Calcium in PDB 3i9h: Crystal Structure of A Betagamma-Crystallin Domain From Clostridium Beijerinckii

The structure of Crystal Structure of A Betagamma-Crystallin Domain From Clostridium Beijerinckii, PDB code: 3i9h was solved by P.Aravind, R.Sankaranarayanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.500, 103.710, 105.200, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Betagamma-Crystallin Domain From Clostridium Beijerinckii (pdb code 3i9h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of A Betagamma-Crystallin Domain From Clostridium Beijerinckii, PDB code: 3i9h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:22.2 occ:1.00 OG1 A:THR40 2.5 22.1 1.0 O A:GLU8 2.6 20.6 1.0 OD1 A:ASP78 2.6 19.4 1.0 O A:HOH96 2.6 20.3 1.0 O A:TRP38 2.6 22.0 1.0 O A:HOH93 2.7 30.2 1.0 O A:HOH92 2.9 27.2 1.0 C A:TRP38 3.5 22.6 1.0 CG A:ASP78 3.5 23.5 1.0 CB A:THR40 3.7 21.1 1.0 C A:GLU8 3.7 23.2 1.0 OD2 A:ASP78 3.8 23.9 1.0 CA A:TRP38 4.1 21.9 1.0 N A:THR40 4.3 17.5 1.0 C A:MET39 4.4 18.0 1.0 OD1 A:ASN77 4.4 20.7 1.0 CA A:GLU8 4.4 21.7 1.0 CG A:GLU8 4.4 24.9 1.0 CA A:THR40 4.5 19.2 1.0 N A:MET39 4.5 19.2 1.0 O A:HOH136 4.6 21.9 1.0 O A:MET39 4.6 17.4 1.0 OD1 A:ASP9 4.7 30.5 1.0 N A:ASP9 4.8 23.4 1.0 CG2 A:THR40 4.8 22.4 1.0 CA A:MET39 4.8 18.2 1.0 CB A:ASP78 4.9 17.4 1.0 CA A:ASP9 4.9 24.1 1.0 O A:HOH382 4.9 21.7 1.0 CG A:TRP38 5.0 23.1 1.0

Calcium binding site 2 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:21.9 occ:1.00 OD1 A:ASP37 2.5 18.2 1.0 O A:GLU54 2.5 19.0 1.0 OG1 A:THR81 2.6 19.1 1.0 O A:HOH98 2.6 17.9 1.0 O A:LYS79 2.6 22.0 1.0 O A:HOH104 2.8 24.5 1.0 O A:HOH100 2.8 27.4 1.0 CG A:ASP37 3.5 21.2 1.0 C A:LYS79 3.5 19.8 1.0 C A:GLU54 3.7 19.1 1.0 CB A:THR81 3.7 17.8 1.0 OD2 A:ASP37 3.9 20.9 1.0 CA A:LYS79 4.0 20.3 1.0 OD1 A:ASN36 4.0 22.3 1.0 O A:HOH215 4.3 42.5 1.0 N A:THR81 4.4 18.0 1.0 CA A:GLU54 4.4 20.1 1.0 CG A:GLU54 4.4 23.3 1.0 C A:MET80 4.5 18.1 1.0 CA A:THR81 4.5 17.6 1.0 CB A:LYS79 4.6 24.1 1.0 O A:HOH216 4.6 31.5 1.0 OD1 A:ASN55 4.6 21.4 1.0 N A:MET80 4.6 17.5 1.0 O A:MET80 4.6 17.1 1.0 N A:ASN55 4.7 19.8 1.0 CG2 A:THR81 4.8 18.5 1.0 CG A:ASN36 4.8 20.5 1.0 CB A:ASP37 4.8 20.7 1.0 CA A:ASN55 4.8 20.2 1.0 ND2 A:ASN36 4.9 21.6 1.0 CA A:MET80 5.0 19.0 1.0

