Atomistry » Calcium » PDB 3whi-3ws5 » 3ws0
Atomistry »
  Calcium »
    PDB 3whi-3ws5 »
      3ws0 »

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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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

Go back to Calcium Binding Sites List in 3ws0
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: Tue Jul 8 18:02:13 2025

Last articles

Fe in 3PCQ
Fe in 3PI4
Fe in 3PI3
Fe in 3PI2
Fe in 3PGH
Fe in 3PI1
Fe in 3PH2
Fe in 3PF7
Fe in 3PER
Fe in 3PEL
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy