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Calcium in PDB 4dk4: Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+:
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+, PDB code: 4dk4 was solved by G.R.Hemsworth, D.Gonzalez-Pacanowska, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.45 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.840, 83.190, 91.180, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.2

Other elements in 4dk4:

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ (pdb code 4dk4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+, PDB code: 4dk4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4dk4

Go back to Calcium Binding Sites List in 4dk4
Calcium binding site 1 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:12.0
occ:1.00
 O2A A:DUN301 2.3 7.9 1.0
O3B A:DUN301 2.3 11.3 1.0
O A:HOH402 2.4 13.9 1.0
OE2 A:GLU51 2.4 12.2 1.0
OE2 A:GLU48 2.5 18.3 1.0
O A:HOH401 2.5 11.3 1.0
CD A:GLU51 3.2 21.0 1.0
CD A:GLU48 3.3 15.0 1.0
OE1 A:GLU48 3.4 14.0 1.0
OE1 A:GLU51 3.4 14.9 1.0
PA A:DUN301 3.4 11.2 1.0
PB A:DUN301 3.5 13.5 1.0
N3A A:DUN301 3.5 11.3 1.0
CA A:CA303 3.7 12.9 1.0
O A:HOH411 4.0 11.9 1.0
NZ B:LYS59 4.1 15.1 1.0
C5' A:DUN301 4.2 10.4 1.0
O5' A:DUN301 4.3 10.2 1.0
O1B A:DUN301 4.4 14.5 1.0
O B:HOH426 4.4 19.1 1.0
O A:HOH405 4.5 27.7 1.0
O1A A:DUN301 4.6 12.0 1.0
CE B:LYS59 4.6 12.7 1.0
CG A:GLU51 4.6 11.6 1.0
CG A:GLU48 4.6 13.3 1.0
O2B A:DUN301 4.7 16.1 1.0
O B:HOH403 5.0 8.1 1.0
O A:HOH403 5.0 16.8 1.0

Calcium binding site 2 out of 4 in 4dk4

Go back to Calcium Binding Sites List in 4dk4
Calcium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.9
occ:1.00
 OE1 A:GLU76 2.2 16.4 1.0
OE1 A:GLU48 2.3 14.0 1.0
OE1 A:GLU51 2.3 14.9 1.0
O3B A:DUN301 2.3 11.3 1.0
OD2 A:ASP79 2.3 14.1 1.0
O A:HOH403 2.4 16.8 1.0
CD A:GLU51 3.3 21.0 1.0
CD A:GLU76 3.4 20.3 1.0
CD A:GLU48 3.4 15.0 1.0
CG A:ASP79 3.4 23.4 1.0
PB A:DUN301 3.5 13.5 1.0
CA A:CA302 3.7 12.0 1.0
NA A:NA304 3.7 19.2 1.0
OE2 A:GLU76 3.8 15.5 1.0
OE2 A:GLU51 3.8 12.2 1.0
OE2 A:GLU48 3.9 18.3 1.0
CB A:ASP79 3.9 12.0 1.0
O2B A:DUN301 4.0 16.1 1.0
O1B A:DUN301 4.0 14.5 1.0
O A:HOH405 4.2 27.7 1.0
OD1 A:ASP79 4.5 15.4 1.0
CG A:GLU51 4.5 11.6 1.0
CB A:GLU51 4.5 11.1 1.0
CA A:GLU76 4.6 9.4 1.0
CG A:GLU76 4.7 13.7 1.0
CG2 A:ILE75 4.7 6.5 1.0
CG A:GLU48 4.7 13.3 1.0
NZ A:LYS208 4.7 13.3 1.0
O A:HOH406 4.7 25.2 1.0
N3A A:DUN301 4.9 11.3 1.0
CB A:GLU76 4.9 11.0 1.0

Calcium binding site 3 out of 4 in 4dk4

Go back to Calcium Binding Sites List in 4dk4
Calcium binding site 3 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:10.7
occ:1.00
 O1A B:DUN301 2.3 7.8 1.0
OE2 B:GLU48 2.3 16.9 1.0
O A:HOH404 2.4 13.4 1.0
O3B B:DUN301 2.4 11.4 1.0
OE2 B:GLU51 2.4 11.6 1.0
O B:HOH401 2.5 10.9 1.0
CD B:GLU48 3.1 7.8 1.0
OE1 B:GLU48 3.2 10.4 1.0
CD B:GLU51 3.2 20.5 1.0
OE1 B:GLU51 3.4 12.3 1.0
PA B:DUN301 3.4 11.7 1.0
PB B:DUN301 3.6 12.9 1.0
N3A B:DUN301 3.6 7.0 1.0
CA B:CA303 3.6 10.7 1.0
NZ A:LYS59 4.1 13.3 1.0
O B:HOH405 4.1 11.9 1.0
O B:HOH411 4.2 19.3 1.0
C5' B:DUN301 4.2 11.2 1.0
O A:HOH445 4.3 21.8 1.0
O5' B:DUN301 4.3 10.9 1.0
O2B B:DUN301 4.4 14.6 1.0
CG B:GLU48 4.5 15.1 1.0
O2A B:DUN301 4.6 10.8 1.0
O1B B:DUN301 4.7 23.8 1.0
CE A:LYS59 4.7 21.7 1.0
CG B:GLU51 4.7 17.8 1.0
O B:HOH481 4.9 13.4 1.0
O B:HOH402 4.9 13.2 1.0
NZ B:LYS227 5.0 44.6 1.0

Calcium binding site 4 out of 4 in 4dk4

Go back to Calcium Binding Sites List in 4dk4
Calcium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:10.7
occ:1.00
 OE1 B:GLU48 2.2 10.4 1.0
OE1 B:GLU76 2.3 18.6 1.0
OD2 B:ASP79 2.3 13.3 1.0
O B:HOH402 2.3 13.2 1.0
OE1 B:GLU51 2.4 12.3 1.0
O3B B:DUN301 2.4 11.4 1.0
CD B:GLU76 3.3 14.9 1.0
CD B:GLU51 3.3 20.5 1.0
CD B:GLU48 3.4 7.8 1.0
CG B:ASP79 3.4 12.7 1.0
PB B:DUN301 3.5 12.9 1.0
CA B:CA302 3.6 10.7 1.0
NA B:NA304 3.7 19.6 1.0
OE2 B:GLU76 3.7 15.8 1.0
OE2 B:GLU51 3.8 11.6 1.0
O2B B:DUN301 3.8 14.6 1.0
OE2 B:GLU48 3.9 16.9 1.0
CB B:ASP79 4.0 14.7 1.0
O1B B:DUN301 4.0 23.8 1.0
OD1 B:ASP79 4.4 8.0 1.0
CG B:GLU51 4.5 17.8 1.0
CB B:GLU51 4.6 12.7 1.0
O B:HOH432 4.6 31.4 1.0
CA B:GLU76 4.6 6.1 1.0
CG B:GLU76 4.7 13.1 1.0
O B:HOH490 4.7 49.7 1.0
CG B:GLU48 4.7 15.1 1.0
NZ B:LYS208 4.7 9.0 1.0
CG2 B:ILE75 4.7 18.0 1.0
N3A B:DUN301 4.9 7.0 1.0
CB B:GLU76 4.9 12.7 1.0

Reference:

G.R.Hemsworth, D.Gonzalez-Pacanowska, K.S.Wilson. On the Catalytic Mechanism of Dimeric Dutpases. Biochem.J. V. 456 81 2013.
ISSN: ISSN 0264-6021
PubMed: 24001052
DOI: 10.1042/BJ20130796
Page generated: Sat Jul 13 23:28:29 2024

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