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Calcium in PDB 3so1: Crystal Structure of A Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii

Protein crystallography data

The structure of Crystal Structure of A Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii, PDB code: 3so1 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 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.582, 103.650, 105.671, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii (pdb code 3so1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii, PDB code: 3so1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3so1

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Calcium binding site 1 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca97

b:26.0
occ:1.00
 O A:GLU9 2.3 21.7 1.0
O A:HOH442 2.4 31.0 1.0
OG A:SER41 2.4 18.7 1.0
OD1 A:ASP79 2.4 20.1 1.0
O A:HOH607 2.5 27.7 1.0
O A:TRP39 2.5 18.9 1.0
O A:HOH481 2.5 29.1 1.0
CG A:ASP79 3.4 21.3 1.0
C A:TRP39 3.5 19.1 1.0
C A:GLU9 3.5 22.0 1.0
CB A:SER41 3.6 18.7 1.0
OD2 A:ASP79 3.6 22.8 1.0
CA A:TRP39 4.2 19.2 1.0
N A:SER41 4.2 18.5 1.0
CA A:GLU9 4.3 21.6 1.0
C A:MET40 4.4 18.5 1.0
OD1 A:ASN78 4.4 23.1 1.0
CA A:SER41 4.4 18.6 1.0
CG A:GLU9 4.5 22.6 1.0
N A:ASP10 4.5 22.5 1.0
N A:MET40 4.5 18.7 1.0
OD1 A:ASP10 4.6 25.3 1.0
CA A:ASP10 4.6 23.3 1.0
O A:MET40 4.7 18.3 1.0
CB A:ASP79 4.8 20.8 1.0
CA A:MET40 4.9 18.5 1.0

Calcium binding site 2 out of 8 in 3so1

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Calcium binding site 2 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca97

b:26.2
occ:1.00
 O B:GLU9 2.3 17.2 1.0
OD1 B:ASP79 2.3 16.8 1.0
O B:HOH582 2.4 30.8 1.0
OG B:SER41 2.5 15.1 1.0
O B:HOH444 2.5 28.9 1.0
O B:TRP39 2.5 17.0 1.0
O B:HOH117 2.9 26.6 1.0
CG B:ASP79 3.3 17.2 1.0
C B:GLU9 3.5 17.5 1.0
C B:TRP39 3.5 16.9 1.0
OD2 B:ASP79 3.6 18.0 1.0
CB B:SER41 3.6 16.0 1.0
CA B:TRP39 4.2 17.5 1.0
N B:SER41 4.3 15.7 1.0
OD1 B:ASN78 4.3 17.8 1.0
CA B:GLU9 4.3 17.4 1.0
C B:MET40 4.4 15.8 1.0
N B:ASP10 4.4 17.7 1.0
CG B:GLU9 4.5 18.7 1.0
N B:MET40 4.5 16.4 1.0
OD1 B:ASP10 4.5 21.8 1.0
CA B:SER41 4.5 15.8 1.0
O B:HOH114 4.5 27.7 1.0
CA B:ASP10 4.5 18.3 1.0
O E:HOH462 4.6 41.9 1.0
O B:MET40 4.7 15.5 1.0
CB B:ASP79 4.7 16.9 1.0
CA B:MET40 4.8 16.0 1.0
CG B:ASP10 5.0 19.7 1.0
CB B:GLU9 5.0 17.5 1.0

Calcium binding site 3 out of 8 in 3so1

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Calcium binding site 3 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca97

b:28.6
occ:1.00
 O C:HOH551 2.3 30.2 1.0
O C:GLU9 2.3 22.4 1.0
OD1 C:ASP79 2.4 22.5 1.0
OG C:SER41 2.4 20.4 1.0
O C:HOH446 2.5 32.1 1.0
O C:TRP39 2.6 21.3 1.0
CG C:ASP79 3.3 22.3 1.0
OD2 C:ASP79 3.4 23.5 1.0
C C:GLU9 3.5 22.6 1.0
C C:TRP39 3.6 21.4 1.0
CB C:SER41 3.7 19.8 1.0
N C:SER41 4.3 19.9 1.0
CA C:GLU9 4.3 22.4 1.0
CA C:TRP39 4.3 21.9 1.0
C C:MET40 4.4 20.2 1.0
CG C:GLU9 4.4 23.7 1.0
OD1 C:ASN78 4.5 21.4 1.0
N C:ASP10 4.5 23.1 1.0
CA C:SER41 4.5 19.6 1.0
N C:MET40 4.6 20.8 1.0
OD1 C:ASP10 4.6 25.6 1.0
CA C:ASP10 4.6 23.5 1.0
CB C:ASP79 4.7 21.5 1.0
O C:MET40 4.7 20.1 1.0
CA C:MET40 4.8 20.5 1.0
O C:HOH604 4.9 33.6 1.0
CB C:GLU9 5.0 22.5 1.0

