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Sodium in PDB 5t8k: 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad

Enzymatic activity of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad

All present enzymatic activity of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad:
3.3.1.1;

Protein crystallography data

The structure of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad, PDB code: 5t8k was solved by G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, B.Bishop, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.686, 182.785, 96.250, 90.00, 100.58, 90.00
R / Rfree (%) 14.1 / 17.3

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad (pdb code 5t8k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad, PDB code: 5t8k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5t8k

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Sodium binding site 1 out of 4 in the 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:28.9
occ:1.00
 O A:HOH717 2.3 29.4 1.0
O A:THR408 2.4 24.5 1.0
O A:HIS410 2.4 22.0 1.0
OE1 A:GLU57 2.5 24.0 1.0
N6 A:ADE503 2.5 23.3 1.0
CD A:GLU57 3.1 25.3 1.0
OE2 A:GLU57 3.4 26.5 1.0
C A:THR408 3.5 24.9 1.0
C A:GLY409 3.5 22.8 1.0
C A:HIS410 3.5 23.1 1.0
O A:GLY409 3.6 22.0 1.0
N A:HIS410 3.7 22.7 1.0
O A:HOH840 3.7 35.2 1.0
CA A:GLY409 3.9 23.3 1.0
C6 A:ADE503 3.9 24.4 1.0
OG1 A:THR55 4.0 23.8 1.0
N A:GLY409 4.1 23.2 1.0
CG A:GLU57 4.1 24.6 1.0
CB A:THR55 4.1 24.9 1.0
OG1 A:THR408 4.2 30.4 1.0
CA A:HIS410 4.2 22.7 1.0
CG2 A:THR55 4.3 24.9 1.0
CB A:THR408 4.4 28.2 1.0
O D:HOH719 4.4 29.3 1.0
N A:PRO411 4.5 23.1 1.0
CA A:THR408 4.6 26.2 1.0
N1 A:ADE503 4.7 23.6 1.0
CA A:PRO411 4.7 23.4 1.0
C5 A:ADE503 4.8 23.3 1.0
O A:HOH708 4.8 34.6 1.0
OE1 A:GLN83 4.8 27.1 1.0
CB A:GLU57 4.9 24.4 1.0
N7 A:ADE503 5.0 24.2 1.0

Sodium binding site 2 out of 4 in 5t8k

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Sodium binding site 2 out of 4 in the 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:26.5
occ:1.00
 O B:HOH880 2.2 31.7 1.0
O B:THR408 2.2 22.7 1.0
O B:HIS410 2.4 22.1 1.0
OE1 B:GLU57 2.5 25.3 1.0
N6 B:ADE503 2.5 23.9 1.0
CD B:GLU57 3.1 25.9 1.0
C B:THR408 3.4 23.3 1.0
C B:GLY409 3.4 21.1 1.0
C B:HIS410 3.4 22.0 1.0
OE2 B:GLU57 3.5 27.2 1.0
O B:GLY409 3.6 21.1 1.0
N B:HIS410 3.7 21.0 1.0
O B:HOH847 3.7 31.7 1.0
CA B:GLY409 3.8 21.8 1.0
C6 B:ADE503 3.8 25.0 1.0
OG1 B:THR55 4.0 24.8 1.0
N B:GLY409 4.0 21.4 1.0
CA B:HIS410 4.1 22.2 1.0
CB B:THR55 4.2 24.8 1.0
CG B:GLU57 4.2 24.5 1.0
OG1 B:THR408 4.2 30.1 1.0
CG2 B:THR55 4.4 24.8 1.0
CB B:THR408 4.4 27.3 1.0
N B:PRO411 4.5 21.7 1.0
CA B:THR408 4.5 25.2 1.0
O C:HOH741 4.5 27.8 1.0
N1 B:ADE503 4.7 23.9 1.0
CA B:PRO411 4.7 21.7 1.0
C5 B:ADE503 4.7 24.5 1.0
OE1 B:GLN83 4.8 26.1 1.0
CB B:GLU57 4.9 24.1 1.0
O B:HOH821 4.9 32.6 1.0
N7 B:ADE503 4.9 25.0 1.0

