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Calcium in PDB 3ws1: N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1B)

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

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

Protein crystallography data

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1B), PDB code: 3ws1 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) 37.68 / 1.80
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 115.125, 115.125, 67.317, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 21.1

Other elements in 3ws1:

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

Caesium (Cs) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-1B) (pdb code 3ws1). 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-1B), PDB code: 3ws1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3ws1

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


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

b:30.2
occ:1.00
 O B:HOH510 2.4 34.0 1.0
OD1 B:ASP187 2.4 37.7 1.0
OD2 B:ASP187 2.5 36.2 1.0
OD2 A:ASP85 2.5 33.5 1.0
OD1 A:ASP85 2.6 30.4 1.0
OD1 A:ASP87 2.6 35.5 1.0
OD2 A:ASP87 2.6 30.9 1.0
CG B:ASP187 2.8 36.3 1.0
CG A:ASP85 2.9 30.4 1.0
CG A:ASP87 2.9 30.6 1.0
CB A:ASP87 4.3 27.7 1.0
CB B:ASP187 4.3 34.6 1.0
CB A:ASP85 4.4 29.8 1.0
O A:HOH675 4.4 32.8 1.0
O B:HOH508 4.5 31.3 1.0
O A:HOH599 4.5 29.4 1.0
N A:ASP87 4.6 25.0 1.0
OD1 B:ASP58 4.6 37.5 1.0
O B:HOH611 4.7 31.5 1.0
CA A:ASP87 4.8 26.0 1.0
NH2 B:ARG196 4.8 53.7 1.0
NH1 B:ARG196 4.9 53.9 1.0
O B:HOH505 4.9 28.9 1.0
N A:ALA88 4.9 26.2 1.0

Calcium binding site 2 out of 10 in 3ws1

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


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

b:42.7
occ:1.00
 OD1 A:ASP124 2.1 40.3 1.0
O A:HOH721 2.2 42.4 1.0
O A:HOH595 2.4 25.9 1.0
O A:HOH674 2.6 32.5 1.0
CG A:ASP124 3.4 40.8 1.0
O A:VAL122 3.9 23.4 1.0
OD2 A:ASP124 4.2 47.7 1.0
CA A:ASP124 4.2 33.1 1.0
N A:ASP124 4.3 31.0 1.0
CB A:ASP124 4.4 37.8 1.0
O A:HOH673 4.7 29.7 1.0
C A:PRO123 4.7 27.8 1.0

Calcium binding site 3 out of 10 in 3ws1

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


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

b:25.3
occ:1.00
 O A:HOH590 2.4 31.9 1.0
O A:HOH584 2.4 30.2 1.0
OD2 A:ASP220 2.4 23.2 1.0
O A:HOH540 2.5 21.2 1.0
O A:HOH567 2.5 31.7 1.0
OD1 A:ASP219 2.5 20.6 1.0
O A:HOH525 2.5 22.1 1.0
CG A:ASP220 3.4 21.4 1.0
CG A:ASP219 3.6 21.4 1.0
OD1 A:ASP220 3.9 23.0 1.0
OD2 A:ASP219 4.0 22.3 1.0
O A:HOH556 4.1 21.0 1.0
O A:HOH610 4.3 28.9 1.0
N A:ASP220 4.4 18.2 1.0
O A:GLY216 4.4 22.1 1.0
CB A:ASP220 4.4 19.5 1.0
O A:HOH517 4.6 24.7 1.0
N A:ASP219 4.7 17.9 1.0
CB A:ASP219 4.9 19.6 1.0
OE1 A:GLU221 5.0 20.7 1.0

Calcium binding site 4 out of 10 in 3ws1

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


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

b:20.7
occ:1.00
 O A:HOH551 2.1 29.9 1.0
O A:HOH563 2.3 27.3 1.0
O A:HOH557 2.4 23.1 1.0
OE1 A:GLU352 2.5 24.2 1.0
OE2 A:GLU352 2.6 22.1 1.0
CD A:GLU352 2.9 22.4 1.0
O A:HOH548 4.3 24.0 1.0
CG A:GLU352 4.4 21.3 1.0
NH2 A:ARG356 4.4 25.8 1.0
O A:HOH562 4.6 28.3 1.0

Calcium binding site 5 out of 10 in 3ws1

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


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

b:35.2
occ:1.00
 O B:HOH559 2.4 37.7 1.0
O B:HOH557 2.4 28.0 1.0
O B:HOH589 2.4 39.4 1.0
OD1 B:ASP199 2.6 38.5 1.0
CG B:ASP199 3.7 37.3 1.0
OD2 B:ASP56 3.8 36.4 1.0
CB A:GLU303 4.1 53.5 1.0
OD1 B:ASP56 4.2 33.4 1.0
O A:GLU303 4.3 55.4 1.0
OD2 B:ASP199 4.4 40.5 1.0
OD2 B:ASP58 4.4 38.3 1.0
CG B:ASP56 4.5 34.6 1.0
CB B:ASP58 4.5 35.1 1.0
O B:HOH538 4.7 28.6 1.0
CB B:ASP199 4.8 34.5 1.0
CG A:GLU303 4.8 55.7 1.0
C A:GLU303 4.9 55.2 1.0
CA B:ASP199 4.9 32.7 1.0
CG B:ASP58 5.0 37.3 1.0
O B:ALA198 5.0 33.6 1.0

