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Calcium in PDB 3wrz: N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)

Enzymatic activity of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)

All present enzymatic activity of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking):
3.5.2.6;

Protein crystallography data

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking), PDB code: 3wrz 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) 29.12 / 1.80
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 114.928, 114.928, 67.567, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 22.1

Other elements in 3wrz:

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking) (pdb code 3wrz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking), PDB code: 3wrz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 3wrz

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Calcium binding site 1 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:33.0
occ:1.00
 OE1 A:GLU303 2.2 58.2 1.0
O B:HOH559 2.2 25.6 1.0
OD1 B:ASP199 2.5 24.7 1.0
O B:HOH627 2.6 36.1 1.0
O B:HOH699 2.6 31.1 1.0
CD A:GLU303 3.4 59.3 1.0
CG B:ASP199 3.6 24.8 1.0
OD2 B:ASP56 3.9 25.9 1.0
OE2 A:GLU303 3.9 59.7 1.0
OD2 B:ASP199 4.1 29.6 1.0
OD2 B:ASP58 4.4 32.1 1.0
OD1 B:ASP56 4.4 23.0 1.0
CB B:ASP58 4.5 27.6 1.0
CG A:GLU303 4.5 58.4 1.0
CG B:ASP56 4.6 23.1 1.0
CB B:ASP199 4.6 22.3 1.0
O A:GLU303 4.7 58.2 1.0
CA B:ASP199 4.8 20.7 1.0
O B:HOH592 4.8 22.2 1.0
O B:ALA198 4.8 22.6 1.0
CG B:ASP58 5.0 29.6 1.0

Calcium binding site 2 out of 11 in 3wrz

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Calcium binding site 2 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.1
occ:1.00
 O B:HOH529 2.4 25.7 1.0
OD1 B:ASP187 2.4 18.4 1.0
OD2 B:ASP187 2.4 17.5 1.0
O B:HOH528 2.4 26.7 1.0
OD1 A:ASP85 2.5 19.0 1.0
OD1 A:ASP87 2.5 18.7 1.0
OD2 A:ASP85 2.5 19.7 1.0
O A:HOH544 2.7 30.8 1.0
CG B:ASP187 2.8 17.3 1.0
CG A:ASP85 2.8 18.1 1.0
CG A:ASP87 3.3 18.3 1.0
OD2 A:ASP87 3.7 20.5 1.0
O B:HOH507 4.1 16.5 1.0
O A:HOH772 4.2 26.7 1.0
CB B:ASP187 4.3 16.2 1.0
CB A:ASP85 4.4 17.5 1.0
CB A:ASP87 4.4 16.3 1.0
OD1 B:ASP58 4.5 30.4 1.0
O B:HOH530 4.5 16.9 1.0
N A:ASP87 4.6 15.1 1.0
O A:HOH570 4.6 17.6 1.0
O B:HOH577 4.7 17.4 1.0
O B:HOH683 4.7 22.9 1.0
CA A:ASP87 4.8 15.1 1.0
O B:HOH516 4.8 15.1 1.0
NH2 B:ARG196 5.0 33.3 1.0

Calcium binding site 3 out of 11 in 3wrz

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Calcium binding site 3 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:35.9
occ:1.00
 OD1 A:ASP124 1.9 28.9 1.0
O A:HOH644 2.4 15.4 1.0
O A:HOH518 2.4 35.8 1.0
O A:HOH744 2.5 36.5 1.0
CG A:ASP124 2.6 25.9 1.0
O A:HOH613 2.7 16.4 1.0
O A:HOH580 2.7 31.6 1.0
OD2 A:ASP124 2.8 29.1 1.0
O A:HOH701 3.8 26.4 1.0
CB A:ASP124 3.9 24.9 1.0
O A:VAL122 4.1 15.2 1.0
CA A:ASP124 4.1 22.2 1.0
N A:ASP124 4.2 20.3 1.0
C A:PRO123 4.8 18.5 1.0
O A:HOH513 4.9 19.5 1.0

Calcium binding site 4 out of 11 in 3wrz

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Calcium binding site 4 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:16.7
occ:1.00
 O A:HOH622 2.3 17.9 1.0
O A:HOH545 2.3 24.4 1.0
O A:HOH623 2.4 24.7 1.0
O A:HOH615 2.4 16.9 1.0
OD2 A:ASP220 2.4 14.5 1.0
O A:HOH528 2.5 14.1 1.0
OD1 A:ASP219 2.5 13.3 1.0
CG A:ASP220 3.4 14.3 1.0
CG A:ASP219 3.6 13.5 1.0
OD1 A:ASP220 4.0 14.7 1.0
O A:HOH546 4.0 17.1 1.0
OD2 A:ASP219 4.0 14.0 1.0
O A:HOH750 4.1 27.8 1.0
N A:ASP220 4.3 12.7 1.0
CB A:ASP220 4.3 13.4 1.0
O A:HOH614 4.4 19.1 1.0
O A:GLY216 4.4 14.0 1.0
O A:HOH771 4.6 24.0 1.0
N A:ASP219 4.7 11.8 1.0
O A:HOH768 4.9 15.1 1.0
CB A:ASP219 4.9 12.9 1.0
CA A:ASP220 5.0 12.7 1.0

