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Magnesium in PDB 2vk6: 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: 2vk6 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) 28.40 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.370, 71.046, 98.900, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.5

Other elements in 2vk6:

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

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates (pdb code 2vk6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structure of Clostridium Perfringens Nani Sialidase and Its Catalytic Intermediates, PDB code: 2vk6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vk6

Go back to Magnesium Binding Sites List in 2vk6
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2693

b:30.8
occ:1.00
 O A:HOH2163 2.3 24.3 1.0
O A:HOH2170 2.7 16.1 1.0
O A:HOH2387 2.8 25.4 1.0
CB A:ASP1322 3.5 10.0 1.0
CB A:PRO1321 3.8 11.1 1.0
CB A:SER1418 4.0 9.1 1.0
O A:HOH2160 4.2 26.0 1.0
CG A:ASP1322 4.2 12.5 1.0
O A:HOH2028 4.2 33.5 1.0
OD1 A:ASP1414 4.2 10.2 1.0
O A:HOH2012 4.3 21.9 1.0
CG A:PRO1321 4.3 11.6 1.0
OD2 A:ASP1322 4.4 13.9 1.0
O A:HOH2094 4.4 17.4 1.0
N A:ASP1322 4.5 9.5 1.0
CA A:ASP1322 4.5 9.2 1.0
OG A:SER1418 4.6 9.2 1.0
OG1 A:THR1420 4.7 11.0 1.0
C A:PRO1321 4.7 10.2 1.0
CA A:PRO1321 4.9 10.4 1.0
OD1 A:ASP1322 5.0 15.6 1.0

Magnesium binding site 2 out of 4 in 2vk6

Go back to Magnesium Binding Sites List in 2vk6
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2694

b:11.5
occ:1.00
 O A:HOH2241 2.4 17.0 1.0
O A:ASP1515 2.4 11.1 1.0
O A:HOH2239 2.4 12.0 1.0
O A:TRP1573 2.5 11.1 1.0
O A:HOH2237 2.5 9.6 1.0
O A:HOH2236 2.6 16.1 1.0
C A:TRP1573 3.6 10.1 1.0
C A:ASP1515 3.6 11.1 1.0
N A:TRP1573 4.0 8.8 1.0
CB A:ASN1516 4.1 11.4 1.0
OE1 A:GLU1511 4.2 12.4 0.9
CA A:TRP1573 4.2 9.2 1.0
O A:ASP1574 4.2 10.3 1.0
O A:ASN1516 4.3 12.0 1.0
C A:ASN1516 4.3 10.4 1.0
C A:ASP1574 4.3 9.7 1.0
O A:SER1512 4.4 7.8 1.0
CB A:TRP1573 4.5 8.5 1.0
N A:ASN1516 4.5 10.6 1.0
CA A:ASN1516 4.5 10.4 1.0
N A:GLU1575 4.5 9.9 1.0
CA A:ASP1515 4.6 9.9 1.0
CA A:GLU1575 4.6 11.2 1.0
N A:ASP1574 4.6 9.1 1.0
O A:PRO1513 4.6 8.6 1.0
ND2 A:ASN1516 4.7 19.0 1.0
CB A:ASP1515 4.7 8.9 1.0
N A:ARG1517 4.8 10.1 1.0
N A:ASP1515 4.8 9.1 1.0
CA A:ASP1574 4.9 9.9 1.0
CG A:ASN1516 5.0 16.0 1.0

Magnesium binding site 3 out of 4 in 2vk6

Go back to Magnesium Binding Sites List in 2vk6
Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg2695

b:28.3
occ:1.00
 O A:HOH2075 2.6 23.9 1.0
O A:HOH2384 2.8 12.8 1.0
O A:HOH2076 2.8 25.0 1.0
CG2 A:VAL1252 3.4 13.6 0.5
O A:GLY1308 3.8 13.9 1.0
CG1 A:VAL1252 3.9 14.6 0.5
CG2 A:VAL1252 4.0 13.5 0.5
CD2 A:TYR1680 4.0 8.6 1.0
OG1 A:THR1249 4.1 14.1 1.0
CE2 A:TYR1680 4.1 7.2 1.0
CB A:THR1249 4.4 13.5 1.0
CB A:VAL1252 4.5 13.3 0.5
CB A:VAL1252 4.6 13.7 0.5
O A:TYR1680 4.7 9.6 1.0
O A:GLU1250 4.8 13.5 1.0
CG2 A:THR1249 4.8 14.5 1.0
C A:GLY1308 4.9 13.8 1.0
NZ A:LYS1309 5.0 26.7 1.0

Magnesium binding site 4 out of 4 in 2vk6

Go back to Magnesium Binding Sites List in 2vk6
Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg2696

b:24.9
occ:1.00
 O A:HOH2095 2.7 19.0 1.0
O A:HOH2167 2.7 15.6 1.0
CG2 A:THR1420 3.8 12.4 1.0
OG A:SER1419 4.0 13.0 1.0
O A:HOH2012 4.3 21.9 1.0
O A:HOH2108 4.6 27.6 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: Wed Aug 14 05:15:08 2024

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