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Calcium in PDB 4zdi: Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)

Enzymatic activity of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)

All present enzymatic activity of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form):
6.3.4.2;

Protein crystallography data

The structure of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form), PDB code: 4zdi was solved by M.Bellinzoni, N.Barilone, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.21 / 3.52
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 196.826, 196.826, 184.047, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) (pdb code 4zdi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form), PDB code: 4zdi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4zdi

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Calcium binding site 1 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


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 the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:95.0
occ:1.00
 CD2 A:LEU77 3.5 90.7 1.0
O A:HIS63 3.5 95.1 1.0
OD1 A:ASP76 3.6 93.2 1.0
OD2 A:ASP76 3.6 96.7 1.0
CG A:ASP76 4.0 92.0 1.0
CG A:LEU77 4.5 87.3 1.0
OD2 A:ASP78 4.7 0.8 1.0
C A:HIS63 4.7 96.8 1.0

Calcium binding site 2 out of 8 in 4zdi

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Calcium binding site 2 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


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 the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:97.1
occ:1.00
 OD1 B:ASP76 3.6 97.6 1.0
O B:HIS63 3.6 83.5 1.0
CD2 B:LEU77 3.7 93.0 1.0
OD2 B:ASP76 3.8 0.3 1.0
CG B:ASP76 4.1 96.4 1.0
CG B:LEU77 4.6 90.3 1.0
OD2 B:ASP78 4.7 0.9 1.0
C B:HIS63 4.8 84.6 1.0

Calcium binding site 3 out of 8 in 4zdi

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Calcium binding site 3 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


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 the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:0.9
occ:1.00
 OD1 C:ASP76 3.4 95.9 1.0
OD2 C:ASP76 3.5 0.2 1.0
O C:HIS63 3.5 91.1 1.0
CD2 C:LEU77 3.6 88.8 1.0
CG C:ASP76 3.9 94.4 1.0
CG C:LEU77 4.6 85.3 1.0
OD2 C:ASP78 4.7 0.5 1.0
C C:HIS63 4.8 92.8 1.0

Calcium binding site 4 out of 8 in 4zdi

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Calcium binding site 4 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


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 the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:0.6
occ:1.00
 OD1 D:ASP76 3.1 0.2 1.0
O D:HIS63 3.3 0.1 1.0
CD2 D:LEU77 3.5 0.8 1.0
OD2 D:ASP76 3.5 0.4 1.0
CG D:ASP76 3.7 0.8 1.0
C D:HIS63 4.5 0.9 1.0
CG D:LEU77 4.6 0.7 1.0

Calcium binding site 5 out of 8 in 4zdi

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Calcium binding site 5 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca601

b:0.7
occ:1.00
 OD2 E:ASP76 3.2 0.4 1.0
OD1 E:ASP76 3.4 1.0 1.0
CD2 E:LEU77 3.6 0.4 1.0
CG E:ASP76 3.7 0.7 1.0
O E:HIS63 4.1 0.5 1.0
OD2 E:ASP78 4.1 0.1 1.0
CG E:LEU77 4.5 0.6 1.0
NZ E:LYS46 4.9 0.8 1.0

Calcium binding site 6 out of 8 in 4zdi

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Calcium binding site 6 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:0.6
occ:1.00
 OD2 F:ASP76 3.2 0.1 1.0
OD1 F:ASP76 3.2 0.7 1.0
CG F:ASP76 3.6 0.1 1.0
CD2 F:LEU77 3.8 0.3 1.0
O F:HIS63 4.0 0.6 1.0
OD2 F:ASP78 4.3 0.3 1.0
CG F:LEU77 4.7 0.5 1.0
NZ F:LYS46 4.9 0.3 1.0

Calcium binding site 7 out of 8 in 4zdi

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Calcium binding site 7 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:0.5
occ:1.00
 CD2 G:LEU77 3.5 0.2 1.0
OD1 G:ASP76 3.5 1.0 1.0
OD2 G:ASP76 3.5 0.8 1.0
O G:HIS63 3.5 0.4 1.0
CG G:ASP76 3.9 0.9 1.0
CG G:LEU77 4.4 0.5 1.0
OD2 G:ASP78 4.6 0.6 1.0
C G:HIS63 4.8 0.8 1.0

Calcium binding site 8 out of 8 in 4zdi

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Calcium binding site 8 out of 8 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca601

b:0.8
occ:1.00
 OD2 H:ASP76 3.3 0.4 1.0
CD2 H:LEU77 3.5 0.1 1.0
OD1 H:ASP76 3.5 0.7 1.0
CG H:ASP76 3.8 0.8 1.0
O H:HIS63 3.9 0.3 1.0
OD2 H:ASP78 4.3 0.8 1.0
CG H:LEU77 4.3 0.1 1.0

Reference:

G.Mori, L.R.Chiarelli, M.Esposito, V.Makarov, M.Bellinzoni, R.C.Hartkoorn, G.Degiacomi, F.Boldrin, S.Ekins, A.L.De Jesus Lopes Ribeiro, L.B.Marino, I.Centarova, Z.Svetlikova, J.Blasko, E.Kazakova, A.Lepioshkin, N.Barilone, G.Zanoni, A.Porta, M.Fondi, R.Fani, A.R.Baulard, K.Mikusova, P.M.Alzari, R.Manganelli, L.P.De Carvalho, G.Riccardi, S.T.Cole, M.R.Pasca. Thiophenecarboxamide Derivatives Activated By Etha Kill Mycobacterium Tuberculosis By Inhibiting the Ctp Synthetase Pyrg. Chem.Biol. V. 22 917 2015.
ISSN: ISSN 1074-5521
PubMed: 26097035
DOI: 10.1016/J.CHEMBIOL.2015.05.016
Page generated: Sat Dec 12 05:15:26 2020

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