Calcium binding site 5 out of 11 in 3wrz

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Calcium binding site 5 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:15.4
occ:1.00
 OE1 A:GLU352 2.4 14.9 1.0
O A:HOH538 2.4 13.4 1.0
O A:HOH542 2.5 20.9 1.0
OE2 A:GLU352 2.6 14.3 1.0
O A:HOH543 2.7 42.0 1.0
CD A:GLU352 2.8 14.2 1.0
O A:HOH788 4.0 29.1 1.0
O A:HOH541 4.3 19.8 1.0
CG A:GLU352 4.3 13.7 1.0
NH2 A:ARG356 4.4 17.4 1.0
O A:HOH539 4.4 22.5 1.0

Calcium binding site 6 out of 11 in 3wrz

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Calcium binding site 6 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:25.9
occ:1.00
 O B:HOH533 2.3 22.1 1.0
O B:HOH531 2.3 30.8 1.0
OD2 B:ASP220 2.4 20.1 1.0
O B:HOH580 2.5 24.4 1.0
O B:HOH532 2.5 27.4 1.0
O B:HOH517 2.5 22.8 1.0
OD1 B:ASP219 2.6 19.2 1.0
CG B:ASP220 3.3 19.5 1.0
CG B:ASP219 3.7 19.5 1.0
O B:HOH656 3.9 26.1 1.0
OD1 B:ASP220 3.9 19.6 1.0
OD2 B:ASP219 4.1 19.9 1.0
O B:HOH700 4.2 35.0 1.0
CB B:ASP220 4.3 18.6 1.0
N B:ASP220 4.3 17.2 1.0
O B:HOH521 4.4 27.8 1.0
O B:HOH518 4.5 44.2 1.0
O B:GLY216 4.6 23.2 1.0
N B:ASP219 4.8 17.9 1.0
O B:HOH541 4.9 25.1 1.0
CA B:ASP220 5.0 17.5 1.0

Calcium binding site 7 out of 11 in 3wrz

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Calcium binding site 7 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:24.1
occ:1.00
 O B:HOH522 2.3 28.9 1.0
OE1 B:GLU295 2.3 24.7 1.0
OD1 B:ASP291 2.4 21.4 1.0
O B:HOH527 2.4 19.4 1.0
CD B:GLU295 3.2 23.1 1.0
OE2 B:GLU295 3.4 25.4 1.0
CG B:ASP291 3.5 21.7 1.0
OD2 B:ASP291 4.1 23.3 1.0
CD1 B:TYR290 4.5 19.8 1.0
CB B:ASP291 4.5 20.3 1.0
CE1 B:TYR290 4.6 20.7 1.0
CG B:GLU295 4.6 21.4 1.0
CA B:ASP291 4.8 19.3 1.0

Calcium binding site 8 out of 11 in 3wrz

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Calcium binding site 8 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:18.6
occ:1.00
 O C:HOH711 2.3 27.5 1.0
O C:HOH510 2.3 23.1 1.0
OD2 C:ASP58 2.4 21.2 1.0
O C:HOH605 2.4 29.7 1.0
O C:HOH512 2.4 25.2 1.0
CG C:ASP58 3.4 19.4 1.0
CB C:ASP58 3.8 17.9 1.0
O C:HOH698 4.4 33.6 1.0
OD1 C:ASP58 4.5 18.5 1.0
O C:HOH656 4.6 22.8 1.0
O C:HOH534 4.6 44.4 1.0
O C:HOH779 4.9 33.5 1.0
OD2 C:ASP199 4.9 20.2 1.0
OD1 C:ASP56 5.0 15.9 1.0

Calcium binding site 9 out of 11 in 3wrz

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Calcium binding site 9 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:30.4
occ:1.00
 O C:HOH732 2.4 27.8 1.0
O A:HOH714 2.5 21.8 1.0
O A:HOH763 2.6 17.5 1.0
OD2 A:ASP56 2.6 20.6 1.0
OE1 C:GLU170 2.8 35.4 1.0
OE2 C:GLU170 3.0 36.6 1.0
CD C:GLU170 3.2 33.1 1.0
CG A:ASP56 3.6 20.1 1.0
O C:HOH736 3.8 24.8 1.0
OD1 A:ASP56 3.9 20.1 1.0
OD1 A:ASP199 4.0 18.6 1.0
O A:HOH732 4.4 31.4 1.0
O A:HOH764 4.6 17.1 1.0
CG C:GLU170 4.7 30.6 1.0
OD2 A:ASP58 4.9 19.4 1.0

Calcium binding site 10 out of 11 in 3wrz

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Calcium binding site 10 out of 11 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Without Soaking)


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 (Without Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:51.5
occ:1.00
 O C:HOH613 2.0 30.2 1.0
O C:HOH735 2.3 30.6 1.0
O A:HOH548 2.3 34.2 1.0
O A:HOH779 2.3 22.0 1.0
OD1 C:ASP219 2.6 12.2 1.0
OD2 C:ASP219 2.9 12.4 1.0
O C:HOH607 3.0 42.2 1.0
CG C:ASP219 3.1 12.1 1.0
O C:HOH548 3.5 29.9 1.0
OD2 C:ASP220 3.9 14.1 1.0
O C:HOH576 4.0 35.4 1.0
O C:HOH714 4.0 39.8 1.0
OD1 C:ASP220 4.1 13.7 1.0
O A:HOH809 4.2 26.2 1.0
CG C:ASP220 4.3 13.8 1.0
O C:GLY216 4.4 12.8 1.0
O C:HOH682 4.5 21.9 1.0
CB C:ASP219 4.6 11.5 1.0
O A:HOH726 4.6 23.9 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 21:20:57 2024

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