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Calcium in PDB 3b9g: Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh

Enzymatic activity of Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh

All present enzymatic activity of Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh:
3.2.2.1;

Protein crystallography data

The structure of Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh, PDB code: 3b9g was solved by A.Vandemeulebroucke, S.De Vos, E.Van Holsbeke, J.Steyaert, W.Versees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.32 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.177, 74.881, 72.424, 90.00, 98.07, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 3b9g:

The structure of Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh (pdb code 3b9g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh, PDB code: 3b9g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3b9g

Go back to Calcium Binding Sites List in 3b9g
Calcium binding site 1 out of 2 in the Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh


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 Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca318

b:10.4
occ:1.00
 O2' A:IMH501 2.3 13.2 0.7
O3' A:IMH501 2.4 14.3 0.3
O A:THR137 2.4 10.8 1.0
O A:HOH514 2.4 11.7 1.0
OD2 A:ASP251 2.4 11.0 1.0
OD2 A:ASP15 2.5 11.1 1.0
OD1 A:ASP10 2.5 12.0 1.0
O3' A:IMH501 2.6 9.3 0.7
OD1 A:ASP15 2.6 10.0 1.0
O2' A:IMH501 2.6 16.4 0.3
CG A:ASP15 2.9 11.4 1.0
C2' A:IMH501 3.4 14.3 0.7
CG A:ASP251 3.4 11.6 1.0
C A:THR137 3.5 11.2 1.0
C3' A:IMH501 3.5 15.4 0.3
C3' A:IMH501 3.5 12.7 0.7
CG A:ASP10 3.5 12.3 1.0
C2' A:IMH501 3.6 16.2 0.3
OD1 A:ASP251 3.7 11.3 1.0
OD2 A:ASP10 4.0 13.1 1.0
C1' A:IMH501 4.1 18.0 0.7
N A:GLY138 4.2 10.4 1.0
CA A:GLY138 4.2 11.4 1.0
OD1 A:ASP14 4.2 13.0 1.0
CB A:ASP15 4.3 10.5 1.0
C1' A:IMH501 4.3 17.5 0.3
CB A:THR137 4.4 11.1 1.0
OG1 A:THR137 4.5 12.1 1.0
N4' A:IMH501 4.5 16.3 0.7
CA A:THR137 4.5 11.0 1.0
C4' A:IMH501 4.5 14.4 0.7
ND2 A:ASN186 4.5 10.6 1.0
C4' A:IMH501 4.6 15.5 0.3
OD1 A:ASN186 4.6 12.5 1.0
N A:ASP10 4.6 10.2 1.0
OD2 A:ASP14 4.6 13.9 1.0
N4' A:IMH501 4.7 16.2 0.3
CB A:ASN12 4.7 13.2 1.0
CB A:ASP251 4.8 10.3 1.0
CG A:ASP14 4.8 11.6 1.0
CB A:ASP10 4.8 10.9 1.0
N A:ASP15 4.8 10.9 1.0
CA A:ASP15 4.9 10.6 1.0
N A:ASN12 5.0 11.7 1.0

Calcium binding site 2 out of 2 in 3b9g

Go back to Calcium Binding Sites List in 3b9g
Calcium binding site 2 out of 2 in the Crystal Structure of Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh


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 Loop Deletion Mutant of Trypanosoma Vivax Nucleoside Hydrolase (3GTVNH) in Complex with Immh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca318

b:11.2
occ:1.00
 O B:THR137 2.4 12.0 1.0
O2' B:IMH502 2.4 15.8 0.5
OD2 B:ASP251 2.4 12.0 1.0
OD1 B:ASP10 2.5 12.8 1.0
OD2 B:ASP15 2.5 11.0 1.0
O B:HOH523 2.5 12.3 1.0
O2' B:IMH502 2.5 11.4 0.5
O3' B:IMH502 2.5 10.5 0.5
O3' B:IMH502 2.5 15.9 0.5
OD1 B:ASP15 2.6 10.7 1.0
CG B:ASP15 2.8 11.4 1.0
CG B:ASP251 3.4 12.6 1.0
C2' B:IMH502 3.5 17.4 0.5
C B:THR137 3.5 12.2 1.0
C2' B:IMH502 3.5 12.4 0.5
C3' B:IMH502 3.5 12.2 0.5
C3' B:IMH502 3.5 17.0 0.5
CG B:ASP10 3.6 13.8 1.0
OD1 B:ASP251 3.7 13.2 1.0
OD2 B:ASP10 4.0 13.9 1.0
C1' B:IMH502 4.1 20.0 0.5
N B:GLY138 4.2 12.3 1.0
CA B:GLY138 4.2 12.5 1.0
C1' B:IMH502 4.3 15.2 0.5
OD1 B:ASP14 4.3 14.4 1.0
CB B:ASP15 4.3 11.0 1.0
CB B:THR137 4.3 12.0 1.0
CA B:THR137 4.5 12.4 1.0
OG1 B:THR137 4.5 13.8 1.0
ND2 B:ASN186 4.5 11.6 1.0
OD1 B:ASN186 4.5 13.9 1.0
C4' B:IMH502 4.5 16.4 0.5
C4' B:IMH502 4.6 11.5 0.5
N4' B:IMH502 4.6 18.5 0.5
N B:ASP10 4.6 11.4 1.0
N4' B:IMH502 4.6 12.3 0.5
OD2 B:ASP14 4.6 14.6 1.0
CB B:ASN12 4.7 13.4 1.0
CG B:ASP14 4.7 14.6 1.0
CB B:ASP251 4.8 11.7 1.0
N B:ASP15 4.8 11.1 1.0
CB B:ASP10 4.8 12.6 1.0
CA B:ASP15 4.8 10.8 1.0
CG B:ASN186 5.0 12.5 1.0

Reference:

A.Vandemeulebroucke, S.De Vos, E.Van Holsbeke, J.Steyaert, W.Versees. A Flexible Loop As A Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase From Trypanosoma Vivax. J.Biol.Chem. V. 283 22272 2008.
ISSN: ISSN 0021-9258
PubMed: 18519562
DOI: 10.1074/JBC.M803705200
Page generated: Tue Jul 8 11:04:04 2025

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