Calcium binding site 4 out of 8 in 3so1

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Calcium binding site 4 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca97

b:41.5
occ:1.00
 O D:HOH603 2.2 25.8 1.0
OD1 D:ASP79 2.4 29.7 1.0
O D:GLU9 2.4 35.6 1.0
OG D:SER41 2.5 29.5 1.0
O D:TRP39 2.5 31.1 1.0
O D:HOH556 2.6 37.3 1.0
O D:HOH620 2.8 35.5 1.0
CG D:ASP79 3.4 29.8 1.0
C D:TRP39 3.6 31.2 1.0
C D:GLU9 3.6 35.6 1.0
CB D:SER41 3.7 29.7 1.0
OD2 D:ASP79 3.8 30.8 1.0
OD1 D:ASN78 4.3 30.6 1.0
N D:SER41 4.3 29.8 1.0
C D:MET40 4.3 30.1 1.0
CA D:TRP39 4.4 31.5 1.0
CA D:GLU9 4.5 35.4 1.0
O D:MET40 4.5 29.8 1.0
CG D:GLU9 4.5 35.8 1.0
N D:MET40 4.6 30.7 1.0
CA D:SER41 4.6 29.4 1.0
OD1 D:ASP10 4.6 37.5 1.0
N D:ASP10 4.6 35.9 1.0
CB D:ASP79 4.7 29.1 1.0
CA D:ASP10 4.7 36.1 1.0
CA D:MET40 4.8 30.3 1.0

Calcium binding site 5 out of 8 in 3so1

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Calcium binding site 5 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca97

b:27.3
occ:1.00
 O E:GLU9 2.3 21.1 1.0
OD1 E:ASP79 2.4 17.8 1.0
O E:HOH525 2.4 27.7 1.0
O E:HOH608 2.4 31.2 1.0
OG E:SER41 2.4 17.3 1.0
O E:HOH447 2.5 32.5 1.0
O E:TRP39 2.6 17.3 1.0
CG E:ASP79 3.3 18.8 1.0
C E:GLU9 3.5 21.0 1.0
OD2 E:ASP79 3.6 20.2 1.0
CB E:SER41 3.6 16.8 1.0
C E:TRP39 3.6 17.7 1.0
N E:SER41 4.3 16.6 1.0
CA E:TRP39 4.3 17.8 1.0
CA E:GLU9 4.4 20.8 1.0
OD1 E:ASN78 4.4 19.6 1.0
CG E:GLU9 4.4 22.2 1.0
C E:MET40 4.4 16.7 1.0
CA E:SER41 4.5 16.8 1.0
N E:ASP10 4.5 21.5 1.0
OD1 E:ASP10 4.5 24.2 1.0
CA E:ASP10 4.6 22.0 1.0
N E:MET40 4.6 17.3 1.0
CB E:ASP79 4.7 18.5 1.0
O E:HOH155 4.8 29.4 1.0
O E:MET40 4.8 16.3 1.0
CA E:MET40 4.9 16.9 1.0

Calcium binding site 6 out of 8 in 3so1

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Calcium binding site 6 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca97

