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Calcium in PDB 2vk7: The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates

Enzymatic activity of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates

All present enzymatic activity of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates:
3.2.1.18;

Protein crystallography data

The structure of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates, PDB code: 2vk7 was solved by S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.2
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.600, 97.400, 72.600, 90.00, 91.00, 90.00
R / Rfree (%) 13.1 / 15.9

Other elements in 2vk7:

The structure of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates (pdb code 2vk7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates, PDB code: 2vk7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2vk7

Go back to Calcium Binding Sites List in 2vk7
Calcium binding site 1 out of 4 in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates


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 Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2692

b:13.0
occ:1.00
 O A:ASP1515 2.6 10.9 1.0
O A:HOH3566 2.6 11.8 1.0
O A:TRP1573 2.7 10.2 1.0
O A:HOH3559 2.8 16.9 1.0
O A:HOH3562 2.8 9.7 1.0
O A:HOH3221 2.9 19.6 1.0
C A:TRP1573 3.8 9.7 1.0
C A:ASP1515 3.8 9.2 1.0
O A:ASN1516 4.0 12.7 1.0
O A:HOH3148 4.0 30.4 1.0
CB A:ASN1516 4.0 11.1 1.0
C A:ASN1516 4.1 10.1 1.0
OE1 A:GLU1511 4.2 12.7 1.0
N A:TRP1573 4.3 9.5 1.0
C A:ASP1574 4.3 10.2 1.0
CA A:GLU1575 4.4 10.7 1.0
O A:ASP1574 4.4 10.1 1.0
N A:GLU1575 4.4 9.7 1.0
CA A:ASN1516 4.5 10.3 1.0
CA A:TRP1573 4.5 9.4 1.0
N A:ASN1516 4.6 9.6 1.0
N A:ARG1517 4.7 9.8 1.0
O A:SER1512 4.7 8.4 1.0
N A:ASP1574 4.8 9.3 1.0
CB A:TRP1573 4.8 10.1 1.0
ND2 A:ASN1516 4.8 17.6 1.0
O A:PRO1513 4.8 9.4 1.0
CA A:ASP1515 4.8 9.2 1.0
O A:HOH3653 4.9 14.8 1.0
CA A:ASP1574 4.9 10.0 1.0
CB A:GLU1575 5.0 11.7 1.0

Calcium binding site 2 out of 4 in 2vk7

Go back to Calcium Binding Sites List in 2vk7
Calcium binding site 2 out of 4 in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates


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 Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2694

b:10.4
occ:1.00
 OD1 A:ASP1296 2.3 12.9 1.0
OD1 A:ASP1319 2.3 13.3 1.0
O A:TYR1320 2.4 11.4 1.0
OD1 A:ASP1298 2.4 10.8 1.0
O A:HOH3144 2.4 14.7 1.0
O A:HOH3145 2.5 10.1 1.0
O A:HOH3142 2.5 12.1 1.0
CG A:ASP1296 3.4 11.5 1.0
CG A:ASP1319 3.4 13.6 1.0
CG A:ASP1298 3.4 10.9 1.0
C A:TYR1320 3.5 11.1 1.0
N A:TYR1320 3.6 10.4 1.0
OD2 A:ASP1296 3.7 12.1 1.0
OD2 A:ASP1298 3.8 13.3 1.0
C A:ASP1319 4.1 12.5 1.0
CA A:ASP1319 4.2 11.9 1.0
CA A:TYR1320 4.2 10.9 1.0
OD2 A:ASP1319 4.2 17.6 1.0
O A:SER1324 4.3 10.9 1.0
CB A:ASP1319 4.3 12.7 1.0
O A:HOH3212 4.3 22.2 1.0
O A:HOH3210 4.4 22.3 1.0
O A:HOH3141 4.5 21.2 1.0
N A:PRO1321 4.5 10.6 1.0
O A:ILE1297 4.5 8.5 1.0
CB A:ASP1296 4.7 10.9 1.0
CA A:PRO1321 4.7 11.1 1.0
C A:ILE1297 4.8 8.7 1.0
CB A:ASP1298 4.8 10.2 1.0
C A:ASP1296 4.8 9.9 1.0
N A:ILE1297 4.8 9.0 1.0
O A:ASP1319 5.0 16.3 1.0

