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Calcium in PDB 3so0: Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii

Protein crystallography data

The structure of Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii, PDB code: 3so0 was solved by S.S.Srivastava, R.Sankaranarayanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.579, 89.509, 101.567, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii (pdb code 3so0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii, PDB code: 3so0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 3so0

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Calcium binding site 1 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca97

b:17.8
occ:1.00
 O A:GLU9 2.3 16.0 1.0
O A:HOH255 2.3 24.6 1.0
OD1 A:ASP79 2.3 15.9 1.0
O A:TRP39 2.4 16.5 1.0
OG A:SER41 2.4 14.0 1.0
O A:HOH254 2.5 28.1 1.0
O A:HOH252 2.8 19.4 1.0
CG A:ASP79 3.4 16.8 1.0
C A:TRP39 3.5 16.4 1.0
C A:GLU9 3.5 16.2 1.0
CB A:SER41 3.6 14.5 1.0
OD2 A:ASP79 3.9 19.3 1.0
CA A:TRP39 4.2 16.8 1.0
N A:SER41 4.2 14.7 1.0
OD1 A:ASN78 4.3 18.2 1.0
CA A:GLU9 4.3 16.2 1.0
C A:MET40 4.3 15.0 1.0
O A:HOH112 4.4 22.5 1.0
O A:HOH354 4.4 25.3 1.0
N A:MET40 4.5 15.8 1.0
CA A:SER41 4.5 14.8 1.0
N A:ASP10 4.5 16.3 1.0
CG A:GLU9 4.5 17.1 1.0
CA A:ASP10 4.6 16.4 1.0
O A:MET40 4.7 14.8 1.0
CB A:ASP79 4.7 16.4 1.0
CA A:MET40 4.7 15.3 1.0

Calcium binding site 2 out of 13 in 3so0

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Calcium binding site 2 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca98

b:34.9
occ:1.00
 O A:HOH364 2.2 27.7 1.0
O A:GLU55 2.3 15.2 1.0
OG1 A:THR82 2.3 15.1 1.0
OD1 A:ASP38 2.3 16.1 1.0
O A:LYS80 2.4 15.0 1.0
C A:LYS80 3.3 14.7 1.0
CG A:ASP38 3.4 17.4 1.0
C A:GLU55 3.4 15.2 1.0
O A:HOH160 3.5 34.3 1.0
CB A:THR82 3.5 13.4 1.0
OD2 A:ASP38 3.7 17.8 1.0
CA A:LYS80 3.7 15.1 1.0
CA A:GLU55 4.0 15.1 1.0
OD1 A:ASN37 4.0 19.2 1.0
N A:THR82 4.0 13.5 1.0
C A:MET81 4.2 13.7 1.0
CB A:LYS80 4.2 15.5 1.0
CG A:GLU55 4.3 17.2 1.0
N A:MET81 4.3 14.3 1.0
CA A:THR82 4.3 13.4 1.0
CD A:LYS80 4.4 19.5 1.0
O A:HOH203 4.5 36.5 1.0
N A:ASN56 4.5 15.3 1.0
O A:MET81 4.6 14.0 1.0
CG2 A:THR82 4.6 11.9 1.0
CB A:GLU55 4.7 15.4 1.0
CB A:ASP38 4.7 17.0 1.0
ND2 A:ASN56 4.7 18.9 1.0
CA A:MET81 4.7 14.0 1.0
O A:TYR54 4.8 14.4 1.0
CA A:ASN56 4.8 15.8 1.0
CG A:ASN37 4.9 18.1 1.0
CA A:ASP38 5.0 17.0 1.0
CG A:LYS80 5.0 16.6 1.0

Calcium binding site 3 out of 13 in 3so0

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Calcium binding site 3 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca97

