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Calcium in PDB 3ws0: N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)

Enzymatic activity of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)

All present enzymatic activity of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A):
3.5.2.6;

Protein crystallography data

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A), PDB code: 3ws0 was solved by S.Arai, Y.Yonezawa, N.Okazaki, F.Matsumoto, R.Shimizu, M.Yamada, M.Adachi, T.Tamada, H.Tokunaga, M.Ishibashi, M.Tokunaga, R.Kuroki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 2.00
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 115.393, 115.393, 67.652, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.4

Other elements in 3ws0:

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) also contains other interesting chemical elements:

Caesium (Cs) 2 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) (pdb code 3ws0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A), PDB code: 3ws0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3ws0

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Calcium binding site 1 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:28.0
occ:1.00
 O B:HOH598 2.1 27.2 1.0
O A:HOH675 2.3 32.7 1.0
OD1 B:ASP187 2.3 33.4 1.0
OD1 A:ASP87 2.5 32.7 1.0
OD2 A:ASP87 2.5 34.6 1.0
OD1 A:ASP85 2.5 33.0 1.0
OD2 B:ASP187 2.5 32.6 1.0
OD2 A:ASP85 2.6 36.8 1.0
CG B:ASP187 2.8 32.0 1.0
CG A:ASP87 2.8 30.5 1.0
CG A:ASP85 2.9 32.1 1.0
O A:HOH686 3.5 46.0 1.0
O A:HOH672 4.0 27.3 1.0
NH1 B:ARG196 4.0 55.5 1.0
CB A:ASP87 4.2 28.3 1.0
CB B:ASP187 4.3 30.4 1.0
CB A:ASP85 4.4 30.8 1.0
OD1 B:ASP58 4.5 37.8 1.0
O B:HOH607 4.6 40.0 1.0
O B:HOH525 4.6 23.5 1.0
O B:HOH543 4.6 30.1 1.0
N A:ASP87 4.6 25.4 1.0
O A:HOH550 4.7 26.9 1.0
O B:HOH578 4.8 27.2 1.0
CA A:ASP87 4.8 25.7 1.0
N A:ALA88 4.9 24.8 1.0
O B:HOH515 5.0 27.4 1.0

Calcium binding site 2 out of 10 in 3ws0

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Calcium binding site 2 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:55.5
occ:1.00
 O A:HOH703 2.3 36.3 1.0
OD1 A:ASP199 2.4 32.5 1.0
O A:HOH646 2.6 25.6 1.0
OE1 C:GLU170 3.0 48.1 1.0
CG A:ASP199 3.6 31.3 1.0
CD C:GLU170 4.0 41.7 1.0
OD2 A:ASP199 4.2 32.1 1.0
OD2 A:ASP56 4.3 35.2 1.0
OE2 C:GLU170 4.4 48.1 1.0
O A:ALA198 4.4 34.4 1.0
O C:HOH712 4.6 38.5 1.0
CB A:ASP199 4.6 29.6 1.0
O A:HOH647 4.7 24.3 1.0
CA A:ASP199 4.7 29.9 1.0
C A:ALA198 4.8 33.8 1.0
OD1 A:ASP56 4.8 32.4 1.0
N A:ASP199 4.9 31.8 1.0
CB A:ASP58 4.9 31.0 1.0
OD2 A:ASP58 4.9 34.0 1.0
CG A:ASP56 5.0 33.9 1.0

Calcium binding site 3 out of 10 in 3ws0

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Calcium binding site 3 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:29.2
occ:1.00
 O A:HOH680 2.2 37.2 1.0
O A:HOH585 2.5 23.8 1.0
O A:HOH523 2.5 28.5 1.0
OD1 A:ASP220 2.5 25.1 1.0
OD1 A:ASP219 2.6 20.5 1.0
CG A:ASP220 3.4 23.4 1.0
CG A:ASP219 3.7 20.8 1.0
OD2 A:ASP220 3.9 23.9 1.0
O A:HOH536 4.0 18.8 1.0
OD2 A:ASP219 4.1 22.4 1.0
O A:HOH642 4.1 28.8 1.0
N A:ASP220 4.3 20.1 1.0
CB A:ASP220 4.4 21.6 1.0
O A:HOH687 4.5 29.8 1.0
O A:GLY216 4.6 24.6 1.0
N A:ASP219 4.8 19.5 1.0
CB A:ASP219 5.0 19.9 1.0

Calcium binding site 4 out of 10 in 3ws0

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Calcium binding site 4 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:25.5
occ:1.00
 O A:HOH531 2.4 25.5 1.0
O A:HOH535 2.4 27.1 1.0
OE1 A:GLU352 2.5 25.6 1.0
OE2 A:GLU352 2.5 27.2 1.0
CD A:GLU352 2.9 25.8 1.0
O A:HOH534 4.2 28.4 1.0
O A:HOH532 4.4 30.4 1.0
CG A:GLU352 4.4 24.6 1.0
NH2 A:ARG356 4.5 28.2 1.0

