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Calcium in PDB 3ws2: N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1C)

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

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

Protein crystallography data

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1C), PDB code: 3ws2 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) 7.50 / 2.10
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 115.308, 115.308, 67.475, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 17.4

Other elements in 3ws2:

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

Caesium (Cs) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1C) (pdb code 3ws2). 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-1C), PDB code: 3ws2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:34.1
occ:1.00
 OD1 A:ASP87 2.4 32.2 1.0
OD1 B:ASP187 2.5 30.5 1.0
O B:HOH510 2.5 23.1 1.0
OD2 A:ASP85 2.6 31.0 1.0
OD2 B:ASP187 2.6 31.2 1.0
OD1 A:ASP85 2.6 33.5 1.0
OD2 A:ASP87 2.6 32.3 1.0
O A:HOH701 2.7 48.0 1.0
CG A:ASP87 2.8 29.6 1.0
CG B:ASP187 2.9 31.4 1.0
CG A:ASP85 2.9 29.0 1.0
NH1 B:ARG196 3.6 55.3 1.0
O A:HOH694 4.2 28.1 1.0
CB A:ASP87 4.3 28.5 1.0
CB B:ASP187 4.4 31.3 1.0
O A:HOH597 4.4 29.9 1.0
CB A:ASP85 4.4 27.4 1.0
OD1 B:ASP58 4.5 26.6 1.0
N A:ASP87 4.6 26.6 1.0
O B:HOH587 4.7 28.6 1.0
O B:HOH568 4.8 39.5 1.0
CZ B:ARG196 4.8 54.9 1.0
CA A:ASP87 4.9 26.5 1.0
N A:ALA88 4.9 24.1 1.0

Calcium binding site 2 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:54.3
occ:1.00
 OD1 A:ASP124 2.2 43.3 1.0
O A:HOH659 2.4 30.8 1.0
O A:HOH594 2.6 31.7 1.0
CG A:ASP124 3.5 41.6 1.0
O A:VAL122 4.1 23.3 1.0
OD2 A:ASP124 4.1 51.3 1.0
N A:ASP124 4.5 34.6 1.0
CA A:ASP124 4.5 36.1 1.0
CB A:ASP124 4.6 37.7 1.0
C A:PRO123 4.9 29.3 1.0
O A:HOH658 5.0 38.0 1.0

Calcium binding site 3 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:30.5
occ:1.00
 O A:HOH566 2.2 34.6 1.0
O A:HOH590 2.3 45.6 1.0
O A:HOH539 2.4 32.3 1.0
OD2 A:ASP220 2.5 25.6 1.0
OD1 A:ASP219 2.6 23.3 1.0
O A:HOH584 2.7 36.2 1.0
O A:HOH525 2.8 26.8 1.0
CG A:ASP220 3.4 21.4 1.0
CG A:ASP219 3.6 22.8 1.0
OD2 A:ASP219 3.9 25.1 1.0
OD1 A:ASP220 4.0 21.6 1.0
O A:HOH555 4.1 28.4 1.0
O A:HOH608 4.4 37.0 1.0
N A:ASP220 4.4 19.1 1.0
CB A:ASP220 4.4 20.5 1.0
O A:GLY216 4.5 22.9 1.0
N A:ASP219 4.8 20.9 1.0
O A:HOH517 4.9 24.6 1.0
CB A:ASP219 5.0 22.2 1.0

Calcium binding site 4 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:24.8
occ:1.00
 O A:HOH550 2.2 29.6 1.0
O A:HOH556 2.4 27.4 1.0
O A:HOH562 2.4 23.6 1.0
OE1 A:GLU352 2.5 18.4 1.0
OE2 A:GLU352 2.7 18.9 1.0
CD A:GLU352 2.9 20.8 1.0
O A:HOH547 4.2 24.9 1.0
NH2 A:ARG356 4.4 17.8 1.0
CG A:GLU352 4.4 20.4 1.0
O A:HOH561 4.5 21.4 1.0

Calcium binding site 5 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:44.2
occ:1.00
 O A:HOH628 2.2 47.3 1.0
O B:HOH554 2.3 37.4 1.0
OD1 B:ASP199 2.3 31.9 1.0
CG B:ASP199 3.5 31.1 1.0
OD2 B:ASP56 3.9 29.2 1.0
O A:GLU303 4.1 52.7 1.0
OD2 B:ASP199 4.2 37.7 1.0
OD1 B:ASP56 4.4 36.3 1.0
OD2 B:ASP58 4.4 35.9 1.0
CB B:ASP58 4.5 28.2 1.0
CB A:GLU303 4.5 53.6 1.0
CG B:ASP56 4.6 29.4 1.0
CB B:ASP199 4.6 33.3 1.0
CA B:ASP199 4.8 31.2 1.0
O B:HOH537 4.8 23.5 1.0
CD A:GLU303 4.8 55.5 1.0
CG A:GLU303 4.8 58.7 1.0
O B:ALA198 4.8 29.8 1.0
OE2 A:GLU303 4.9 62.6 1.0
CG B:ASP58 5.0 30.5 1.0
C A:GLU303 5.0 53.5 1.0