Calcium binding site 3 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:21.6 occ:1.00 OG1 B:THR40 2.5 15.1 1.0 O B:GLU8 2.5 19.6 1.0 OD1 B:ASP78 2.6 20.6 1.0 O B:TRP38 2.7 21.9 1.0 O B:HOH93 2.8 19.7 1.0 O B:HOH384 2.8 36.9 1.0 O B:HOH100 2.9 27.5 1.0 CG B:ASP78 3.6 24.4 1.0 CB B:THR40 3.6 17.9 1.0 C B:TRP38 3.7 22.5 1.0 C B:GLU8 3.7 22.6 1.0 OD2 B:ASP78 4.0 24.6 1.0 OD1 B:ASN77 4.2 17.4 1.0 N B:THR40 4.2 18.2 1.0 CA B:TRP38 4.3 22.4 1.0 C B:MET39 4.4 19.1 1.0 OD1 B:ASP9 4.4 24.8 1.0 CA B:THR40 4.5 16.2 1.0 CA B:ASP9 4.6 22.2 1.0 CA B:GLU8 4.6 23.2 1.0 N B:ASP9 4.6 21.6 1.0 O B:MET39 4.6 19.4 1.0 N B:MET39 4.6 20.9 1.0 CG B:GLU8 4.6 23.7 1.0 CG2 B:THR40 4.7 17.0 1.0 CA B:MET39 4.9 19.4 1.0 CB B:ASP78 4.9 22.9 1.0 CG B:ASN77 5.0 18.3 1.0

Calcium binding site 4 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:25.5 occ:1.00 OD1 B:ASP37 2.5 24.6 1.0 OG1 B:THR81 2.5 15.1 1.0 O B:GLU54 2.5 17.4 1.0 O B:LYS79 2.6 16.6 1.0 O B:HOH115 2.7 22.8 1.0 O B:HOH91 2.7 15.9 1.0 O B:HOH105 2.7 27.3 1.0 C B:LYS79 3.6 19.1 1.0 CG B:ASP37 3.6 23.7 1.0 C B:GLU54 3.7 17.9 1.0 CB B:THR81 3.8 16.2 1.0 OD1 B:ASN36 3.9 18.8 1.0 OD2 B:ASP37 4.0 26.7 1.0 CA B:LYS79 4.0 20.4 1.0 N B:THR81 4.4 16.9 1.0 C B:MET80 4.5 18.2 1.0 O B:HOH440 4.5 27.8 1.0 CA B:GLU54 4.5 18.6 1.0 O B:HOH500 4.6 32.0 1.0 CA B:THR81 4.6 16.1 1.0 OD1 B:ASN55 4.6 21.8 1.0 N B:MET80 4.6 18.1 1.0 CB B:LYS79 4.6 21.9 1.0 CG B:GLU54 4.7 21.1 1.0 O B:MET80 4.7 18.3 1.0 N B:ASN55 4.7 17.9 1.0 CG B:ASN36 4.8 19.6 1.0 CG2 B:THR81 4.8 14.3 1.0 CA B:ASN55 4.8 17.0 1.0 CB B:ASP37 4.8 22.8 1.0 ND2 B:ASN36 5.0 13.9 1.0 CA B:MET80 5.0 18.6 1.0

Calcium binding site 5 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca105 b:29.7 occ:1.00 OG1 C:THR40 2.6 24.5 1.0 OD1 C:ASP78 2.6 26.2 1.0 O C:GLU8 2.6 30.0 1.0 O C:TRP38 2.6 26.7 1.0 O C:HOH93 2.7 28.3 1.0 O C:HOH223 2.8 37.3 1.0 O C:HOH792 2.9 47.7 1.0 CG C:ASP78 3.4 26.4 1.0 OD2 C:ASP78 3.5 23.5 1.0 C C:TRP38 3.7 27.1 1.0 C C:GLU8 3.7 29.1 1.0 CB C:THR40 3.7 24.9 1.0 CA C:TRP38 4.3 27.9 1.0 N C:THR40 4.3 26.0 1.0 CA C:GLU8 4.4 28.5 1.0 CG C:GLU8 4.5 28.6 1.0 C C:MET39 4.5 26.1 1.0 OD1 C:ASN77 4.5 25.3 1.0 CA C:THR40 4.6 25.5 1.0 N C:ASP9 4.6 31.3 1.0 N C:MET39 4.7 26.5 1.0 OD1 C:ASP9 4.7 36.1 1.0 O C:MET39 4.7 25.5 1.0 CA C:ASP9 4.8 30.9 1.0 CB C:ASP78 4.8 26.1 1.0 CG2 C:THR40 4.8 26.7 1.0 CA C:MET39 4.9 24.7 1.0

