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Calcium in PDB 6k92: Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin

Protein crystallography data

The structure of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin, PDB code: 6k92 was solved by S.Are, S.Gatreddi, I.A.Qureshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.57 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.740, 71.520, 76.670, 90.00, 99.27, 90.00
R / Rfree (%) 17.9 / 21.4

Other elements in 6k92:

The structure of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin (pdb code 6k92). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin, PDB code: 6k92:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6k92

Go back to Calcium Binding Sites List in 6k92
Calcium binding site 1 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:16.1
occ:1.00
 O1B A:ADP801 2.3 13.3 1.0
O1A A:ADP801 2.4 16.2 1.0
O A:HOH997 2.4 18.3 1.0
OD2 A:ASP124 2.5 16.5 1.0
O3 A:PO4807 2.5 22.7 1.0
O A:HOH987 2.5 14.6 1.0
OD1 A:ASP124 2.5 15.8 1.0
CG A:ASP124 2.8 15.1 1.0
PB A:ADP801 3.4 14.4 1.0
PA A:ADP801 3.6 14.1 1.0
P A:PO4807 3.7 20.2 1.0
O3B A:ADP801 3.8 13.1 1.0
O3A A:ADP801 3.8 13.5 1.0
O A:HOH973 3.9 17.3 1.0
CA A:CA804 3.9 17.3 1.0
O4 A:PO4807 4.0 33.5 1.0
O A:HOH974 4.2 17.5 1.0
O A:HOH936 4.2 22.1 1.0
CB A:ASP124 4.3 15.6 1.0
ND2 A:ASN151 4.3 12.4 1.0
O A:HOH939 4.3 17.5 1.0
O1 A:PO4807 4.3 35.7 1.0
O A:HOH953 4.4 16.1 1.0
CB A:ASN151 4.6 13.7 1.0
O2A A:ADP801 4.6 15.5 1.0
O5' A:ADP801 4.7 14.5 1.0
O A:HOH921 4.7 14.9 1.0
O2B A:ADP801 4.8 14.0 1.0
CG A:ASN151 4.8 14.0 1.0
O2 A:PO4807 4.9 30.9 1.0
OG1 A:THR229 4.9 16.2 1.0

Calcium binding site 2 out of 7 in 6k92

Go back to Calcium Binding Sites List in 6k92
Calcium binding site 2 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:17.3
occ:1.00
 O A:TYR226 2.3 15.9 1.0
OD2 A:ASP124 2.3 16.5 1.0
O A:HOH939 2.4 17.5 1.0
O A:HOH1000 2.5 13.4 1.0
O A:HOH987 2.5 14.6 1.0
O A:HOH910 2.6 15.9 1.0
O A:HOH973 2.6 17.3 1.0
C A:TYR226 3.5 17.9 1.0
CG A:ASP124 3.5 15.1 1.0
CA A:CA803 3.9 16.1 1.0
CB A:ASP124 4.2 15.6 1.0
OD2 A:ASP125 4.2 37.0 1.0
O A:HOH936 4.3 22.1 1.0
N A:THR227 4.3 17.1 1.0
O A:HOH953 4.3 16.1 1.0
CA A:THR227 4.3 16.6 1.0
N A:TYR226 4.4 23.2 1.0
O3B A:ADP801 4.5 13.1 1.0
OD1 A:ASP124 4.5 15.8 1.0
O3 A:PO4807 4.5 22.7 1.0
OD1 A:ASP125 4.5 27.6 1.0
O1B A:ADP801 4.6 13.3 1.0
CA A:TYR226 4.6 20.2 1.0
CG2 A:THR227 4.6 21.3 1.0
CG A:ASP125 4.7 32.9 1.0
OG1 A:THR229 4.7 16.2 1.0

