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Calcium in PDB 2bf6: Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC).

Enzymatic activity of Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC).

All present enzymatic activity of Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC).:
3.2.1.18;

Protein crystallography data

The structure of Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC)., PDB code: 2bf6 was solved by S.Newstead, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.00 / 0.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.981, 69.413, 72.694, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 13.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC). (pdb code 2bf6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC)., PDB code: 2bf6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2bf6

Go back to Calcium Binding Sites List in 2bf6
Calcium binding site 1 out of 2 in the Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1693

b:5.9
occ:1.00
 OD1 A:ASP296 2.3 7.1 1.0
OD1 A:ASP319 2.3 7.9 1.0
O A:TYR320 2.4 6.0 1.0
OD1 A:ASP298 2.4 6.2 1.0
O A:HOH2042 2.4 8.6 1.0
O A:HOH2071 2.4 5.4 1.0
O A:HOH2039 2.5 8.6 1.0
CG A:ASP296 3.3 6.5 1.0
CG A:ASP319 3.4 8.4 1.0
CG A:ASP298 3.4 6.0 1.0
C A:TYR320 3.5 5.5 1.0
N A:TYR320 3.6 5.6 1.0
O A:HOH2041 3.6 51.9 1.0
OD2 A:ASP296 3.7 6.8 1.0
OD2 A:ASP298 3.8 8.2 1.0
C A:ASP319 4.0 7.1 1.0
CA A:ASP319 4.1 6.8 1.0
O A:HOH2064 4.2 47.9 1.0
CA A:TYR320 4.2 5.3 1.0
CB A:ASP319 4.2 8.4 1.0
OD2 A:ASP319 4.2 12.2 1.0
O A:SER324 4.3 7.5 1.0
O A:HOH2062 4.4 33.0 1.0
O A:ILE297 4.5 4.7 1.0
N A:PRO321 4.6 6.0 1.0
CB A:ASP296 4.6 6.6 1.0
C A:ILE297 4.7 4.7 1.0
CA A:PRO321 4.7 6.1 1.0
CB A:ASP298 4.8 5.3 1.0
C A:ASP296 4.8 5.5 1.0
N A:ILE297 4.8 5.0 1.0
O A:ASP319 4.9 10.6 1.0
N A:ASP298 5.0 4.8 1.0

Calcium binding site 2 out of 2 in 2bf6

Go back to Calcium Binding Sites List in 2bf6
Calcium binding site 2 out of 2 in the Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Atomic Resolution Structure of the Bacterial Sialidase Nani From Clostridium Perfringens in Complex with Alpha-Sialic Acid (NEU5AC). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1694

b:7.8
occ:1.00
 O A:ASP515 2.6 5.9 1.0
O A:TRP573 2.6 5.6 1.0
O A:HOH2309 2.6 7.4 1.0
O A:HOH2193 2.7 23.9 1.0
O A:HOH2303 2.8 11.6 1.0
O A:HOH2306 2.8 5.4 1.0
C A:TRP573 3.7 4.8 1.0
C A:ASP515 3.8 5.1 1.0
CB A:ASN516 4.0 7.4 1.0
O A:ASN516 4.0 7.8 1.0
C A:ASN516 4.2 5.9 1.0
OE1 A:GLU511 4.2 7.5 1.0
N A:TRP573 4.3 4.9 1.0
C A:ASP574 4.3 4.7 1.0
N A:GLU575 4.4 4.8 1.0
O A:ASP574 4.4 4.9 1.0
CA A:ASN516 4.5 6.0 1.0
CA A:GLU575 4.5 5.4 1.0
CA A:TRP573 4.5 4.5 1.0
N A:ASN516 4.6 5.6 1.0
N A:ARG517 4.7 5.5 1.0
O A:SER512 4.7 4.3 1.0
CB A:TRP573 4.7 5.3 1.0
N A:ASP574 4.8 4.9 1.0
ND2 A:ASN516 4.8 14.2 1.0
CA A:ASP515 4.9 5.0 1.0
O A:PRO513 4.9 5.4 1.0
CA A:ASP574 4.9 4.7 1.0
O A:HOH2370 5.0 11.0 1.0
CB A:ASP515 5.0 5.1 1.0
CG A:ASN516 5.0 10.1 1.0

Reference:

S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor. The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates. J.Biol.Chem. V. 283 9080 2008.
ISSN: ISSN 0021-9258
PubMed: 18218621
DOI: 10.1074/JBC.M710247200
Page generated: Sat Dec 12 03:32:23 2020

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