Atomistry » Sodium » PDB 5syu-5tde » 5t8k
Atomistry »
  Sodium »
    PDB 5syu-5tde »
      5t8k »

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

Go back to Sodium Binding Sites List in 5t8k
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

Go back to Sodium Binding Sites List in 5t8k
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

Go back to Sodium Binding Sites List in 5t8k
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy