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Calcium in PDB 1jtd: Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase

Enzymatic activity of Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase

All present enzymatic activity of Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase, PDB code: 1jtd was solved by D.C.Lim, H.U.Park, L.De Castro, S.G.Kang, H.S.Lee, S.Jensen, K.J.Lee, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.54 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.525, 84.918, 147.694, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase (pdb code 1jtd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase, PDB code: 1jtd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1jtd

Go back to Calcium Binding Sites List in 1jtd
Calcium binding site 1 out of 5 in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase


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 Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:17.6
occ:1.00
 O A:HOH503 2.3 13.8 1.0
O A:HOH509 2.3 22.8 1.0
OE2 A:GLU37 2.4 17.5 1.0
CD A:GLU37 3.6 22.3 1.0
CB A:GLU37 3.8 16.9 1.0
NH2 A:ARG61 4.1 18.1 1.0
CG A:GLU37 4.3 18.7 1.0
OD1 A:ASP38 4.4 19.8 1.0
OE1 A:GLU37 4.6 15.8 1.0
O A:LYS34 4.8 19.6 1.0
O A:HOH533 4.9 18.1 1.0

Calcium binding site 2 out of 5 in 1jtd

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Calcium binding site 2 out of 5 in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase


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 Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:29.9
occ:1.00
 O B:HOH506 2.2 15.4 1.0
O B:HOH586 2.4 23.7 1.0
O B:HOH683 2.4 25.5 1.0
O B:HOH534 2.5 10.6 1.0
OD2 B:ASP187 2.5 12.6 1.0
O B:GLY188 2.6 14.7 1.0
OD1 B:ASP187 2.6 21.0 1.0
CG B:ASP187 2.9 16.8 1.0
C B:GLY188 3.7 15.0 1.0
O B:HOH606 3.8 21.6 1.0
N B:GLY188 3.8 11.0 1.0
O B:GLY227 4.3 14.9 1.0
CA B:GLY188 4.3 15.2 1.0
CB B:ASP187 4.3 13.0 1.0
O B:HOH667 4.4 29.0 1.0
O B:ALA149 4.4 14.1 1.0
O B:HOH601 4.5 24.4 1.0
N B:GLY227 4.5 16.0 1.0
O B:HOH511 4.6 13.3 1.0
C B:ASP187 4.7 12.6 1.0
N B:GLY189 4.7 12.3 1.0
O B:SER266 4.8 11.0 1.0
CA B:ASP187 4.9 11.7 1.0
O B:HOH628 4.9 19.8 1.0
CA B:GLY189 5.0 10.7 1.0

Calcium binding site 3 out of 5 in 1jtd

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Calcium binding site 3 out of 5 in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase


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 Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:51.3
occ:1.00
 O B:HOH703 2.3 29.2 1.0
OD1 B:ASP106 2.6 29.7 1.0
O B:GLY104 2.7 22.1 1.0
OD1 B:ASP120 2.7 23.4 1.0
OD2 B:ASP106 2.9 25.8 1.0
CG B:ASP106 3.1 29.4 1.0
C B:GLY104 3.6 21.8 1.0
CG B:ASP120 3.8 27.9 1.0
CA B:GLY104 4.0 21.2 1.0
OD2 B:ASP120 4.3 34.0 1.0
CB B:ASP106 4.5 25.1 1.0
N B:ASP120 4.6 21.3 1.0
C B:VAL105 4.7 19.8 1.0
N B:VAL105 4.7 20.3 1.0
N B:ASP106 4.7 17.4 1.0
O B:VAL105 4.9 17.6 1.0
CA B:ASP120 5.0 23.1 1.0

Calcium binding site 4 out of 5 in 1jtd

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Calcium binding site 4 out of 5 in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase


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 Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:47.2
occ:1.00
 O B:HOH608 2.3 28.5 1.0
O B:HOH697 2.3 32.8 1.0
O B:HOH671 2.6 30.1 1.0
O B:GLY166 2.6 10.9 1.0
C B:GLY166 3.7 12.3 1.0
N B:GLY166 4.1 13.5 1.0
O B:HOH698 4.2 33.1 1.0
O B:HOH568 4.3 21.1 1.0
CA B:GLY166 4.3 13.9 1.0
O B:ASP131 4.5 16.9 1.0
OG1 B:THR173 4.7 14.6 1.0
CB B:ASP168 4.8 17.5 1.0
N B:ASP167 4.8 15.6 1.0
N B:ASP168 4.9 14.5 1.0
C B:ASP167 4.9 14.9 1.0
CA B:ASP167 5.0 15.6 1.0

Calcium binding site 5 out of 5 in 1jtd

Go back to Calcium Binding Sites List in 1jtd
Calcium binding site 5 out of 5 in the Crystal Structure of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase


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 Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:57.1
occ:1.00
 O B:HOH590 2.5 28.6 1.0
O B:HOH607 2.6 26.9 1.0
O B:THR184 2.6 13.3 1.0
O B:HOH591 2.8 25.6 1.0
O B:HOH700 2.8 33.0 1.0
C B:THR184 3.8 17.1 1.0
CA B:THR184 4.4 17.1 1.0
CB B:THR184 4.5 19.0 1.0
OD2 B:ASP145 4.6 29.4 1.0
O B:HOH694 4.7 25.7 1.0
N B:ALA185 4.8 15.8 1.0

Reference:

D.Lim, H.U.Park, L.De Castro, S.G.Kang, H.S.Lee, S.Jensen, K.J.Lee, N.C.Strynadka. Crystal Structure and Kinetic Analysis of Beta-Lactamase Inhibitor Protein-II in Complex with Tem-1 Beta-Lactamase. Nat.Struct.Biol. V. 8 848 2001.
ISSN: ISSN 1072-8368
PubMed: 11573088
DOI: 10.1038/NSB1001-848
Page generated: Thu Jul 11 10:53:47 2024

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