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Sodium in PDB 4jos: Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335)

Enzymatic activity of Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335)

All present enzymatic activity of Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335):
3.2.2.9;

Protein crystallography data

The structure of Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335), PDB code: 4jos was solved by P.Sampathkumar, V.L.Schramm, S.C.Almo, New York Structural Genomicsresearch Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.06 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.747, 74.937, 114.542, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335) (pdb code 4jos). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335), PDB code: 4jos:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4jos

Go back to Sodium Binding Sites List in 4jos
Sodium binding site 1 out of 2 in the Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:14.3
occ:1.00
 O A:ASP83 2.3 14.5 1.0
OD2 A:ASP88 2.4 11.3 1.0
O A:HOH588 2.4 18.3 1.0
O A:HOH499 2.5 21.7 1.0
CG A:ASP88 3.3 11.9 1.0
C A:ASP83 3.5 14.5 1.0
OD1 A:ASP88 3.6 13.0 1.0
NE2 A:HIS141 3.9 16.3 1.0
N A:GLN85 3.9 12.1 1.0
CA A:LEU84 4.1 12.2 1.0
CE1 A:HIS141 4.1 15.6 1.0
CG A:GLN85 4.2 15.0 1.0
N A:LEU84 4.2 12.5 1.0
CB A:GLN85 4.3 13.3 1.0
C A:LEU84 4.4 11.8 1.0
CB A:ASP83 4.5 15.2 1.0
CA A:ASP83 4.5 14.6 1.0
CB A:ASP88 4.6 11.5 1.0
OD2 A:ASP83 4.7 19.7 1.0
O A:HOH436 4.7 13.6 1.0
CA A:GLN85 4.8 12.3 1.0
O A:HOH605 4.8 36.0 1.0
CD2 A:HIS141 4.9 15.7 1.0
CG A:ASP83 5.0 16.6 1.0

Sodium binding site 2 out of 2 in 4jos

Go back to Sodium Binding Sites List in 4jos
Sodium binding site 2 out of 2 in the Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Putative 5'-Methylthioadenosine/S- Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:40.5
occ:1.00
 O A:HOH596 2.2 15.9 0.5
O A:HOH583 2.2 28.3 1.0
O A:HOH538 2.6 33.0 1.0
O A:HOH612 2.7 33.4 1.0
O A:HOH577 3.1 23.0 1.0
O A:LEU21 3.3 24.1 1.0
CD1 A:TYR39 3.8 19.1 1.0
C A:LEU21 4.2 22.3 1.0
CA A:LEU21 4.2 20.2 1.0
CE1 A:TYR39 4.3 20.9 1.0
O A:HOH596 4.4 23.9 0.5
CD2 A:LEU21 4.5 21.6 1.0
O A:ASN38 4.6 14.5 1.0
O A:LYS20 4.7 21.4 1.0
OD1 A:ASN40 4.7 36.4 0.5
CA A:TYR39 4.9 17.9 1.0
CB A:LEU21 4.9 19.9 1.0
CG A:TYR39 4.9 18.0 1.0

Reference:

P.Sampathkumar, A.Gizzi, M.Ahmed, N.Banu, R.Bhosle, J.Bonanno, S.Chamala, S.Chowdhury, A.Fiser, A.S.Glenn, J.Hammonds, B.Hillerich, K.Khafizov, J.Lafleur, L.L.Morisco, S.S.Sojitra, S.R.Wasserman, A.Haapalainen, J.D.Love, M.Stead, R.Seidel, R.Toro, V.L.Schramm, S.C.Almo. Crystal Structure of A Putative 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase From Francisella Philomiragia Atcc 25017 (Target Nysgrc-029335) To Be Published.
Page generated: Tue Dec 15 06:46:55 2020

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