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Strontium in PDB 3e4p: Crystal Structure of Malonate Occupied Dctb

Enzymatic activity of Crystal Structure of Malonate Occupied Dctb

All present enzymatic activity of Crystal Structure of Malonate Occupied Dctb:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of Malonate Occupied Dctb, PDB code: 3e4p 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 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.980, 39.100, 111.540, 90.00, 94.78, 90.00
R / Rfree (%) 19.6 / 26.2

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Malonate Occupied Dctb (pdb code 3e4p). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 3 binding sites of Strontium where determined in the Crystal Structure of Malonate Occupied Dctb, PDB code: 3e4p:
Jump to Strontium binding site number: 1; 2; 3;

Strontium binding site 1 out of 3 in 3e4p

Go back to Strontium Binding Sites List in 3e4p
Strontium binding site 1 out of 3 in the Crystal Structure of Malonate Occupied Dctb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Malonate Occupied Dctb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr502

b:43.5
occ:0.50
ND2 A:ASN299 3.4 36.4 1.0
NE1 A:TRP300 3.6 28.1 1.0
CE2 A:TRP300 3.6 27.5 1.0
N A:ASN299 3.7 32.9 1.0
CB A:THR298 3.7 31.0 1.0
CD1 A:TRP300 3.9 27.7 1.0
CD2 A:TRP300 3.9 28.4 1.0
OE1 A:GLU165 4.0 33.2 1.0
CA A:THR298 4.1 31.6 1.0
CG A:TRP300 4.1 30.0 1.0
CZ2 A:TRP300 4.1 25.7 1.0
CG A:ASN299 4.2 37.2 1.0
CG2 A:THR298 4.3 28.6 1.0
C A:THR298 4.4 32.1 1.0
NH2 A:ARG80 4.6 19.7 1.0
CE3 A:TRP300 4.6 28.7 1.0
OD1 A:ASN299 4.7 41.0 1.0
CA A:ASN299 4.7 33.6 1.0
CH2 A:TRP300 4.7 26.6 1.0
OG1 A:THR298 4.8 29.6 1.0
N A:TRP300 4.9 31.6 1.0
CZ3 A:TRP300 5.0 26.1 1.0

Strontium binding site 2 out of 3 in 3e4p

Go back to Strontium Binding Sites List in 3e4p
Strontium binding site 2 out of 3 in the Crystal Structure of Malonate Occupied Dctb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Malonate Occupied Dctb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr501

b:54.3
occ:0.50
O B:HOH652 2.8 40.6 1.0
O B:HOH623 3.7 29.5 1.0
N B:ASP153 3.7 30.0 1.0
CG B:ASP153 3.9 27.7 1.0
OD2 B:ASP153 4.0 27.7 1.0
OD1 B:ASP153 4.1 26.4 1.0
NE2 B:HIS166 4.3 26.8 1.0
CB B:ASP153 4.3 29.1 1.0
OE1 B:GLN252 4.3 49.0 1.0
CA B:ARG152 4.3 29.1 1.0
CD2 B:HIS166 4.3 26.4 1.0
O B:PHE151 4.5 26.4 1.0
C B:ARG152 4.5 29.7 1.0
CD B:ARG152 4.6 26.8 1.0
O B:SER250 4.6 42.2 1.0
CA B:ASP153 4.6 29.3 1.0
O B:HOH622 4.8 45.2 1.0
O B:GLU249 4.9 44.6 1.0

Strontium binding site 3 out of 3 in 3e4p

Go back to Strontium Binding Sites List in 3e4p
Strontium binding site 3 out of 3 in the Crystal Structure of Malonate Occupied Dctb


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Malonate Occupied Dctb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr503

b:38.9
occ:0.50
ND2 B:ASN299 3.4 23.1 1.0
NE1 B:TRP300 3.5 23.5 1.0
CE2 B:TRP300 3.6 24.3 1.0
N B:ASN299 3.8 27.1 1.0
CB B:THR298 3.8 25.0 1.0
CD1 B:TRP300 3.9 24.4 1.0
CD2 B:TRP300 4.0 23.3 1.0
CZ2 B:TRP300 4.1 25.7 1.0
OE1 B:GLU165 4.1 31.8 1.0
CG B:ASN299 4.1 26.9 1.0
CG B:TRP300 4.1 26.0 1.0
CA B:THR298 4.2 25.3 1.0
CG2 B:THR298 4.4 21.8 1.0
OD1 B:ASN299 4.5 26.2 1.0
C B:THR298 4.5 25.9 1.0
N B:TRP300 4.7 27.5 1.0
CE3 B:TRP300 4.7 22.7 1.0
CA B:ASN299 4.7 27.6 1.0
CH2 B:TRP300 4.8 26.1 1.0
OG1 B:THR298 4.8 23.1 1.0
O B:HOH643 4.9 24.9 1.0
C B:ASN299 4.9 27.9 1.0
NH2 B:ARG80 4.9 27.7 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: Wed Dec 16 02:22:38 2020

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