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Calcium in PDB 3lez: Crystal Structure of A Halotolerant Bacterial Beta-Lactamase

Enzymatic activity of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase

All present enzymatic activity of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase, PDB code: 3lez 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) 41.85 / 1.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 55.980, 55.980, 165.890, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 17.4

Other elements in 3lez:

The structure of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase (pdb code 3lez). 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 A Halotolerant Bacterial Beta-Lactamase, PDB code: 3lez:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3lez

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Calcium binding site 1 out of 8 in the Crystal Structure of A Halotolerant Bacterial 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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:18.9
occ:1.00
O A:MET175 2.4 16.3 1.0
OE2 A:GLU174 2.4 12.3 0.4
OE1 A:GLU162 2.4 14.9 1.0
OD2 A:ASP159 2.4 20.8 1.0
OD1 A:ASP176 2.5 18.6 1.0
CG A:ASP176 3.2 17.9 1.0
OD2 A:ASP176 3.5 19.4 1.0
CD A:GLU162 3.5 15.1 1.0
C A:MET175 3.5 14.7 1.0
CD A:GLU174 3.5 13.2 0.4
CG A:ASP159 3.6 19.4 1.0
CA A:CA2 3.7 19.0 1.0
OE2 A:GLU162 3.8 17.8 1.0
N A:MET175 3.9 13.6 1.0
OE1 A:GLU174 4.2 14.4 0.4
O A:HOH773 4.2 36.6 1.0
OD1 A:ASP159 4.3 18.7 1.0
CA A:MET175 4.3 13.7 1.0
N A:ASP176 4.3 15.2 1.0
CA A:ASP176 4.3 15.3 1.0
CB A:ASP176 4.3 16.8 1.0
CG A:GLU174 4.4 13.2 0.4
CA A:ASP159 4.5 16.9 1.0
CB A:ASP159 4.5 17.7 1.0
OE1 A:GLU174 4.5 21.4 0.6
O A:HOH518 4.7 20.5 1.0
C A:GLU174 4.7 13.9 1.0
CG A:GLU162 4.7 14.9 1.0
O A:HOH755 4.8 40.8 1.0
CB A:GLU162 4.9 13.9 1.0
O A:HOH517 4.9 20.7 1.0

Calcium binding site 2 out of 8 in 3lez

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Calcium binding site 2 out of 8 in the Crystal Structure of A Halotolerant Bacterial 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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:19.0
occ:1.00
O A:HOH517 2.5 20.7 1.0
O A:HOH516 2.5 20.8 1.0
OD1 A:ASP176 2.5 18.6 1.0
O A:HOH518 2.5 20.5 1.0
OD1 A:ASP159 2.6 18.7 1.0
O A:HOH519 2.6 23.3 1.0
OD2 A:ASP159 2.8 20.8 1.0
CG A:ASP159 3.0 19.4 1.0
CG A:ASP176 3.6 17.9 1.0
CA A:CA1 3.7 18.9 1.0
CB A:ASP176 4.0 16.8 1.0
O A:HOH773 4.2 36.6 1.0
CA A:ASP176 4.3 15.3 1.0
O A:MET175 4.5 16.3 1.0
CB A:ASP159 4.5 17.7 1.0
O A:ASP176 4.6 17.6 1.0
OD2 A:ASP176 4.7 19.4 1.0
O A:HOH648 4.8 43.8 1.0
O A:HOH500 4.9 20.3 1.0
CL A:CL20 5.0 22.2 1.0
C A:ASP176 5.0 15.6 1.0

Calcium binding site 3 out of 8 in 3lez

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Calcium binding site 3 out of 8 in the Crystal Structure of A Halotolerant Bacterial 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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:21.5
occ:1.00
O A:HOH521 2.4 24.1 1.0
O A:HOH522 2.4 21.1 1.0
O A:HOH520 2.4 21.9 1.0
OD2 A:ASP213 2.5 15.9 1.0
CG A:ASP213 3.5 14.6 1.0
O A:HOH23 3.9 30.0 1.0
CA A:CA8 4.1 34.4 1.0
OD1 A:ASP213 4.2 17.6 1.0
O A:HOH529 4.2 20.1 1.0
CB A:ASP213 4.3 13.2 1.0
NE A:ARG216 4.4 20.4 1.0
O A:HOH596 4.5 25.1 1.0
CZ A:ARG216 4.6 20.0 1.0
NH2 A:ARG216 4.6 21.8 1.0
O A:HOH24 4.7 30.9 1.0
OD1 A:ASP101 4.7 28.1 1.0
O A:HOH489 4.8 15.3 1.0
CD A:ARG216 4.9 18.8 1.0
OD1 A:ASP215 5.0 17.1 1.0

Calcium binding site 4 out of 8 in 3lez

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Calcium binding site 4 out of 8 in the Crystal Structure of A Halotolerant Bacterial 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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:19.2
occ:0.50
OD1 A:ASP70 2.4 25.2 1.0
O A:THR67 2.4 19.6 1.0
O A:HOH523 2.5 34.3 1.0
CG A:ASP70 3.5 25.4 1.0
C A:THR67 3.6 17.7 1.0
OD2 A:ASP70 3.9 27.4 1.0
CA A:THR67 4.2 16.1 1.0
O A:HOH751 4.6 53.1 1.0
N A:GLY68 4.6 18.1 1.0
OE1 A:GLU269 4.7 30.0 0.5
CB A:THR67 4.7 16.5 1.0
CB A:ASP70 4.7 22.9 1.0
O A:HOH768 4.7 53.4 1.0
O A:HOH32 4.7 54.9 0.5
CA A:GLY68 4.8 19.2 1.0
CA A:ASP70 4.9 20.2 1.0
O A:GLY68 4.9 23.4 1.0