Calcium binding site 6 out of 10 in 3ws1

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


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

b:51.4
occ:1.00
 OD1 B:ASP219 2.4 34.2 1.0
OD2 B:ASP220 2.4 36.0 1.0
O B:HOH568 2.4 43.0 1.0
O B:HOH554 2.5 40.0 1.0
CG B:ASP220 3.4 35.0 1.0
CG B:ASP219 3.5 33.6 1.0
OD2 B:ASP219 3.9 34.6 1.0
O B:HOH599 3.9 48.6 1.0
OD1 B:ASP220 4.0 34.9 1.0
O B:HOH562 4.1 37.5 1.0
N B:ASP220 4.3 32.0 1.0
O B:GLY216 4.4 37.4 1.0
CB B:ASP220 4.4 34.3 1.0
O B:HOH512 4.5 32.1 1.0
N B:ASP219 4.6 32.3 1.0
CB B:ASP219 4.8 31.7 1.0
OE1 B:GLU221 4.9 34.5 1.0
CA B:ASP220 5.0 32.4 1.0

Calcium binding site 7 out of 10 in 3ws1

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


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

b:37.0
occ:1.00
 O B:HOH537 2.2 33.0 1.0
OD1 B:ASP291 2.4 34.0 1.0
O B:HOH563 2.6 36.7 1.0
OE1 B:GLU295 2.6 34.5 1.0
OE2 B:GLU295 2.9 33.0 1.0
CD B:GLU295 3.1 32.1 1.0
CG B:ASP291 3.4 31.2 1.0
OD2 B:ASP291 3.9 33.9 1.0
CE1 B:TYR290 4.4 30.7 1.0
CD1 B:TYR290 4.5 29.0 1.0
CG B:GLU295 4.5 30.2 1.0
CB B:ASP291 4.6 29.8 1.0
CA B:ASP291 4.9 28.7 1.0
O B:HOH588 4.9 36.2 1.0

Calcium binding site 8 out of 10 in 3ws1

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


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

b:35.9
occ:1.00
 O C:HOH743 1.6 23.7 1.0
O C:HOH744 2.2 39.6 1.0
OD2 C:ASP58 2.4 39.4 1.0
O C:HOH549 2.4 30.4 1.0
O C:HOH684 2.5 29.5 1.0
CG C:ASP58 3.4 36.0 1.0
CB C:ASP58 3.7 33.8 1.0
O C:HOH639 4.0 28.9 1.0
O C:HOH600 4.2 30.0 1.0
OD1 C:ASP58 4.5 35.4 1.0
OD1 C:ASP57 4.5 46.5 1.0
OD2 C:ASP199 4.8 32.1 1.0
OD1 C:ASP199 4.9 34.7 1.0
OD2 C:ASP56 5.0 37.7 1.0

Calcium binding site 9 out of 10 in 3ws1

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


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

b:47.9
occ:1.00
 O C:HOH637 2.3 41.9 1.0
O C:HOH692 2.5 25.6 1.0
OD1 C:ASP219 2.6 20.1 1.0
OD2 C:ASP220 2.6 17.9 1.0
O C:HOH574 2.8 22.8 1.0
CG C:ASP220 3.4 17.2 1.0
CG C:ASP219 3.7 19.4 1.0
OD1 C:ASP220 3.7 18.1 1.0
O C:HOH739 3.8 30.1 1.0
OD2 C:ASP219 4.0 22.9 1.0
O C:HOH533 4.3 21.9 1.0
N C:ASP220 4.4 15.4 1.0
CB C:ASP220 4.5 15.7 1.0
O C:GLY216 4.6 21.2 1.0
O C:HOH558 4.7 27.9 1.0
N C:ASP219 4.9 15.7 1.0

Calcium binding site 10 out of 10 in 3ws1

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


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

b:25.9
occ:1.00
 OE1 C:GLU352 2.3 27.0 1.0
OE2 C:GLU352 2.6 25.0 1.0
CD C:GLU352 2.8 25.1 1.0
O C:HOH745 3.0 19.6 1.0
NH2 C:ARG285 4.3 33.2 1.0
NH1 C:ARG356 4.3 31.5 1.0
CG C:GLU352 4.3 24.4 1.0
O C:HOH569 4.4 24.8 1.0
O C:HOH630 4.6 29.8 1.0
NE C:ARG356 5.0 28.5 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 21:21:32 2024

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