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Calcium in PDB 7c23: Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase

Protein crystallography data

The structure of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase, PDB code: 7c23 was solved by Z.Li, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.82 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.655, 37.019, 99.747, 90.00, 99.06, 90.00
R / Rfree (%) 16.3 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase (pdb code 7c23). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase, PDB code: 7c23:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7c23

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Calcium binding site 1 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:19.4
occ:1.00
 O A:HOH477 2.3 19.9 1.0
OD2 A:ASP200 2.3 17.5 1.0
OE2 B:GLU159 2.4 20.8 1.0
O B:HOH413 2.4 19.6 1.0
CD B:GLU159 3.4 25.2 1.0
CG A:ASP200 3.5 17.5 1.0
OE1 B:GLU159 3.7 22.1 1.0
HB3 A:ASP200 3.7 18.2 1.0
HA A:ARG201 3.9 17.2 1.0
CA A:CA303 3.9 18.1 1.0
OD2 A:ASP204 4.1 19.1 1.0
CB A:ASP200 4.2 15.2 1.0
HB2 A:ARG201 4.2 17.0 1.0
O B:HOH476 4.2 32.9 1.0
HD2 A:ARG201 4.2 26.7 1.0
HD3 A:ARG201 4.4 26.7 1.0
N A:ARG201 4.4 16.9 1.0
OD1 A:ASP200 4.5 19.7 1.0
CA A:ARG201 4.5 14.4 1.0
C A:ASP200 4.5 17.8 1.0
CG B:GLU159 4.6 24.5 1.0
H A:ARG201 4.7 20.3 1.0
HG3 A:GLN197 4.7 19.9 1.0
HG2 B:GLU159 4.7 29.4 1.0
CD A:ARG201 4.8 22.2 1.0
CB A:ARG201 4.8 14.2 1.0
O A:ASP200 4.8 17.9 1.0
HB2 A:ASP200 4.9 18.2 1.0
HG3 B:GLU159 4.9 29.4 1.0
O A:GLN197 4.9 17.4 1.0

Calcium binding site 2 out of 7 in 7c23

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Calcium binding site 2 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:19.6
occ:1.00
 O A:HOH441 2.3 20.8 1.0
OD1 A:ASP200 2.4 19.7 1.0
O A:HOH541 2.4 33.3 1.0
O A:HOH540 2.5 30.6 1.0
CG A:ASP200 3.6 17.5 1.0
HA A:ASP200 3.9 22.8 1.0
CA A:CA303 3.9 18.1 1.0
HB2 A:ASP200 4.0 18.2 1.0
CB A:ASP200 4.3 15.2 1.0
OD2 A:ASP203 4.5 32.9 1.0
CA A:ASP200 4.6 19.0 1.0
OD2 A:ASP200 4.6 17.5 1.0
OD1 A:ASP204 4.6 20.0 1.0
HB3 A:ASP203 4.7 22.9 1.0
O A:HOH440 4.9 26.4 1.0

Calcium binding site 3 out of 7 in 7c23

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Calcium binding site 3 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:18.1
occ:1.00
 OD2 A:ASP204 2.4 19.1 1.0
OD1 A:ASP200 2.5 19.7 1.0
OD2 A:ASP200 2.5 17.5 1.0
CG A:ASP200 2.9 17.5 1.0
CG A:ASP204 3.4 21.1 1.0
OD1 A:ASP204 3.8 20.0 1.0
CA A:CA301 3.9 19.4 1.0
CA A:CA302 3.9 19.6 1.0
O A:HOH477 4.0 19.9 1.0
O A:HOH441 4.1 20.8 1.0
CB A:ASP200 4.3 15.2 1.0
O A:HOH541 4.4 33.3 1.0
O A:ASP200 4.7 17.9 1.0
CB A:ASP204 4.7 21.6 1.0
HB2 A:ASP200 4.8 18.2 1.0
HB3 A:ASP200 4.8 18.2 1.0
HB2 A:ASP204 4.8 25.9 1.0
HA A:ASP200 5.0 22.8 1.0
HB3 A:ASP204 5.0 25.9 1.0

