2 16.1 1.0
CB C:ALA366 4.3 12.9 1.0
CB C:GLN367 4.4 16.1 1.0
CB C:GLU377 4.4 17.4 1.0
CA C:ALA366 4.5 13.1 1.0
N C:GLN367 4.6 14.2 1.0
O C:HOH746 4.7 28.1 1.0
N C:GLN378 4.7 16.0 1.0
CA C:GLN367 4.7 15.1 1.0
CG C:GLU377 4.9 23.4 1.0
O B:HOH763 4.9 26.9 1.0
C C:GLN378 5.0 15.5 1.0
CA C:GLN378 5.0 16.8 1.0

Calcium binding site 4 out of 4 in 3fha

Go back to Calcium Binding Sites List in 3fha
Calcium binding site 4 out of 4 in the Structure of Endo-Beta-N-Acetylglucosaminidase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Endo-Beta-N-Acetylglucosaminidase A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:32.6
occ:1.00
 O D:HOH1669 2.5 21.4 1.0
O D:ALA366 2.5 13.3 1.0
OE1 A:GLU309 2.5 16.5 1.0
O D:GLU377 2.6 16.2 1.0
O A:HOH743 2.9 18.2 1.0
O A:HOH633 3.0 22.2 1.0
OE1 D:GLU377 3.0 36.6 1.0
CD A:GLU309 3.6 18.7 1.0
C D:GLU377 3.7 16.2 1.0
C D:ALA366 3.7 13.1 1.0
OE2 A:GLU309 4.0 17.2 1.0
CD D:GLU377 4.2 31.9 1.0
CA D:GLU377 4.2 16.9 1.0
CB D:ALA366 4.3 12.7 1.0
CB D:GLU377 4.4 18.5 1.0
CB D:GLN367 4.4 16.1 1.0
CA D:ALA366 4.5 13.0 1.0
N D:GLN367 4.6 14.0 1.0
CA D:GLN367 4.7 15.1 1.0
N D:GLN378 4.7 16.7 1.0
CG A:GLU309 4.9 14.4 1.0
CG D:GLU377 4.9 25.5 1.0
O A:HOH859 5.0 24.2 1.0

Reference:

J.Yin, L.Li, N.Shaw, Y.Li, J.K.Song, W.Zhang, C.Xia, R.Zhang, A.Joachimiak, H.C.Zhang, L.X.Wang, Z.J.Liu, P.Wang. Structural Basis and Catalytic Mechanism For the Dual Functional Endo-Beta-N-Acetylglucosaminidase A. Plos One V. 4 E4658 2009.
ISSN: ESSN 1932-6203
PubMed: 19252736
DOI: 10.1371/JOURNAL.PONE.0004658
Page generated: Tue Jul 8 12:17:33 2025

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