Calcium binding site 3 out of 7 in 6k92

Go back to Calcium Binding Sites List in 6k92
Calcium binding site 3 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:18.1
occ:1.00
 O A:HOH919 2.2 13.7 1.0
O2B A:ADP801 2.3 14.0 1.0
O A:HOH955 2.3 13.0 1.0
O A:HOH924 2.4 14.6 1.0
O A:HOH936 2.7 22.1 1.0
PB A:ADP801 3.4 14.4 1.0
O1B A:ADP801 3.9 13.3 1.0
OH A:TYR129 4.0 32.8 1.0
O A:HOH970 4.0 14.5 1.0
O3B A:ADP801 4.0 13.1 1.0
NZ A:LYS187 4.1 15.4 1.0
ND2 A:ASN151 4.1 12.4 1.0
OE2 A:GLU154 4.3 14.3 1.0
CA A:GLY230 4.4 12.6 1.0
CG2 A:VAL121 4.4 16.4 1.0
OD2 A:ASP119 4.5 17.1 1.0
OD1 A:ASP119 4.6 14.5 1.0
OE1 A:GLU154 4.6 14.8 1.0
O3A A:ADP801 4.6 13.5 1.0
C5 A:GT0802 4.7 15.8 1.0
OD1 A:ASP231 4.7 15.7 1.0
O2 A:GT0802 4.8 21.2 1.0
N A:GLY230 4.8 11.8 1.0
O A:HOH939 4.8 17.5 1.0
CD A:GLU154 4.9 15.9 1.0
CG1 A:VAL121 4.9 16.6 1.0
CG A:ASN151 4.9 14.0 1.0
CG A:ASP119 5.0 15.2 1.0

Calcium binding site 4 out of 7 in 6k92

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Calcium binding site 4 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:16.5
occ:1.00
 O B:TYR226 2.1 14.8 1.0
OD2 B:ASP124 2.3 15.2 1.0
O B:HOH767 2.4 27.1 1.0
O B:HOH804 2.4 16.8 1.0
O B:HOH704 2.5 16.4 1.0
O B:HOH732 2.5 15.9 1.0
O B:HOH794 2.5 13.6 1.0
C B:TYR226 3.4 17.2 1.0
CG B:ASP124 3.6 16.0 1.0
CA B:CA604 3.9 17.7 1.0
CA B:THR227 4.2 17.9 1.0
N B:THR227 4.2 17.7 1.0
O B:HOH761 4.2 16.2 1.0
CB B:ASP124 4.3 16.9 1.0
N B:TYR226 4.3 20.4 1.0
OD2 B:ASP125 4.4 37.1 1.0
O B:HOH751 4.4 39.0 1.0
O2B B:ADP601 4.4 15.4 1.0
OD1 B:ASP125 4.5 31.4 1.0
CA B:TYR226 4.5 20.7 1.0
O3B B:ADP601 4.5 11.9 1.0
O1 B:PO4607 4.5 25.8 1.0
OD1 B:ASP124 4.5 17.5 1.0
CG2 B:THR227 4.5 19.0 1.0
OG1 B:THR229 4.8 13.1 1.0
CG B:ASP125 4.8 30.6 1.0
CB B:THR227 5.0 20.1 1.0

Calcium binding site 5 out of 7 in 6k92

Go back to Calcium Binding Sites List in 6k92
Calcium binding site 5 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:17.7
occ:1.00
 O2A B:ADP601 2.3 14.1 1.0
O3B B:ADP601 2.3 11.9 1.0
O B:HOH792 2.4 18.7 1.0
O1 B:PO4607 2.5 25.8 1.0
OD2 B:ASP124 2.5 15.2 1.0
OD1 B:ASP124 2.5 17.5 1.0
O B:HOH794 2.5 13.6 1.0
CG B:ASP124 2.8 16.0 1.0
PB B:ADP601 3.4 13.4 1.0
PA B:ADP601 3.6 14.5 1.0
O3A B:ADP601 3.8 13.6 1.0
P B:PO4607 3.8 28.8 1.0
O2B B:ADP601 3.8 15.4 1.0
CA B:CA603 3.9 16.5 1.0
O B:HOH732 4.0 15.9 1.0
O2 B:PO4607 4.1 42.6 1.0
O B:HOH756 4.1 17.2 1.0
O B:HOH704 4.2 16.4 1.0
CB B:ASP124 4.3 16.9 1.0
ND2 B:ASN151 4.3 12.6 1.0
O4 B:PO4607 4.4 42.7 1.0
O B:HOH751 4.5 39.0 1.0
CB B:ASN151 4.5 12.8 1.0
O1A B:ADP601 4.5 15.8 1.0
O B:HOH761 4.5 16.2 1.0
O5' B:ADP601 4.6 15.1 1.0
O1B B:ADP601 4.7 12.0 1.0
O B:HOH741 4.7 15.8 1.0
CG B:ASN151 4.8 14.3 1.0
O3 B:PO4607 4.9 44.0 1.0

