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Sodium in PDB 4ypo: Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+, PDB code: 4ypo was solved by Y.Lv, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.74 / 1.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.697, 54.797, 92.230, 90.00, 123.25, 90.00
R / Rfree (%) 15.5 / 16.3

Other elements in 4ypo:

The structure of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 13 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ (pdb code 4ypo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+, PDB code: 4ypo:

Sodium binding site 1 out of 1 in 4ypo

Go back to Sodium Binding Sites List in 4ypo
Sodium binding site 1 out of 1 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:12.9
occ:1.00
O B:ASN94 2.3 13.2 1.0
O B:ALA68 2.3 13.9 1.0
O B:HOH583 2.4 14.6 1.0
O B:ALA71 2.4 13.1 1.0
OD2 B:ASP99 2.4 13.5 1.0
HZ2 B:LYS96 3.0 25.4 1.0
HA B:LEU95 3.3 15.2 1.0
H B:LYS96 3.5 15.7 1.0
HZ1 B:LYS96 3.5 25.4 1.0
CG B:ASP99 3.5 13.8 1.0
C B:ALA68 3.5 12.8 1.0
C B:ASN94 3.5 11.4 1.0
C B:ALA71 3.6 12.4 1.0
NZ B:LYS96 3.6 21.1 1.0
HG3 B:LYS96 3.7 32.0 1.0
HA B:LYS69 3.7 18.4 1.0
HA B:ASP72 3.8 16.1 1.0
HD23 B:LEU95 3.9 17.7 1.0
O B:LYS69 3.9 15.9 1.0
HB3 B:ASN94 4.0 14.6 1.0
HZ3 B:LYS96 4.0 25.4 1.0
OD1 B:ASP99 4.1 14.4 1.0
CA B:LEU95 4.1 12.6 1.0
H B:ALA71 4.1 16.4 1.0
HB3 B:ALA71 4.1 15.5 1.0
C B:LYS69 4.2 14.7 1.0
CA B:LYS69 4.2 15.3 1.0
N B:LYS96 4.3 13.1 1.0
N B:LEU95 4.3 12.0 1.0
N B:ALA71 4.3 13.7 1.0
N B:LYS69 4.3 13.9 1.0
HG23 B:VAL74 4.4 17.1 1.0
HG21 B:VAL74 4.4 17.1 1.0
O B:HOH853 4.4 22.1 1.0
HA B:ALA68 4.4 14.9 1.0
CA B:ALA71 4.4 13.3 1.0
N B:ASP72 4.5 13.4 1.0
HB1 B:ALA68 4.5 16.2 1.0
HB3 B:ASP99 4.5 14.6 1.0
CA B:ALA68 4.6 12.4 1.0
CA B:ASP72 4.6 13.4 1.0
CG B:LYS96 4.6 26.6 1.0
CA B:ASN94 4.6 11.4 1.0
CB B:ASP99 4.6 12.2 1.0
CB B:ASN94 4.7 12.2 1.0
CG2 B:VAL74 4.7 14.2 1.0
HG22 B:VAL74 4.7 17.1 1.0
C B:LEU95 4.8 12.8 1.0
CB B:ALA71 4.8 12.9 1.0
HA B:ASN94 4.8 13.7 1.0
CD2 B:LEU95 4.8 14.7 1.0
CE B:LYS96 4.9 27.7 1.0
HB2 B:ASN94 4.9 14.6 1.0
HB2 B:ASP99 4.9 14.6 1.0
C B:TRP70 4.9 14.0 1.0
HD3 B:LYS96 4.9 35.8 1.0
HB2 B:LYS96 5.0 22.8 1.0
N B:TRP70 5.0 14.5 1.0

Reference:

Y.Lv, A.Kandale, S.J.Wun, R.P.Mcgeary, S.J.Williams, B.Kobe, V.Sieber, M.A.Schembri, G.Schenk, L.W.Guddat. Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase at 1.0 Angstrom Resolution - A Potential Target For Anti-Tuberculosis Drug Discovery. Febs J. V. 283 1184 2016.
ISSN: ISSN 1742-464X
PubMed: 26876563
DOI: 10.1111/FEBS.13672
Page generated: Tue Dec 15 10:04:25 2020

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