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Sodium in PDB 2zsa: Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate

Enzymatic activity of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate

All present enzymatic activity of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate:
2.7.1.33;

Protein crystallography data

The structure of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate, PDB code: 2zsa was solved by B.Chetnani, S.Das, P.Kumar, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.14 / 2.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.092, 104.092, 90.440, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 23.6

Other elements in 2zsa:

The structure of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate (pdb code 2zsa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate, PDB code: 2zsa:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2zsa

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Sodium binding site 1 out of 4 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:56.1
occ:1.00
 OD2 A:ASP124 3.1 51.4 1.0
OD1 A:ASP124 3.3 52.5 1.0
N A:ARG193 3.5 43.7 1.0
CG A:ASP124 3.6 49.4 1.0
O A:VAL191 3.8 44.7 1.0
CA A:VAL192 4.1 41.0 1.0
CD A:ARG122 4.1 61.0 1.0
C A:VAL192 4.3 41.6 1.0
CB A:ARG193 4.3 46.4 1.0
CA A:ARG193 4.4 45.0 1.0
NE A:ARG122 4.4 64.1 1.0
O A:ARG193 4.6 46.1 1.0
CG A:ARG193 4.6 48.9 1.0
C A:VAL191 4.7 43.9 1.0
CG A:ARG122 4.7 57.7 1.0
CZ A:ARG122 4.8 65.6 1.0
NH1 A:ARG122 4.8 67.5 1.0
N A:VAL192 4.9 42.7 1.0
C A:ARG193 4.9 46.4 1.0
CD A:ARG193 5.0 51.3 1.0

Sodium binding site 2 out of 4 in 2zsa

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Sodium binding site 2 out of 4 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:60.9
occ:1.00
 OE2 A:GLU42 2.4 55.5 1.0
O A:HOH391 2.7 50.9 1.0
O A:HOH418 2.8 42.9 1.0
O A:ALA100 2.9 35.4 1.0
CD A:GLU42 3.5 56.7 1.0
C A:ALA100 3.6 34.0 1.0
N A:GLY102 3.7 38.1 1.0
NE2 A:HIS302 3.8 46.0 1.0
CD2 A:HIS302 3.9 45.8 1.0
C A:VAL101 3.9 36.8 1.0
CG A:GLU42 3.9 54.7 1.0
CA A:GLY102 4.0 38.9 1.0
N A:VAL101 4.3 35.0 1.0
CA A:ALA100 4.3 33.2 1.0
O A:VAL101 4.3 37.5 1.0
CA A:VAL101 4.4 35.9 1.0
CE3 A:TRP234 4.4 37.0 1.0
O1B A:ADP800 4.5 32.2 1.0
OE1 A:GLU42 4.6 59.6 1.0
O A:HOH330 4.6 41.1 1.0
O A:LEU40 4.6 45.3 1.0
C A:GLY41 4.8 50.6 1.0
O A:GLY41 4.8 50.6 1.0
NH1 A:ARG238 4.8 30.0 1.0
CB A:TRP234 4.8 38.2 1.0
CD2 A:TRP234 4.9 36.7 1.0
N A:GLU42 4.9 52.8 1.0
O A:HOH392 5.0 44.1 1.0
CB A:ALA100 5.0 29.2 1.0
CZ3 A:TRP234 5.0 37.1 1.0

Sodium binding site 3 out of 4 in 2zsa

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Sodium binding site 3 out of 4 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:49.2
occ:1.00
 OD1 A:ASP225 2.4 39.7 1.0
OH A:TYR223 2.7 31.8 1.0
O A:HOH474 2.9 40.2 1.0
O A:HOH337 2.9 29.7 1.0
CE1 A:TYR223 3.2 32.3 1.0
CZ A:TYR223 3.4 33.2 1.0
CD2 A:LEU286 3.5 34.4 1.0
CG A:ASP225 3.5 38.1 1.0
CD1 A:LEU281 3.9 32.4 1.0
CA A:ASP225 4.1 36.6 1.0
O A:ALA226 4.1 41.2 1.0
CG A:LEU286 4.1 36.1 1.0
CB A:ASP225 4.2 37.5 1.0
N A:ALA226 4.2 38.2 1.0
CD1 A:ILE231 4.4 31.1 1.0
O A:VAL224 4.5 35.8 1.0
CD1 A:TYR223 4.5 31.2 1.0
OD2 A:ASP225 4.5 42.8 1.0
O A:HOH515 4.5 65.9 1.0
C A:ASP225 4.7 37.8 1.0
NH1 A:ARG289 4.7 38.0 1.0
O A:HOH475 4.8 49.0 1.0
CE2 A:TYR223 4.8 30.4 1.0
CD1 A:LEU286 4.9 37.6 1.0
CG A:LEU281 4.9 34.3 1.0
CD2 A:LEU281 4.9 31.6 1.0

Sodium binding site 4 out of 4 in 2zsa

Go back to Sodium Binding Sites List in 2zsa
Sodium binding site 4 out of 4 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Phosphopantothenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:64.9
occ:1.00
 OE1 A:GLU283 3.1 43.4 1.0
ND2 A:ASN284 3.3 27.9 1.0
O A:HOH482 3.3 65.4 1.0
OD1 A:ASN284 3.5 35.1 1.0
NH2 A:ARG146 3.7 44.1 1.0
CG A:ASN284 3.8 32.5 1.0
CD2 A:PHE149 3.8 32.3 1.0
CE2 A:PHE149 4.0 32.0 1.0
O A:HOH380 4.1 46.2 1.0
CB A:GLU283 4.1 36.1 1.0
O A:HOH510 4.1 64.2 1.0
CD A:GLU283 4.2 40.9 1.0
CG A:GLU283 4.7 38.9 1.0
CZ A:ARG146 4.7 47.7 1.0
OE2 A:GLU151 4.8 49.8 1.0
OE1 A:GLU151 4.8 44.5 1.0

Reference:

B.Chetnani, S.Das, P.Kumar, A.Surolia, M.Vijayan. Mycobacterium Tuberculosis Pantothenate Kinase: Possible Changes in Location of Ligands During Enzyme Action Acta Crystallogr.,Sect.D V. 65 312 2009.
ISSN: ISSN 0907-4449
PubMed: 19307712
DOI: 10.1107/S0907444909002170
Page generated: Mon Oct 7 05:39:51 2024

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