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Sodium in PDB 3tx2: Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus

Protein crystallography data

The structure of Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus, PDB code: 3tx2 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.18 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.350, 41.180, 44.970, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus (pdb code 3tx2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus, PDB code: 3tx2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tx2

Go back to Sodium Binding Sites List in 3tx2
Sodium binding site 1 out of 2 in the Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na248

b:15.6
occ:1.00
O A:HOH449 2.3 18.8 1.0
OD1 A:ASN65 2.4 16.1 1.0
O A:HOH330 2.4 17.3 1.0
O A:HOH577 2.4 17.9 1.0
O A:HOH282 2.5 15.4 1.0
O A:THR64 2.5 14.5 1.0
O A:HOH566 3.3 9.5 1.0
C A:THR64 3.4 14.2 1.0
CG A:ASN65 3.5 15.4 1.0
CA A:ASN65 3.5 13.4 1.0
N A:ASN65 3.8 13.6 1.0
O A:HOH428 4.0 30.7 1.0
CB A:ASN65 4.1 14.2 1.0
O A:HOH501 4.3 30.3 1.0
O A:HOH327 4.3 23.9 1.0
OG1 A:THR64 4.3 16.0 1.0
NE2 A:HIS67 4.3 12.8 1.0
O A:HOH514 4.4 15.2 1.0
ND2 A:ASN65 4.6 16.1 1.0
CA A:THR64 4.6 14.5 1.0
O A:HOH584 4.6 16.1 1.0
O A:GLY35 4.7 13.4 1.0
CB A:THR64 4.7 15.7 1.0
CE1 A:HIS67 4.7 13.1 1.0
C A:ASN65 4.7 12.3 1.0
ND2 A:ASN102 5.0 12.3 1.0

Sodium binding site 2 out of 2 in 3tx2

Go back to Sodium Binding Sites List in 3tx2
Sodium binding site 2 out of 2 in the Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Probable 6-Phosphogluconolactonase From Mycobacterium Abscessus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na249

b:17.7
occ:1.00
O A:HOH473 2.2 17.8 1.0
O A:HOH319 2.4 11.8 1.0
O A:MET103 2.4 10.1 1.0
O A:HOH531 2.4 22.6 1.0
O A:HOH318 2.4 16.4 1.0
O A:HOH322 2.5 20.0 1.0
C A:MET103 3.6 10.0 1.0
O A:HOH270 3.7 22.1 1.0
O A:LEU100 3.8 11.4 1.0
O A:HOH430 4.2 27.9 1.0
ND1 A:HIS104 4.2 9.6 1.0
CA A:HIS104 4.2 9.1 1.0
O A:HOH340 4.2 20.3 1.0
N A:HIS104 4.3 9.4 1.0
O A:HOH255 4.3 22.6 1.0
CA A:MET103 4.7 10.4 1.0
N A:ALA105 4.8 8.7 1.0
CE1 A:HIS104 4.8 9.9 1.0
N A:MET103 4.8 10.6 1.0
C A:LEU100 4.9 11.6 1.0
CB A:MET103 4.9 11.1 1.0
CG A:HIS104 4.9 9.4 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Tue Dec 15 06:26:43 2020

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