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Sodium in PDB 4a44: CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen

Enzymatic activity of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen

All present enzymatic activity of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen:
3.2.1.50;

Protein crystallography data

The structure of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen, PDB code: 4a44 was solved by E.Ficko-Blean, C.P.Stuart, M.D.Suits, M.Cid, M.Tessier, R.J.Woods, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.50 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.800, 59.260, 67.430, 90.00, 90.00, 90.00
R / Rfree (%) 18.758 / 22.249

Other elements in 4a44:

The structure of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen (pdb code 4a44). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen, PDB code: 4a44:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4a44

Go back to Sodium Binding Sites List in 4a44
Sodium binding site 1 out of 3 in the CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2496

b:3.9
occ:1.00
NE2 A:HIS1471 2.1 16.5 1.0
OE1 A:GLU1408 2.2 26.2 1.0
O A:HOH2120 2.7 33.5 1.0
CE1 A:HIS1471 3.0 13.7 1.0
O A:HOH2223 3.0 47.0 1.0
CD2 A:HIS1471 3.1 14.5 1.0
CD A:GLU1408 3.2 24.4 1.0
CG A:GLU1408 3.7 18.9 1.0
CB A:GLU1408 4.1 14.7 1.0
O A:HOH2118 4.1 39.2 1.0
ND1 A:HIS1471 4.2 14.5 1.0
CG A:HIS1471 4.2 14.4 1.0
O A:HOH2007 4.3 40.7 1.0
O A:HOH2170 4.3 26.5 1.0
OE2 A:GLU1408 4.3 27.6 1.0
O A:HOH2030 4.7 47.9 1.0
CA A:GLY1442 4.7 19.4 1.0

Sodium binding site 2 out of 3 in 4a44

Go back to Sodium Binding Sites List in 4a44
Sodium binding site 2 out of 3 in the CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2497

b:31.1
occ:1.00
CA A:FLC2499 2.8 64.8 1.0
OG2 A:FLC2499 3.1 64.4 1.0
CBC A:FLC2499 3.5 64.2 1.0
OB2 A:FLC2499 3.6 64.1 1.0
CGC A:FLC2499 3.6 64.4 1.0
CB A:FLC2499 3.6 64.5 1.0
CAC A:FLC2499 4.0 65.5 1.0
OB1 A:FLC2499 4.1 64.4 1.0
CG A:FLC2499 4.1 64.5 1.0
OG1 A:FLC2499 4.3 64.8 1.0
O A:HOH2226 4.3 43.9 1.0
OA1 A:FLC2499 4.4 65.9 1.0
O A:HOH2224 4.8 54.1 1.0
OHB A:FLC2499 5.0 65.0 1.0
OA2 A:FLC2499 5.0 66.4 1.0

Sodium binding site 3 out of 3 in 4a44

Go back to Sodium Binding Sites List in 4a44
Sodium binding site 3 out of 3 in the CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CPGH89CBM32-5, From Clostridium Perfringens, in Complex with the Tn Antigen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2498

b:48.4
occ:1.00
OHB A:FLC2499 2.6 65.0 1.0
OA2 A:FLC2499 3.5 66.4 1.0
CB A:FLC2499 3.8 64.5 1.0
CAC A:FLC2499 3.8 65.5 1.0
CG A:FLC2499 4.0 64.5 1.0
O A:HOH2225 4.1 66.2 1.0
OA1 A:FLC2499 4.2 65.9 1.0
CA A:FLC2499 4.4 64.8 1.0
CBC A:FLC2499 4.9 64.2 1.0
OG1 A:FLC2499 4.9 64.8 1.0
CGC A:FLC2499 5.0 64.4 1.0

Reference:

E.Ficko-Blean, C.P.Stuart, M.D.Suits, M.Cid, M.Tessier, R.J.Woods, A.B.Boraston. Carbohydrate Recognition By An Architecturally Complex Alpha-N-Acetylglucosaminidase From Clostridium Perfringens. Plos One V. 7 33524 2012.
ISSN: ISSN 1932-6203
PubMed: 22479408
DOI: 10.1371/JOURNAL.PONE.0033524
Page generated: Tue Dec 15 06:32:30 2020

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