Calcium binding site 4 out of 7 in 7c23

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Calcium binding site 4 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:20.4
occ:1.00
 O A:HOH529 2.3 23.7 1.0
OD1 A:ASP123 2.4 20.0 1.0
O A:ASP120 2.4 21.2 1.0
OD1 A:ASP120 2.4 20.8 1.0
C A:ASP120 3.3 19.9 1.0
HA A:ASP123 3.5 24.4 1.0
CG A:ASP120 3.5 26.9 1.0
CG A:ASP123 3.6 28.4 1.0
HA A:ASP120 3.6 26.1 1.0
H A:ASP123 3.8 23.7 1.0
CA A:CA305 3.9 18.8 1.0
CA A:ASP120 3.9 21.8 1.0
CA A:CA306 4.0 21.3 1.0
HA A:GLN121 4.1 29.1 1.0
CA A:ASP123 4.2 20.4 1.0
CB A:ASP120 4.3 20.7 1.0
N A:GLN121 4.3 21.2 1.0
N A:ASP123 4.3 19.8 1.0
OD2 A:ASP120 4.5 23.3 1.0
OD2 A:ASP123 4.5 26.0 1.0
CB A:ASP123 4.5 22.8 1.0
CA A:GLN121 4.6 24.2 1.0
O A:HOH539 4.6 25.2 1.0
HB3 A:ASP120 4.7 24.8 1.0
O A:HOH553 4.8 36.4 1.0
C A:GLN121 4.9 33.7 1.0
HB3 A:ASP123 4.9 27.4 1.0

Calcium binding site 5 out of 7 in 7c23

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Calcium binding site 5 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:18.8
occ:1.00
 OD2 A:ASP123 2.4 26.0 1.0
O A:HOH539 2.4 25.2 1.0
OD1 A:ASP123 2.7 20.0 1.0
CG A:ASP123 2.8 28.4 1.0
CA A:CA304 3.9 20.4 1.0
CB A:ASP123 4.3 22.8 1.0
HB3 A:ASP123 4.5 27.4 1.0
O A:HOH529 4.6 23.7 1.0
O A:HOH463 4.7 32.4 1.0
HB2 A:ASP123 4.7 27.4 1.0
O A:HOH468 4.8 33.9 1.0

Calcium binding site 6 out of 7 in 7c23

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Calcium binding site 6 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:21.3
occ:1.00
 O A:HOH509 2.4 38.2 1.0
OD2 A:ASP120 2.4 23.3 1.0
O A:HOH518 2.6 32.2 1.0
OD1 A:ASP120 2.7 20.8 1.0
CG A:ASP120 2.9 26.9 1.0
CA A:CA304 4.0 20.4 1.0
O A:HOH529 4.3 23.7 1.0
O A:HOH418 4.3 32.2 1.0
CB A:ASP120 4.4 20.7 1.0
O A:HOH464 4.6 28.8 1.0
HB3 A:ASP120 4.8 24.8 1.0
HB2 A:ASP120 4.8 24.8 1.0
O A:HOH553 4.9 36.4 1.0

Calcium binding site 7 out of 7 in 7c23

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Calcium binding site 7 out of 7 in the Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of CRME10, A Sgnh-Hydrolase Family Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca309

b:52.1
occ:1.00
 O A:HOH456 2.1 37.9 1.0
O A:HOH443 2.5 33.8 1.0
O A:ASP203 2.6 22.2 1.0
O A:HOH437 2.6 31.5 1.0
O A:LEU205 3.0 32.4 1.0
C A:ASP203 3.7 23.4 1.0
HA A:ASP203 4.1 23.8 1.0
C A:LEU205 4.1 35.2 1.0
H A:LEU205 4.2 29.6 1.0
N A:LEU205 4.3 24.7 1.0
HA A:ASP204 4.3 22.0 1.0
O A:HOH569 4.4 44.5 1.0
C A:ASP204 4.5 24.6 1.0
CA A:ASP203 4.5 19.8 1.0
O A:ILE202 4.5 17.9 1.0
N A:ASP204 4.6 16.8 1.0
HB2 A:LEU205 4.6 34.2 1.0
CA A:ASP204 4.7 18.4 1.0
OD1 A:ASP203 4.7 32.4 1.0
CA A:LEU205 4.7 24.1 1.0
O A:HOH453 4.8 26.6 1.0

Reference:

Z.Li, J.Li. C-Terminal Swapped Dimers Revealed A New Catalytic Mechanism of Sgnh-Hydrolase Family Esterase To Be Published.
Page generated: Thu Jul 18 23:25:38 2024

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