Calcium binding site 3 out of 4 in 2vk7

Go back to Calcium Binding Sites List in 2vk7
Calcium binding site 3 out of 4 in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates


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 Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2693

b:19.5
occ:1.00
 O B:ASP1515 2.5 16.9 1.0
O B:HOH3482 2.6 17.9 1.0
O B:TRP1573 2.6 15.7 1.0
O B:HOH3480 2.8 20.5 1.0
O B:HOH3479 2.8 15.7 1.0
O B:HOH3201 2.8 33.3 1.0
C B:ASP1515 3.8 16.4 1.0
C B:TRP1573 3.8 14.3 1.0
CB B:ASN1516 4.0 18.8 1.0
O B:ASN1516 4.1 18.2 1.0
C B:ASN1516 4.2 17.2 1.0
OE1 B:GLU1511 4.2 20.4 1.0
N B:TRP1573 4.2 14.9 1.0
O B:HOH3133 4.3 36.9 1.0
C B:ASP1574 4.3 15.8 1.0
O B:ASP1574 4.4 15.8 1.0
N B:GLU1575 4.4 16.4 1.0
CA B:ASN1516 4.4 16.9 1.0
CA B:GLU1575 4.4 18.3 1.0
CA B:TRP1573 4.5 13.6 1.0
N B:ASN1516 4.5 16.5 1.0
O B:SER1512 4.7 13.7 1.0
N B:ARG1517 4.7 16.9 1.0
N B:ASP1574 4.7 15.1 1.0
ND2 B:ASN1516 4.8 23.3 1.0
CB B:TRP1573 4.8 13.6 1.0
CA B:ASP1515 4.8 15.7 1.0
O B:PRO1513 4.8 15.5 1.0
CA B:ASP1574 4.9 15.4 1.0
O B:HOH3551 4.9 22.7 1.0
CB B:ASP1515 5.0 16.6 1.0
CG B:ASN1516 5.0 20.3 1.0
O B:HOH3137 5.0 37.0 1.0

Calcium binding site 4 out of 4 in 2vk7

Go back to Calcium Binding Sites List in 2vk7
Calcium binding site 4 out of 4 in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2694

b:11.6
occ:1.00
 OD1 B:ASP1319 2.3 13.6 1.0
OD1 B:ASP1296 2.3 13.6 1.0
O B:TYR1320 2.4 12.2 1.0
OD1 B:ASP1298 2.4 11.4 1.0
O B:HOH3129 2.4 15.0 1.0
O B:HOH3126 2.4 13.6 1.0
O B:HOH3215 2.5 10.4 1.0
CG B:ASP1296 3.4 13.0 1.0
CG B:ASP1319 3.4 14.0 1.0
CG B:ASP1298 3.5 12.2 1.0
C B:TYR1320 3.5 12.1 1.0
N B:TYR1320 3.6 11.0 1.0
OD2 B:ASP1296 3.7 15.1 1.0
OD2 B:ASP1298 3.8 13.7 1.0
C B:ASP1319 4.1 12.7 1.0
CA B:ASP1319 4.2 12.2 1.0
OD2 B:ASP1319 4.2 17.0 1.0
CA B:TYR1320 4.2 11.3 1.0
O B:HOH3193 4.2 22.8 1.0
O B:SER1324 4.3 13.1 1.0
CB B:ASP1319 4.3 12.9 1.0
O B:HOH3190 4.3 22.3 1.0
O B:HOH3127 4.4 25.1 1.0
O B:ILE1297 4.5 9.2 1.0
N B:PRO1321 4.5 12.3 1.0
CB B:ASP1296 4.6 11.4 1.0
CA B:PRO1321 4.7 12.5 1.0
C B:ILE1297 4.8 9.5 1.0
CB B:ASP1298 4.8 10.1 1.0
C B:ASP1296 4.8 10.4 1.0
N B:ILE1297 4.9 9.5 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: Tue Jul 8 08:38:58 2025

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