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Strontium in PDB 3ws4: N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)

Enzymatic activity of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)

All present enzymatic activity of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A):
3.5.2.6;

Protein crystallography data

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A), PDB code: 3ws4 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) 28.02 / 1.90
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 115.019, 115.019, 67.800, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 21.6

Other elements in 3ws4:

The structure of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) (pdb code 3ws4). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 8 binding sites of Strontium where determined in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A), PDB code: 3ws4:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 3ws4

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Strontium binding site 1 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr401

b:35.2
occ:1.00
 OD1 B:ASP58 2.4 33.6 1.0
O B:HOH523 2.5 25.4 1.0
O B:HOH636 2.5 27.8 1.0
OD2 A:ASP87 2.6 34.1 1.0
O B:HOH628 2.7 14.8 1.0
CG A:ASP87 3.5 37.2 1.0
CG B:ASP58 3.6 36.2 1.0
CB A:ASP87 3.8 33.2 1.0
O B:HOH657 3.9 30.0 1.0
OD2 B:ASP187 4.3 28.8 1.0
OD2 B:ASP57 4.3 31.7 0.5
OD2 B:ASP58 4.4 36.7 1.0
CA B:ASP58 4.5 29.8 1.0
OD1 A:ASP85 4.5 35.9 1.0
CB B:ASP58 4.5 32.9 1.0
OD1 A:ASP87 4.6 34.3 1.0
O B:ASP57 4.6 30.1 1.0
OD1 B:ASP187 4.7 33.6 1.0
CG B:ASP57 4.7 32.6 0.5
N B:ASP58 4.9 29.1 1.0
C B:ASP57 4.9 28.8 1.0
CG B:ASP187 4.9 29.2 1.0
O B:HOH598 4.9 23.0 1.0

Strontium binding site 2 out of 8 in 3ws4

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Strontium binding site 2 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr402

b:28.5
occ:1.00
 O A:HOH571 2.4 30.5 1.0
O A:HOH577 2.5 33.5 1.0
O A:HOH655 2.5 35.4 1.0
O A:HOH517 2.6 20.8 1.0
OD2 A:ASP220 2.6 26.2 1.0
OD1 A:ASP219 2.6 26.4 1.0
CG A:ASP220 3.6 26.1 1.0
CG A:ASP219 3.7 25.1 1.0
OD2 A:ASP219 4.1 29.2 1.0
OD1 A:ASP220 4.1 30.0 1.0
O A:HOH529 4.3 23.3 1.0
O A:GLY216 4.6 28.0 1.0
N A:ASP220 4.6 25.8 1.0
CB A:ASP220 4.6 24.4 1.0
N A:ASP219 4.8 23.0 1.0

Strontium binding site 3 out of 8 in 3ws4

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Strontium binding site 3 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr403

b:21.7
occ:1.00
 O A:HOH659 2.5 30.0 1.0
O A:HOH656 2.5 26.1 1.0
O A:HOH525 2.6 22.9 1.0
OE1 A:GLU352 2.6 26.3 1.0
OE2 A:GLU352 2.8 28.3 1.0
CD A:GLU352 3.0 25.3 1.0
O A:HOH528 4.3 21.5 1.0
CG A:GLU352 4.5 23.8 1.0
O A:HOH526 4.5 30.3 1.0
NH2 A:ARG285 4.6 20.3 0.6
NH2 A:ARG356 4.8 30.5 1.0

Strontium binding site 4 out of 8 in 3ws4

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Strontium binding site 4 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr401

b:30.9
occ:1.00
 O B:HOH549 2.6 26.7 1.0
OD1 B:ASP219 2.6 29.3 1.0
OD2 B:ASP220 2.6 29.5 1.0
O B:HOH515 2.6 25.3 1.0
O B:HOH525 2.6 26.8 1.0
O B:HOH629 2.7 28.0 1.0
CG B:ASP220 3.6 30.1 1.0
CG B:ASP219 3.6 30.1 1.0
OD2 B:ASP219 4.0 30.7 1.0
OD1 B:ASP220 4.2 32.9 1.0
O B:HOH586 4.4 24.0 1.0
O B:GLY216 4.5 31.4 1.0
N B:ASP220 4.5 27.1 1.0
O B:HOH516 4.6 18.4 1.0
CB B:ASP220 4.6 29.0 1.0
O B:HOH626 4.6 36.3 1.0
N B:ASP219 4.8 31.9 1.0
CB B:ASP219 5.0 29.2 1.0

Strontium binding site 5 out of 8 in 3ws4

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Strontium binding site 5 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr402

b:22.7
occ:1.00
 O B:HOH632 2.3 29.1 1.0
OD1 B:ASP291 2.6 23.2 1.0
OE1 B:GLU295 2.7 29.4 1.0
O B:HOH611 2.7 25.2 1.0
OE2 B:GLU295 2.8 32.2 1.0
CD B:GLU295 3.1 31.0 1.0
CG B:ASP291 3.5 26.6 1.0
OD2 B:ASP291 3.8 25.3 1.0
O B:HOH539 4.5 17.7 1.0
CG B:GLU295 4.6 28.0 1.0
CB B:ASP291 4.7 24.3 1.0
CE1 B:TYR290 4.8 28.6 1.0

Strontium binding site 6 out of 8 in 3ws4

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Strontium binding site 6 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr401

b:48.4
occ:1.00
 OD2 C:ASP58 2.4 46.6 1.0
O C:HOH691 2.5 30.0 1.0
O C:HOH665 2.7 40.1 1.0
O C:HOH647 3.2 42.9 1.0
CG C:ASP58 3.4 44.1 1.0
CB C:ASP58 3.7 42.2 1.0
OD1 C:ASP58 4.5 35.5 1.0
OD1 C:ASP57 4.9 73.8 1.0

Strontium binding site 7 out of 8 in 3ws4

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Strontium binding site 7 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr402

b:31.6
occ:1.00
 O C:HOH539 2.5 27.9 1.0
OD2 C:ASP220 2.7 22.4 1.0
OD1 C:ASP219 2.7 27.4 1.0
O C:HOH636 2.7 31.1 1.0
O C:HOH617 2.8 22.3 1.0
CG C:ASP220 3.6 24.1 1.0
CG C:ASP219 3.7 26.4 1.0
OD2 C:ASP219 4.0 31.6 1.0
O C:HOH643 4.1 20.5 1.0
OD1 C:ASP220 4.2 26.7 1.0
O A:HOH648 4.4 24.8 1.0
O C:HOH525 4.5 29.8 1.0
N C:ASP220 4.6 21.7 1.0
CB C:ASP220 4.7 20.5 1.0
O C:GLY216 4.7 27.6 1.0
OD2 A:ASP58 4.7 44.2 1.0
N C:ASP219 5.0 24.1 1.0
O C:HOH649 5.0 31.7 1.0

Strontium binding site 8 out of 8 in 3ws4

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Strontium binding site 8 out of 8 in the N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of N288Q-N321Q Mutant Beta-Lactamase Derived From Chromohalobacter Sp.560 (Condition-2A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr403

b:21.6
occ:1.00
 O C:HOH532 2.6 28.8 1.0
OE2 C:GLU352 2.7 25.9 1.0
OE1 C:GLU352 2.7 23.6 1.0
CD C:GLU352 3.0 23.8 1.0
CG C:GLU352 4.5 23.7 1.0
O C:HOH560 4.6 25.1 1.0
NH1 C:ARG356 4.6 29.0 1.0
NH2 C:ARG285 4.6 26.5 1.0
O C:HOH598 5.0 23.5 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: Fri Oct 11 05:25:30 2024

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