Calcium binding site 6 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:42.9
occ:1.00
 OD2 B:ASP220 2.3 32.9 1.0
O B:HOH558 2.4 29.5 1.0
OD1 B:ASP219 2.6 36.7 1.0
CG B:ASP220 3.3 29.9 1.0
CG B:ASP219 3.7 33.6 1.0
OD2 B:ASP219 4.0 36.2 1.0
OD1 B:ASP220 4.0 32.5 1.0
CB B:ASP220 4.2 30.2 1.0
N B:ASP220 4.3 30.5 1.0
O B:GLY216 4.5 38.4 1.0
O B:HOH512 4.6 21.7 1.0
N B:ASP219 4.8 30.5 1.0
CA B:ASP220 4.9 29.3 1.0
OE1 B:GLU221 4.9 34.3 1.0

Calcium binding site 7 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:35.8
occ:1.00
 O B:HOH536 2.2 28.1 1.0
OD1 B:ASP291 2.4 29.2 1.0
OE1 B:GLU295 2.6 35.6 1.0
OE2 B:GLU295 2.8 37.3 1.0
CD B:GLU295 3.0 32.7 1.0
CG B:ASP291 3.5 30.8 1.0
OD2 B:ASP291 4.2 36.7 1.0
CE1 B:TYR290 4.5 28.7 1.0
CG B:GLU295 4.5 31.0 1.0
CD1 B:TYR290 4.5 27.2 1.0
CB B:ASP291 4.6 27.1 1.0
CA B:ASP291 4.8 24.4 1.0
O B:HOH574 4.8 37.2 1.0

Calcium binding site 8 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:46.1
occ:1.00
 OD2 C:ASP58 2.2 33.0 1.0
O C:HOH711 2.4 29.3 1.0
O C:HOH550 2.6 33.9 1.0
O C:HOH665 2.7 41.1 1.0
CG C:ASP58 3.2 30.0 1.0
CB C:ASP58 3.6 30.9 1.0
O C:HOH634 4.2 23.5 1.0
O C:HOH599 4.3 42.9 1.0
OD1 C:ASP58 4.3 38.0 1.0
OD1 C:ASP57 4.3 48.0 1.0
OD1 C:ASP199 4.7 39.8 1.0
OD2 C:ASP199 4.8 32.5 1.0

Calcium binding site 9 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:39.1
occ:1.00
 OD2 C:ASP220 2.5 22.8 1.0
O C:HOH632 2.5 34.8 1.0
OD1 C:ASP219 2.6 22.0 1.0
O C:HOH574 2.6 19.1 1.0
O C:HOH672 2.8 22.0 1.0
CG C:ASP220 3.3 17.1 1.0
CG C:ASP219 3.6 21.7 1.0
OD1 C:ASP220 3.8 15.9 1.0
OD2 C:ASP219 3.9 28.3 1.0
O C:HOH709 4.0 30.0 1.0
O C:HOH534 4.2 25.4 1.0
N C:ASP220 4.3 15.8 1.0
CB C:ASP220 4.4 16.4 1.0
O C:HOH559 4.4 27.7 1.0
O C:GLY216 4.6 24.3 1.0
N C:ASP219 4.8 18.6 1.0
CA C:ASP220 5.0 15.5 1.0
CB C:ASP219 5.0 20.9 1.0

Calcium binding site 10 out of 10 in 3ws2

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


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-1C) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:30.1
occ:1.00
 O C:HOH712 1.9 27.6 1.0
OE1 C:GLU352 2.4 24.4 1.0
O C:HOH635 2.6 40.4 1.0
OE2 C:GLU352 2.7 25.5 1.0
CD C:GLU352 2.9 23.5 1.0
NH2 C:ARG285 4.3 28.0 1.0
NH1 C:ARG356 4.3 24.7 1.0
O C:HOH626 4.4 27.6 1.0
CG C:GLU352 4.4 21.9 1.0
O C:HOH570 4.5 27.1 1.0
NH1 C:ARG285 4.8 28.2 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 21:21:54 2024

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