Calcium binding site 6 out of 7 in 6k92

Go back to Calcium Binding Sites List in 6k92
Calcium binding site 6 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:17.0
occ:1.00
 O B:HOH706 2.1 16.7 1.0
O1B B:ADP601 2.2 12.0 1.0
O B:HOH712 2.3 11.3 1.0
O B:HOH717 2.4 11.1 1.0
O B:HOH751 2.8 39.0 1.0
PB B:ADP601 3.4 13.4 1.0
O3B B:ADP601 3.8 11.9 1.0
OH B:TYR129 4.0 30.5 1.0
O B:HOH780 4.0 13.9 1.0
O2B B:ADP601 4.0 15.4 1.0
NZ B:LYS187 4.1 12.2 1.0
ND2 B:ASN151 4.1 12.6 1.0
OE2 B:GLU154 4.2 14.5 1.0
O2 B:GT0602 4.3 33.7 1.0
OE1 B:GLU154 4.4 14.0 1.0
CA B:GLY230 4.4 12.0 1.0
OD2 B:ASP119 4.4 13.4 1.0
CG2 B:VAL121 4.4 13.1 1.0
OD1 B:ASP119 4.6 12.3 1.0
C5 B:GT0602 4.6 17.4 1.0
O3A B:ADP601 4.6 13.6 1.0
O B:HOH704 4.6 16.4 1.0
CD B:GLU154 4.7 15.2 1.0
CG1 B:VAL121 4.7 13.8 1.0
OD1 B:ASP231 4.8 11.8 1.0
N B:GLY230 4.8 13.1 1.0
CG B:ASP119 4.9 12.2 1.0
CG B:ASN151 4.9 14.3 1.0

Calcium binding site 7 out of 7 in 6k92

Go back to Calcium Binding Sites List in 6k92
Calcium binding site 7 out of 7 in the Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pyridoxal Kinase From Leishmania Donovani in Complex with Adp and Ginkgotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:29.0
occ:1.00
 O B:HOH764 2.3 24.2 1.0
O B:HOH715 2.3 20.1 1.0
O B:HOH798 2.3 33.5 1.0
O B:GLY180 2.3 23.1 1.0
O B:THR143 2.4 19.4 1.0
C B:GLY180 3.3 22.6 1.0
C B:THR143 3.6 17.8 1.0
CA B:GLY180 3.7 22.8 1.0
N B:HIS144 4.4 15.3 1.0
CA B:THR143 4.5 17.5 1.0
N B:THR181 4.5 19.0 1.0
CA B:HIS144 4.5 15.6 1.0
O B:ALA145 4.6 16.2 1.0
CD B:PRO182 4.7 18.4 1.0
C B:HIS144 4.9 14.7 1.0
O B:HOH753 4.9 20.8 1.0
CA B:THR181 5.0 16.5 1.0

Reference:

S.Are, S.Gatreddi, P.Jakkula, I.A.Qureshi. Structural Attributes and Substrate Specificity of Pyridoxal Kinase From Leishmania Donovani. Int.J.Biol.Macromol. V. 152 812 2020.
ISSN: ISSN 0141-8130
PubMed: 32105687
DOI: 10.1016/J.IJBIOMAC.2020.02.257
Page generated: Tue Jul 16 10:20:12 2024

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