b:27.1
occ:1.00
 O F:GLU9 2.3 21.1 1.0
OD1 F:ASP79 2.4 24.3 1.0
O F:HOH449 2.4 27.8 1.0
O F:HOH450 2.4 31.3 1.0
O F:TRP39 2.5 18.7 1.0
OG F:SER41 2.5 18.4 1.0
O F:HOH609 2.8 29.6 1.0
CG F:ASP79 3.4 23.4 1.0
C F:TRP39 3.5 18.9 1.0
C F:GLU9 3.6 21.0 1.0
OD2 F:ASP79 3.6 25.1 1.0
CB F:SER41 3.7 17.9 1.0
CA F:TRP39 4.2 19.2 1.0
N F:SER41 4.3 17.6 1.0
CG F:GLU9 4.4 21.3 1.0
CA F:GLU9 4.4 20.5 1.0
C F:MET40 4.4 17.6 1.0
OD1 F:ASP10 4.4 24.3 1.0
OD1 F:ASN78 4.5 22.9 1.0
N F:MET40 4.5 18.1 1.0
CA F:SER41 4.5 17.8 1.0
N F:ASP10 4.6 21.4 1.0
O F:MET40 4.7 17.2 1.0
CA F:ASP10 4.7 22.0 1.0
CB F:ASP79 4.7 22.5 1.0
CA F:MET40 4.8 17.8 1.0
O F:HOH347 4.8 30.0 1.0
CB F:GLU9 5.0 20.6 1.0

Calcium binding site 7 out of 8 in 3so1

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Calcium binding site 7 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca97

b:31.3
occ:1.00
 O G:HOH569 2.2 33.1 1.0
OG G:SER41 2.3 21.3 1.0
OD1 G:ASP79 2.3 23.1 1.0
O G:GLU9 2.4 24.4 1.0
O G:HOH530 2.4 27.3 1.0
O G:TRP39 2.6 23.2 1.0
O G:HOH159 2.8 29.6 1.0
CG G:ASP79 3.3 23.5 1.0
OD2 G:ASP79 3.6 25.2 1.0
CB G:SER41 3.6 21.0 1.0
C G:GLU9 3.6 24.7 1.0
C G:TRP39 3.7 23.3 1.0
OD1 G:ASN78 4.1 22.5 1.0
N G:SER41 4.3 21.1 1.0
C G:MET40 4.3 21.7 1.0
OD1 G:ASP10 4.4 28.2 1.0
CA G:TRP39 4.4 23.8 1.0
CA G:SER41 4.4 20.8 1.0
O G:HOH245 4.5 28.5 1.0
CA G:GLU9 4.5 24.3 1.0
CG G:GLU9 4.6 25.7 1.0
O G:MET40 4.6 21.4 1.0
N G:ASP10 4.6 25.3 1.0
N G:MET40 4.6 22.6 1.0
CA G:ASP10 4.6 26.1 1.0
CB G:ASP79 4.7 22.6 1.0
O F:HOH502 4.8 34.0 1.0
CA G:MET40 4.8 22.0 1.0
CG G:ASN78 4.9 22.6 1.0
O G:HOH299 4.9 32.2 1.0
ND2 G:ASN78 4.9 22.7 1.0

Calcium binding site 8 out of 8 in 3so1

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Calcium binding site 8 out of 8 in the Crystal Structure of A Double Mutant T41S T82S 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 Double Mutant T41S T82S of A Betagamma- Crystallin Domain From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca97

b:30.3
occ:1.00
 O H:HOH611 2.3 41.2 1.0
O H:GLU9 2.3 23.2 1.0
OD1 H:ASP79 2.3 22.8 1.0
O H:HOH453 2.4 30.0 1.0
OG H:SER41 2.5 20.1 1.0
O H:TRP39 2.5 21.7 1.0
O H:HOH549 2.7 31.9 1.0
CG H:ASP79 3.3 23.1 1.0
C H:GLU9 3.5 23.6 1.0
OD2 H:ASP79 3.5 24.4 1.0
C H:TRP39 3.6 21.9 1.0
CB H:SER41 3.7 20.3 1.0
CA H:TRP39 4.3 22.4 1.0
N H:SER41 4.3 20.3 1.0
C H:MET40 4.4 20.6 1.0
CA H:GLU9 4.4 23.4 1.0
CG H:GLU9 4.5 24.7 1.0
OD1 H:ASN78 4.5 22.4 1.0
N H:ASP10 4.5 24.0 1.0
OD1 H:ASP10 4.5 27.7 1.0
CA H:SER41 4.5 20.3 1.0
N H:MET40 4.6 21.2 1.0
CA H:ASP10 4.6 24.5 1.0
O H:MET40 4.6 20.1 1.0
O H:HOH390 4.6 38.7 1.0
CB H:ASP79 4.7 22.2 1.0
O H:HOH105 4.8 38.0 1.0
CA H:MET40 4.8 20.8 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: Sat Jul 13 19:21:15 2024

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