b:35.1
occ:1.00
 O B:HOH375 2.3 28.6 1.0
O B:GLU9 2.3 24.6 1.0
O B:TRP39 2.3 18.6 1.0
OD1 B:ASP79 2.4 19.5 1.0
OG B:SER41 2.5 19.0 1.0
C B:TRP39 3.4 18.6 1.0
CG B:ASP79 3.4 18.1 1.0
C B:GLU9 3.4 25.0 1.0
CB B:SER41 3.5 18.4 1.0
OD2 B:ASP79 3.7 19.8 1.0
N B:SER41 3.9 18.2 1.0
O B:HOH245 3.9 29.9 1.0
C B:MET40 4.0 18.3 1.0
CA B:GLU9 4.1 24.7 1.0
CA B:SER41 4.2 18.4 1.0
CA B:TRP39 4.2 18.6 1.0
N B:MET40 4.2 18.6 1.0
O B:HOH108 4.3 25.3 1.0
O B:MET40 4.4 18.3 1.0
CA B:MET40 4.4 18.4 1.0
OD1 B:ASN78 4.5 19.1 1.0
CG B:GLU9 4.5 26.3 1.0
N B:ASP10 4.5 25.6 1.0
CB B:ASP79 4.8 17.5 1.0
CA B:ASP10 4.8 26.5 1.0
O B:TYR8 4.9 23.2 1.0
CB B:GLU9 4.9 24.9 1.0
OD1 B:ASP10 5.0 31.2 1.0

Calcium binding site 4 out of 13 in 3so0

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Calcium binding site 4 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca98

b:35.0
occ:1.00
 OG1 B:THR82 2.3 13.6 1.0
O B:GLU55 2.3 14.6 1.0
O B:HOH362 2.3 30.6 1.0
O B:LYS80 2.4 15.4 1.0
OD1 B:ASP38 2.4 18.9 1.0
C B:LYS80 3.3 14.9 1.0
C B:GLU55 3.4 15.1 1.0
CG B:ASP38 3.5 19.4 1.0
CB B:THR82 3.5 13.2 1.0
O B:HOH363 3.5 44.8 1.0
OD2 B:ASP38 3.8 20.4 1.0
CA B:LYS80 3.8 15.5 1.0
CA B:GLU55 3.9 15.3 1.0
N B:THR82 4.0 13.6 1.0
OD1 B:ASN37 4.1 18.0 1.0
CG B:GLU55 4.2 17.9 1.0
C B:MET81 4.3 14.2 1.0
CA B:THR82 4.3 13.3 1.0
N B:MET81 4.4 14.6 1.0
O B:HOH306 4.5 38.5 1.0
CB B:LYS80 4.5 15.6 1.0
N B:ASN56 4.5 15.2 1.0
CG2 B:THR82 4.6 13.2 1.0
O B:MET81 4.7 14.2 1.0
CB B:GLU55 4.7 15.7 1.0
CA B:MET81 4.8 14.2 1.0
CD B:LYS80 4.8 18.8 1.0
O B:TYR54 4.8 14.9 1.0
ND2 B:ASN56 4.8 17.3 1.0
CB B:ASP38 4.8 18.3 1.0
CA B:ASN56 4.8 15.5 1.0
CG B:ASN37 5.0 18.4 1.0
O B:HOH221 5.0 22.2 1.0
O B:HOH231 5.0 40.0 1.0

Calcium binding site 5 out of 13 in 3so0

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Calcium binding site 5 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca97

b:36.7
occ:1.00
 O C:GLU9 2.3 21.0 1.0
OD1 C:ASP79 2.4 19.8 1.0
O C:TRP39 2.4 20.1 1.0
OG C:SER41 2.4 17.6 1.0
O C:HOH243 2.5 49.0 1.0
O C:HOH292 2.5 25.9 1.0
O C:HOH325 2.8 39.5 1.0
CG C:ASP79 3.4 19.9 1.0
C C:TRP39 3.4 19.8 1.0
CB C:SER41 3.5 17.9 1.0
C C:GLU9 3.5 21.2 1.0
OD2 C:ASP79 3.8 19.6 1.0
N C:SER41 3.9 18.2 1.0
C C:MET40 4.0 18.5 1.0
CA C:SER41 4.2 17.8 1.0
OD1 C:ASN78 4.2 20.7 1.0
N C:MET40 4.3 19.3 1.0
CA C:TRP39 4.3 20.1 1.0
CA C:GLU9 4.3 21.2 1.0
O C:MET40 4.3 18.6 1.0
CA C:MET40 4.4 18.8 1.0
N C:ASP10 4.5 21.4 1.0
CG C:GLU9 4.6 23.3 1.0
CA C:ASP10 4.7 21.9 1.0
CB C:ASP79 4.7 19.4 1.0
CA C:ASP79 5.0 19.3 1.0
O C:TYR8 5.0 19.6 1.0

