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Calcium in PDB 3e4q: Crystal Structure of Apo Dctb

Enzymatic activity of Crystal Structure of Apo Dctb

All present enzymatic activity of Crystal Structure of Apo Dctb:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of Apo Dctb, PDB code: 3e4q was solved by Y.F.Zhou, J.Nan, B.Y.Nan, Y.H.Liang, S.Panjikar, X.D.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.988, 38.735, 111.172, 90.00, 94.47, 90.00
R / Rfree (%) 19.5 / 27.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Apo Dctb (pdb code 3e4q). 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 Apo Dctb, PDB code: 3e4q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3e4q

Go back to Calcium Binding Sites List in 3e4q
Calcium binding site 1 out of 2 in the Crystal Structure of Apo Dctb


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 Apo Dctb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:49.0
occ:0.80
ND2 A:ASN299 2.2 63.4 1.0
N A:ASN299 3.1 50.8 1.0
CG A:ASN299 3.5 59.3 1.0
CB A:THR298 3.5 48.6 1.0
NE1 A:TRP300 3.6 49.4 1.0
CD1 A:TRP300 3.7 51.3 1.0
CA A:THR298 3.8 48.8 1.0
CE2 A:TRP300 3.9 50.5 1.0
C A:THR298 3.9 49.2 1.0
CG A:TRP300 4.0 52.6 1.0
CA A:ASN299 4.1 53.0 1.0
CD2 A:TRP300 4.1 51.0 1.0
CG2 A:THR298 4.3 48.7 1.0
OD1 A:ASN299 4.3 65.2 1.0
N A:TRP300 4.3 52.9 1.0
OE1 A:GLU165 4.4 51.7 1.0
CB A:ASN299 4.4 53.5 1.0
C A:ASN299 4.5 53.1 1.0
OG1 A:THR298 4.6 45.8 1.0
CZ2 A:TRP300 4.6 52.8 1.0
NH2 A:ARG80 4.7 38.5 1.0
CB A:TRP300 4.9 52.3 1.0
CE3 A:TRP300 5.0 51.3 1.0

Calcium binding site 2 out of 2 in 3e4q

Go back to Calcium Binding Sites List in 3e4q
Calcium binding site 2 out of 2 in the Crystal Structure of Apo Dctb


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 Apo Dctb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:45.9
occ:0.80
ND2 B:ASN299 3.4 52.3 1.0
NE1 B:TRP300 3.4 50.0 1.0
CE2 B:TRP300 3.5 52.8 1.0
N B:ASN299 3.6 52.6 1.0
CD1 B:TRP300 3.8 52.2 1.0
CB B:THR298 3.9 51.0 1.0
CZ2 B:TRP300 3.9 56.2 1.0
CA B:THR298 4.0 50.4 1.0
CD2 B:TRP300 4.0 52.4 1.0
CG B:ASN299 4.1 52.8 1.0
CG B:TRP300 4.2 53.0 1.0
OE1 B:GLU165 4.3 52.6 1.0
C B:THR298 4.3 51.0 1.0
OD1 B:ASN299 4.5 54.2 1.0
N B:TRP300 4.6 54.3 1.0
CA B:ASN299 4.6 53.3 1.0
CH2 B:TRP300 4.7 53.2 1.0
CG2 B:THR298 4.8 48.6 1.0
CE3 B:TRP300 4.8 50.4 1.0
OG1 B:THR298 4.8 51.7 1.0
C B:ASN299 4.9 53.8 1.0
CB B:ASN299 5.0 52.7 1.0

Reference:

Y.F.Zhou, B.Y.Nan, J.Nan, Q.J.Ma, S.Panjikar, Y.H.Liang, Y.P.Wang, X.D.Su. C4-Dicarboxylates Sensing Mechanism Revealed By the Crystal Structures of Dctb Sensor Domain. J.Mol.Biol. V. 383 49 2008.
ISSN: ISSN 0022-2836
PubMed: 18725229
DOI: 10.1016/J.JMB.2008.08.010
Page generated: Sat Dec 12 04:09:41 2020

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