Calcium binding site 5 out of 8 in 3lez

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Calcium binding site 5 out of 8 in the Crystal Structure of A Halotolerant Bacterial 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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:41.5
occ:1.00
O A:HOH12 2.3 43.8 1.0
O A:HOH10 2.4 43.0 1.0
O A:HOH13 2.5 34.5 1.0
O A:HOH11 2.5 37.9 1.0
O A:HOH9 2.7 42.4 1.0
O A:HOH622 3.3 48.8 1.0
O A:HOH360 4.2 56.4 1.0
O A:HOH527 4.4 20.0 1.0
O A:HOH548 4.5 27.9 1.0
O A:HOH578 4.6 24.0 1.0
O A:HOH510 4.7 49.9 1.0
O A:HOH566 4.7 35.9 1.0
OE1 A:GLU123 4.8 18.4 1.0
CB A:LEU115 4.8 19.7 1.0
OE2 A:GLU112 4.8 37.0 0.6
O A:VAL116 4.9 16.2 1.0
O A:LEU115 4.9 22.4 1.0

Calcium binding site 6 out of 8 in 3lez

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Calcium binding site 6 out of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase


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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca6

b:29.4
occ:1.00
OG A:SER74 2.4 25.6 1.0
O A:HOH16 2.5 29.1 1.0
O A:HOH15 2.6 30.5 1.0
O A:HOH14 2.6 28.8 1.0
OE2 A:GLU77 2.9 26.8 1.0
CD A:GLU77 3.2 21.6 1.0
OE1 A:GLU77 3.2 22.4 1.0
CB A:SER74 3.4 23.1 1.0
O A:HOH31 3.4 57.4 0.5
O A:SER74 4.2 18.6 1.0
CA A:SER74 4.3 18.1 1.0
C A:SER74 4.3 16.2 1.0
CG A:GLU77 4.3 16.8 1.0
O A:HOH389 4.5 43.2 1.0
OE1 A:GLU72 4.6 20.8 1.0
N A:SER74 4.7 16.1 1.0
OE2 A:GLU72 4.7 21.6 1.0
O A:HOH41 4.8 19.3 1.0
N A:TYR75 5.0 15.3 1.0

Calcium binding site 7 out of 8 in 3lez

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Calcium binding site 7 out of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase


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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:32.1
occ:1.00
O A:HOH22 2.3 35.2 1.0
O A:GLY169 2.4 17.4 1.0
O A:HOH17 2.4 35.6 1.0
O A:HOH21 2.5 31.3 1.0
O A:HOH19 2.5 32.6 1.0
O A:HOH18 2.6 36.3 1.0
O A:HOH524 2.7 34.8 1.0
C A:GLY169 3.5 15.5 1.0
CA A:GLY169 4.1 16.1 1.0
CG A:GLU171 4.2 25.3 0.5
O A:HOH413 4.2 40.0 1.0
OE2 A:GLU171 4.2 32.5 0.5
CD A:GLU171 4.3 30.1 0.5
O A:HOH569 4.4 41.7 1.0
N A:GLU171 4.5 15.6 1.0
OE1 A:GLU171 4.5 31.4 0.5
N A:ASP170 4.6 15.0 1.0
CB A:GLU171 4.7 19.8 0.5
O A:HOH692 4.7 36.0 1.0
CB A:GLU171 4.7 20.2 0.5
CD A:GLU171 4.8 30.0 0.5
CG A:GLU171 4.8 24.6 0.5
O A:HOH549 4.8 23.4 1.0
CA A:ASP170 4.8 14.4 1.0
OE1 A:GLU171 5.0 31.4 0.5

Calcium binding site 8 out of 8 in 3lez

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Calcium binding site 8 out of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase


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 A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8

b:34.4
occ:1.00
O A:HOH26 2.2 34.8 1.0
O A:HOH24 2.5 30.9 1.0
O A:HOH23 2.5 30.0 1.0
OD2 A:ASP215 2.5 23.4 1.0
O A:HOH520 2.6 21.9 1.0
O A:HOH25 2.8 37.3 1.0
O A:HOH521 3.3 24.1 1.0
CG A:ASP215 3.6 17.7 1.0
OD1 A:ASP101 3.7 28.1 1.0
OD2 A:ASP101 3.7 28.7 1.0
OD1 A:ASP215 3.9 17.1 1.0
O A:HOH757 4.1 42.6 1.0
CA A:CA3 4.1 21.5 1.0
CG A:ASP101 4.1 28.0 1.0
O A:HOH353 4.3 50.7 1.0
O A:HOH529 4.5 20.1 1.0
O A:HOH372 4.7 56.6 1.0
O A:HOH557 4.8 36.0 1.0
CB A:ASP215 4.9 16.5 1.0
NE A:ARG216 4.9 20.4 1.0

Reference:

M.Toth, C.Smith, H.Frase, S.Mobashery, S.Vakulenko. An Antibiotic-Resistance Enzyme From A Deep-Sea Bacterium J.Am.Chem.Soc. V. 132 816 2010.
ISSN: ISSN 0002-7863
PubMed: 20000704
DOI: 10.1021/JA908850P
Page generated: Sat Dec 12 04:18:51 2020

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