Calcium binding site 6 out of 13 in 3so0

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Calcium binding site 6 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca98

b:35.8
occ:1.00
 OD1 C:ASP38 2.3 19.1 1.0
O C:HOH365 2.3 40.3 1.0
OG1 C:THR82 2.4 17.4 1.0
O C:GLU55 2.4 16.2 1.0
O C:LYS80 2.4 18.3 1.0
C C:LYS80 3.3 18.5 1.0
CG C:ASP38 3.4 20.6 1.0
C C:GLU55 3.5 16.9 1.0
CB C:THR82 3.6 16.6 1.0
CA C:LYS80 3.7 19.2 1.0
OD2 C:ASP38 3.8 21.4 1.0
CA C:GLU55 4.1 17.2 1.0
OD1 C:ASN37 4.2 20.0 1.0
N C:THR82 4.2 16.9 1.0
CB C:LYS80 4.3 19.3 1.0
C C:MET81 4.3 17.3 1.0
N C:MET81 4.4 18.1 1.0
CG C:GLU55 4.4 20.0 1.0
CA C:THR82 4.4 16.6 1.0
N C:ASN56 4.6 16.7 1.0
CG2 C:THR82 4.6 16.8 1.0
O C:MET81 4.7 17.1 1.0
CD C:LYS80 4.7 23.6 1.0
ND2 C:ASN56 4.7 19.2 1.0
CB C:ASP38 4.7 20.6 1.0
CA C:MET81 4.8 17.6 1.0
CB C:GLU55 4.8 17.6 1.0
O C:TYR54 4.9 16.7 1.0
CA C:ASN56 4.9 17.0 1.0
CG C:ASN37 5.0 20.7 1.0
CA C:ASP38 5.0 20.3 1.0
ND2 C:ASN37 5.0 21.4 1.0

Calcium binding site 7 out of 13 in 3so0

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Calcium binding site 7 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


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 A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca97

b:35.7
occ:1.00
 O D:GLU9 2.3 21.5 1.0
OD1 D:ASP79 2.4 21.9 1.0
O D:TRP39 2.4 18.8 1.0
O D:HOH263 2.5 29.9 1.0
O D:HOH260 2.6 28.6 1.0
OG D:SER41 2.6 17.4 1.0
CG D:ASP79 3.3 20.7 1.0
C D:GLU9 3.4 21.5 1.0
C D:TRP39 3.4 18.9 1.0
CB D:SER41 3.5 16.9 1.0
OD2 D:ASP79 3.6 21.7 1.0
N D:SER41 3.9 17.2 1.0
C D:MET40 4.1 17.4 1.0
CA D:GLU9 4.1 21.4 1.0
O D:HOH376 4.1 30.7 1.0
CA D:SER41 4.2 17.1 1.0
CA D:TRP39 4.3 19.5 1.0
N D:MET40 4.3 18.2 1.0
CG D:GLU9 4.3 23.3 1.0
OD1 D:ASN78 4.5 20.6 1.0
N D:ASP10 4.5 21.8 1.0
CA D:MET40 4.5 17.6 1.0
O D:MET40 4.5 17.1 1.0
CB D:ASP79 4.7 19.3 1.0
CA D:ASP10 4.7 22.1 1.0
CB D:GLU9 4.9 21.8 1.0
O D:TYR8 4.9 19.9 1.0

Calcium binding site 8 out of 13 in 3so0

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Calcium binding site 8 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca98

b:39.2
occ:1.00
 OG1 D:THR82 2.3 12.8 1.0
O D:GLU55 2.3 16.6 1.0
O D:HOH366 2.4 34.6 1.0
OD1 D:ASP38 2.4 22.2 1.0
O D:LYS80 2.4 17.1 1.0
C D:LYS80 3.3 17.1 1.0
CG D:ASP38 3.4 22.1 1.0
C D:GLU55 3.5 17.0 1.0
CB D:THR82 3.6 14.3 1.0
OD2 D:ASP38 3.7 24.4 1.0
CA D:LYS80 3.8 17.8 1.0
N D:THR82 4.0 14.7 1.0
CA D:GLU55 4.1 17.1 1.0
OD1 D:ASN37 4.2 21.7 1.0
C D:MET81 4.3 15.3 1.0
CB D:LYS80 4.3 18.2 1.0
CA D:THR82 4.3 14.2 1.0
N D:MET81 4.4 16.2 1.0
CG D:GLU55 4.5 20.2 1.0
N D:ASN56 4.6 17.4 1.0
CG2 D:THR82 4.6 13.8 1.0
O D:MET81 4.7 15.1 1.0
O G:HOH228 4.7 39.2 1.0
CB D:ASP38 4.8 21.4 1.0
CA D:MET81 4.8 15.7 1.0
ND2 D:ASN37 4.8 22.9 1.0
O D:TYR54 4.8 15.3 1.0
CA D:ASN56 4.9 17.7 1.0
CB D:GLU55 4.9 17.5 1.0
CG D:ASN37 4.9 21.9 1.0
CG D:LYS80 4.9 20.2 1.0
ND2 D:ASN56 5.0 19.6 1.0

