Calcium in PDB 6p96: Oxa-48 Carbapanemase, Apo Form

Enzymatic activity of Oxa-48 Carbapanemase, Apo Form

All present enzymatic activity of Oxa-48 Carbapanemase, Apo Form:
3.5.2.6;

Protein crystallography data

The structure of Oxa-48 Carbapanemase, Apo Form, PDB code: 6p96 was solved by C.A.Smith, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.41 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.746, 76.827, 100.044, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.9

Other elements in 6p96:

The structure of Oxa-48 Carbapanemase, Apo Form also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Oxa-48 Carbapanemase, Apo Form (pdb code 6p96). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Oxa-48 Carbapanemase, Apo Form, PDB code: 6p96:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6p96

Go back to Calcium Binding Sites List in 6p96
Calcium binding site 1 out of 3 in the Oxa-48 Carbapanemase, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Oxa-48 Carbapanemase, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:14.2
occ:1.00
OD1 A:ASP143 2.2 26.4 1.0
OE1 A:GLU147 2.2 31.3 1.0
O A:HOH425 2.3 24.4 1.0
CG A:ASP143 3.2 22.6 1.0
CD A:GLU147 3.2 28.0 1.0
OD2 A:ASP143 3.5 26.3 1.0
CD A:CD305 3.6 25.8 1.0
CG A:GLU147 4.0 21.9 1.0
OE2 A:GLU147 4.1 22.8 1.0
O A:HOH555 4.2 39.3 1.0
O A:GLY145 4.3 22.4 1.0
O A:HOH439 4.3 34.2 1.0
CB A:ASP143 4.5 20.6 1.0
CA A:ASP143 4.9 22.4 1.0

Calcium binding site 2 out of 3 in 6p96

Go back to Calcium Binding Sites List in 6p96
Calcium binding site 2 out of 3 in the Oxa-48 Carbapanemase, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Oxa-48 Carbapanemase, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:25.0
occ:1.00
ND1 A:HIS34 2.2 32.9 1.0
O A:HOH476 2.2 40.3 1.0
OE2 A:GLU37 2.3 27.9 1.0
O A:HOH564 2.4 36.8 1.0
OE2 A:GLU256 2.6 27.9 1.0
CE1 A:HIS34 2.8 30.2 1.0
CD A:GLU37 3.1 39.0 1.0
OE1 A:GLU37 3.3 43.9 1.0
CD A:GLU256 3.4 35.0 1.0
CG A:HIS34 3.4 29.8 1.0
CD A:CD306 3.5 27.9 1.0
CB A:HIS34 4.0 30.9 1.0
CG A:GLU256 4.1 26.5 1.0
NE2 A:HIS34 4.1 30.1 1.0
CB A:GLU256 4.1 24.8 1.0
OE1 A:GLU256 4.1 30.8 1.0
CA A:HIS34 4.2 28.6 1.0
CD2 A:HIS34 4.4 30.4 1.0
CG A:GLU37 4.6 33.5 1.0
O A:HOH431 4.7 34.7 1.0
N A:HIS34 4.9 25.6 1.0

Calcium binding site 3 out of 3 in 6p96

Go back to Calcium Binding Sites List in 6p96
Calcium binding site 3 out of 3 in the Oxa-48 Carbapanemase, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Oxa-48 Carbapanemase, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:17.4
occ:1.00
OE1 B:GLU37 2.3 38.6 1.0
O B:HOH401 2.3 37.7 1.0
ND1 B:HIS34 2.4 29.2 1.0
OE1 B:GLU256 2.4 42.0 1.0
CD B:GLU256 3.1 39.6 1.0
CD B:GLU37 3.1 39.2 1.0
CE1 B:HIS34 3.1 27.2 1.0
OE2 B:GLU37 3.3 42.3 1.0
CG B:HIS34 3.5 32.9 1.0
OE2 B:GLU256 3.7 49.1 1.0
CG B:GLU256 3.9 31.5 1.0
CB B:HIS34 3.9 32.5 1.0
CB B:GLU256 4.0 26.9 1.0
CA B:HIS34 4.0 29.7 1.0
NE2 B:HIS34 4.3 32.5 1.0
CG B:GLU37 4.5 38.0 1.0
CD2 B:HIS34 4.5 29.8 1.0
O B:HOH567 4.6 35.5 1.0
N B:HIS34 4.8 31.4 1.0
CE1 B:HIS38 4.8 33.8 1.0
CB B:GLU37 4.9 36.8 1.0

Reference:

C.A.Smith, N.K.Stewart, M.Toth, S.B.Vakulenko. Structural Insights Into the Mechanism of Carbapenemase Activity of the Oxa-48 Beta-Lactamase. Antimicrob.Agents Chemother. V. 63 2019.
ISSN: ESSN 1098-6596
PubMed: 31358584
DOI: 10.1128/AAC.01202-19
Page generated: Sat Dec 12 07:24:59 2020

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