Calcium binding site 5 out of 10 in 3ws0

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Calcium binding site 5 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:41.8
occ:1.00
 OD1 B:ASP199 2.4 35.4 1.0
O B:HOH608 2.4 36.5 1.0
O B:HOH585 2.5 34.3 1.0
CG B:ASP199 3.5 34.2 1.0
OD2 B:ASP56 3.8 33.9 1.0
OD2 B:ASP199 4.1 36.5 1.0
OD1 B:ASP56 4.3 31.1 1.0
OE1 A:GLU303 4.3 69.4 1.0
OD2 B:ASP58 4.3 39.0 1.0
CB B:ASP58 4.4 35.5 1.0
CG B:ASP56 4.5 32.2 1.0
O B:HOH553 4.6 26.4 1.0
CB B:ASP199 4.7 32.3 1.0
CB A:GLU303 4.7 61.0 1.0
O A:GLU303 4.8 62.2 1.0
CA B:ASP199 4.8 31.3 1.0
CG B:ASP58 4.9 37.4 1.0
O B:ALA198 4.9 33.2 1.0

Calcium binding site 6 out of 10 in 3ws0

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Calcium binding site 6 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:43.2
occ:1.00
 O B:HOH545 2.3 35.8 1.0
O B:HOH618 2.5 41.1 1.0
OD1 B:ASP220 2.6 30.9 1.0
OD1 B:ASP219 2.6 31.5 1.0
O B:HOH516 2.6 36.6 1.0
CG B:ASP220 3.5 30.2 1.0
CG B:ASP219 3.7 31.8 1.0
OD2 B:ASP220 4.0 29.8 1.0
OD2 B:ASP219 4.1 34.0 1.0
O B:HOH573 4.2 30.7 1.0
N B:ASP220 4.4 28.6 1.0
CB B:ASP220 4.5 29.5 1.0
O B:GLY216 4.5 34.4 1.0
O B:HOH519 4.6 29.7 1.0
N B:ASP219 4.8 30.1 1.0

Calcium binding site 7 out of 10 in 3ws0

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Calcium binding site 7 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:36.6
occ:1.00
 O B:HOH603 2.3 33.5 1.0
OD1 B:ASP291 2.4 35.4 1.0
OE1 B:GLU295 2.5 37.5 1.0
O B:HOH524 2.6 35.9 1.0
OE2 B:GLU295 2.8 36.8 1.0
CD B:GLU295 3.0 35.2 1.0
CG B:ASP291 3.6 34.0 1.0
OD2 B:ASP291 4.3 35.1 1.0
CE1 B:TYR290 4.4 34.7 1.0
CD1 B:TYR290 4.4 33.7 1.0
CG B:GLU295 4.5 33.1 1.0
CB B:ASP291 4.6 31.8 1.0
O B:HOH595 4.7 29.4 1.0
CA B:ASP291 4.7 30.7 1.0

Calcium binding site 8 out of 10 in 3ws0

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Calcium binding site 8 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:35.1
occ:1.00
 O C:HOH511 2.2 31.4 1.0
OD1 C:ASP58 2.3 40.7 1.0
O C:HOH706 2.4 38.7 1.0
CG C:ASP58 3.3 37.5 1.0
CB C:ASP58 3.7 34.9 1.0
O C:HOH668 3.9 27.9 1.0
OD2 C:ASP58 4.4 37.9 1.0
O C:HOH700 4.5 47.9 1.0
O C:HOH616 4.7 38.1 1.0
OD1 C:ASP56 5.0 29.6 1.0

Calcium binding site 9 out of 10 in 3ws0

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Calcium binding site 9 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:30.0
occ:1.00
 O C:HOH724 2.4 30.0 1.0
OD1 C:ASP220 2.6 22.0 1.0
O C:HOH540 2.7 23.4 1.0
O C:HOH632 2.8 25.5 1.0
OD1 C:ASP219 2.8 20.6 1.0
CG C:ASP220 3.4 20.9 1.0
O C:HOH723 3.5 28.1 1.0
CG C:ASP219 3.8 20.1 1.0
OD2 C:ASP220 3.9 21.5 1.0
OD2 C:ASP219 4.2 22.7 1.0
O C:HOH661 4.4 27.7 1.0
N C:ASP220 4.5 17.4 1.0
O C:HOH527 4.5 34.7 1.0
CB C:ASP220 4.5 19.1 1.0
O C:GLY216 4.8 22.1 1.0
OD2 A:ASP58 5.0 34.0 1.0

Calcium binding site 10 out of 10 in 3ws0

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Calcium binding site 10 out of 10 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:26.6
occ:1.00
 OE1 C:GLU352 2.5 24.9 1.0
OE2 C:GLU352 2.6 24.2 1.0
O C:HOH707 2.6 40.2 1.0
CD C:GLU352 2.9 24.5 1.0
CG C:GLU352 4.4 23.5 1.0
O C:HOH534 4.4 29.1 1.0
NH2 C:ARG285 4.5 33.4 1.0
NH1 C:ARG356 4.5 28.4 1.0
O C:HOH605 4.8 27.1 1.0

Reference:

S.Arai, Y.Yonezawa, N.Okazaki, F.Matsumoto, C.Shibazaki, R.Shimizu, M.Yamada, M.Adachi, T.Tamada, T.Kawamoto, H.Tokunaga, M.Ishibashi, M.Blaber, M.Tokunaga, R.Kuroki. Crystal Structure of Highly Acidic Beta-Lactamase From Moderate Halophile Chromohalobacter Sp. 560 and the Discovery of A Cs+ Selective Binding Site To Be Published.
Page generated: Sat Jul 13 21:21:31 2024

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