Calcium binding site 9 out of 13 in 3so0

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Calcium binding site 9 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca97

b:29.0
occ:1.00
 O E:GLU9 2.3 16.3 1.0
O E:TRP39 2.4 17.2 1.0
OD1 E:ASP79 2.4 17.3 1.0
OG E:SER41 2.5 15.2 1.0
O E:HOH302 2.6 26.9 1.0
O E:HOH378 2.7 56.2 1.0
O E:HOH370 3.0 42.4 1.0
CG E:ASP79 3.4 18.0 1.0
C E:TRP39 3.4 17.0 1.0
C E:GLU9 3.4 16.6 1.0
CB E:SER41 3.5 15.3 1.0
OD2 E:ASP79 3.5 19.6 1.0
N E:SER41 3.9 15.5 1.0
C E:MET40 4.1 15.6 1.0
CA E:GLU9 4.1 16.4 1.0
CA E:TRP39 4.1 17.5 1.0
O E:HOH307 4.1 27.7 1.0
CA E:SER41 4.3 15.2 1.0
N E:MET40 4.3 16.6 1.0
O E:HOH377 4.4 40.5 1.0
CG E:GLU9 4.4 18.5 1.0
O E:MET40 4.5 15.3 1.0
OD1 E:ASN78 4.5 19.6 1.0
N E:ASP10 4.5 17.1 1.0
CA E:MET40 4.5 15.9 1.0
OD1 E:ASP10 4.7 20.3 1.0
CA E:ASP10 4.8 17.7 1.0
CB E:ASP79 4.8 17.9 1.0
O E:TYR8 4.9 14.3 1.0
CB E:GLU9 4.9 16.5 1.0

Calcium binding site 10 out of 13 in 3so0

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Calcium binding site 10 out of 13 in the Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Mutant T41S of A Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca98

b:35.8
occ:1.00
 O E:GLU55 2.2 15.6 1.0
OG1 E:THR82 2.3 16.1 1.0
O E:LYS80 2.4 17.3 1.0
O E:HOH250 2.4 27.5 1.0
OD1 E:ASP38 2.5 19.0 1.0
O E:HOH381 3.2 48.8 1.0
C E:GLU55 3.2 16.0 1.0
C E:LYS80 3.3 17.3 1.0
CB E:THR82 3.5 16.1 1.0
CG E:ASP38 3.5 19.8 1.0
CA E:GLU55 3.7 16.2 1.0
OD2 E:ASP38 3.8 22.3 1.0
CG E:GLU55 3.9 19.1 1.0
N E:THR82 3.9 16.5 1.0
CA E:LYS80 4.0 17.8 1.0
C E:MET81 4.2 16.5 1.0
OD1 E:ASN37 4.2 19.9 1.0
CA E:THR82 4.3 15.9 1.0
N E:MET81 4.3 17.0 1.0
N E:ASN56 4.4 15.9 1.0
CB E:GLU55 4.4 16.7 1.0
O E:MET81 4.6 16.5 1.0
CG2 E:THR82 4.6 15.7 1.0
CB E:LYS80 4.6 17.9 1.0
CA E:MET81 4.7 16.8 1.0
O E:TYR54 4.7 15.1 1.0
CA E:ASN56 4.8 16.2 1.0
CB E:ASP38 4.9 18.9 1.0
ND2 E:ASN37 4.9 20.1 1.0
CG E:ASN37 4.9 19.4 1.0
ND2 E:ASN56 5.0 19.6 1.0
N E:GLU55 5.0 15.7 1.0
CD E:LYS80 5.0 22.3 1.0

Reference:

A.Mishra, S.K.Suman, S.S.Srivastava, R.Sankaranarayanan, Y.Sharma. Decoding the Molecular Design Principles Underlying Ca(2+) Binding to Beta Gamma-Crystallin Motifs J.Mol.Biol. V. 415 75 2012.
ISSN: ISSN 0022-2836
PubMed: 22099475
DOI: 10.1016/J.JMB.2011.10.037
Page generated: Tue Jul 8 16:42:06 2025

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