Sodium binding site 3 out of 4 in 5t8k

Go back to Sodium Binding Sites List in 5t8k
Sodium binding site 3 out of 4 in the 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:28.9
occ:1.00
 O C:THR408 2.3 22.3 1.0
O C:HOH859 2.3 28.6 1.0
O C:HIS410 2.4 19.0 1.0
OE1 C:GLU57 2.5 24.8 1.0
N6 C:ADE503 2.5 20.1 1.0
CD C:GLU57 3.1 25.1 1.0
C C:THR408 3.4 23.6 1.0
C C:GLY409 3.4 19.1 1.0
OE2 C:GLU57 3.5 28.8 1.0
C C:HIS410 3.5 20.0 1.0
O C:GLY409 3.6 17.5 1.0
N C:HIS410 3.6 19.3 1.0
O C:HOH920 3.7 38.1 1.0
CA C:GLY409 3.8 20.5 1.0
C6 C:ADE503 3.8 21.0 1.0
N C:GLY409 4.0 20.8 1.0
CA C:HIS410 4.1 19.6 1.0
OG1 C:THR55 4.2 23.2 1.0
CG C:GLU57 4.2 23.9 1.0
CB C:THR55 4.2 22.6 1.0
OG1 C:THR408 4.2 28.5 1.0
CB C:THR408 4.4 26.9 1.0
CG2 C:THR55 4.5 21.6 1.0
O B:HOH678 4.5 26.7 1.0
N C:PRO411 4.5 20.8 1.0
CA C:THR408 4.5 24.7 1.0
N1 C:ADE503 4.7 21.4 1.0
C5 C:ADE503 4.7 21.3 1.0
CA C:PRO411 4.7 20.8 1.0
OE1 C:GLN83 4.8 27.6 1.0
N7 C:ADE503 4.9 19.2 1.0
O C:HOH778 4.9 36.5 1.0
CB C:GLU57 5.0 23.4 1.0

Sodium binding site 4 out of 4 in 5t8k

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Sodium binding site 4 out of 4 in the 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:39.5
occ:1.00
 O D:HOH950 2.1 36.2 1.0
O D:THR408 2.2 28.5 1.0
O D:HIS410 2.5 23.6 1.0
OE1 D:GLU57 2.6 27.5 1.0
N6 D:ADE503 2.7 25.9 1.0
CD D:GLU57 3.2 29.3 1.0
C D:THR408 3.3 27.4 1.0
C D:GLY409 3.5 24.4 1.0
OE2 D:GLU57 3.5 33.6 1.0
C D:HIS410 3.6 23.7 1.0
O D:GLY409 3.6 23.1 1.0
O D:HOH905 3.6 40.1 1.0
N D:HIS410 3.8 24.2 1.0
CA D:GLY409 3.9 26.0 1.0
C6 D:ADE503 4.0 25.9 1.0
N D:GLY409 4.0 25.5 1.0
OG1 D:THR408 4.1 33.5 1.0
OG1 D:THR55 4.2 26.3 1.0
CB D:THR55 4.2 26.1 1.0
CG D:GLU57 4.2 27.3 1.0
CB D:THR408 4.2 30.3 1.0
CA D:HIS410 4.3 24.0 1.0
O A:HOH720 4.4 33.9 1.0
CG2 D:THR55 4.4 25.4 1.0
CA D:THR408 4.4 28.8 1.0
N D:PRO411 4.5 24.2 1.0
OE1 D:GLN83 4.7 29.7 1.0
CA D:PRO411 4.7 23.4 1.0
N1 D:ADE503 4.8 25.6 1.0
C5 D:ADE503 4.9 26.2 1.0
O D:HOH820 4.9 43.8 1.0

Reference:

G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, B.Bishop, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.95 Angstrom Crystal Structure of S-Adenosylhomocysteinase From Cryptosporidium Parvum in Complex with Adenine and Nad. To Be Published.
Page generated: Tue Oct 8 00:04:45 2024

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