Calcium binding site 6 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca106 b:32.7 occ:1.00 OD1 C:ASP37 2.5 29.1 1.0 O C:GLU54 2.5 22.8 1.0 OG1 C:THR81 2.5 19.5 1.0 O C:LYS79 2.7 27.3 1.0 O C:HOH825 2.8 43.5 1.0 O C:HOH122 2.9 31.9 1.0 O C:HOH130 3.0 38.7 1.0 CG C:ASP37 3.6 31.6 1.0 C C:LYS79 3.7 25.9 1.0 C C:GLU54 3.7 22.0 1.0 CB C:THR81 3.8 18.9 1.0 OD1 C:ASN36 3.9 23.7 1.0 OD2 C:ASP37 3.9 34.5 1.0 CA C:LYS79 4.1 27.0 1.0 O C:HOH317 4.1 44.7 1.0 CA C:GLU54 4.4 22.3 1.0 N C:THR81 4.5 19.4 1.0 C C:MET80 4.6 22.5 1.0 OD1 C:ASN55 4.6 28.6 1.0 CA C:THR81 4.7 19.9 1.0 CB C:LYS79 4.7 26.5 1.0 N C:ASN55 4.7 23.0 1.0 CG2 C:THR81 4.7 20.4 1.0 O C:MET80 4.7 20.2 1.0 CG C:ASN36 4.8 27.1 1.0 N C:MET80 4.8 24.5 1.0 CA C:ASN55 4.8 23.4 1.0 CB C:ASP37 4.8 29.2 1.0 CB C:GLU54 4.8 24.1 1.0 ND2 C:ASN36 4.9 27.3 1.0 O C:HOH730 4.9 31.0 1.0 CD C:LYS79 5.0 30.9 1.0

Calcium binding site 7 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca107 b:38.0 occ:1.00 OD1 D:ASP78 2.6 28.4 1.0 O D:GLU8 2.7 33.0 1.0 OG1 D:THR40 2.7 28.0 1.0 O D:HOH416 2.8 40.4 1.0 O D:TRP38 2.8 29.2 1.0 O D:HOH94 2.8 40.0 1.0 O D:HOH824 2.9 37.6 1.0 CG D:ASP78 3.5 29.0 1.0 OD2 D:ASP78 3.6 30.9 1.0 C D:GLU8 3.8 33.6 1.0 C D:TRP38 3.8 29.8 1.0 CB D:THR40 3.9 26.4 1.0 OD1 D:ASN77 4.4 29.8 1.0 N D:THR40 4.4 27.9 1.0 CA D:TRP38 4.4 31.6 1.0 CG D:GLU8 4.5 33.9 1.0 C D:MET39 4.5 29.6 1.0 CA D:GLU8 4.6 32.8 1.0 OD1 D:ASP9 4.6 34.7 1.0 N D:ASP9 4.6 33.1 1.0 O D:HOH595 4.7 37.9 1.0 CA D:ASP9 4.7 32.4 1.0 CA D:THR40 4.7 26.7 1.0 O D:HOH330 4.7 31.5 1.0 N D:MET39 4.7 29.6 1.0 O D:MET39 4.8 29.1 1.0 CB D:ASP78 4.9 28.2 1.0 CA D:MET39 4.9 28.5 1.0 CG2 D:THR40 5.0 25.1 1.0

Calcium binding site 8 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca108 b:35.2 occ:1.00 O D:GLU54 2.5 22.5 1.0 OD1 D:ASP37 2.6 34.0 1.0 OG1 D:THR81 2.6 27.5 1.0 O D:LYS79 2.7 29.8 1.0 O D:HOH197 2.7 26.8 1.0 O D:HOH90 2.9 32.3 1.0 O D:HOH184 2.9 35.1 1.0 C D:LYS79 3.6 28.8 1.0 CG D:ASP37 3.7 34.3 1.0 C D:GLU54 3.7 21.5 1.0 CB D:THR81 3.8 27.6 1.0 CA D:LYS79 3.9 28.9 1.0 OD2 D:ASP37 4.1 35.1 1.0 OD1 D:ASN36 4.1 27.7 1.0 CB D:LYS79 4.3 32.6 1.0 CG D:GLU54 4.4 25.6 1.0 N D:THR81 4.4 26.5 1.0 CA D:GLU54 4.5 22.2 1.0 OD1 D:ASN55 4.6 24.6 1.0 CA D:THR81 4.6 26.5 1.0 C D:MET80 4.6 27.9 1.0 N D:ASN55 4.7 19.6 1.0 N D:MET80 4.7 27.5 1.0 CA D:ASN55 4.7 21.6 1.0 CG2 D:THR81 4.9 27.3 1.0 CG D:ASN36 4.9 27.9 1.0 O D:MET80 4.9 27.8 1.0 ND2 D:ASN36 4.9 27.8 1.0 CB D:ASP37 4.9 32.9 1.0 O D:HOH610 5.0 42.6 1.0

Calcium binding site 9 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca109 b:24.8 occ:1.00 O E:GLU8 2.5 28.3 1.0 OD1 E:ASP78 2.5 21.6 1.0 OG1 E:THR40 2.6 23.2 1.0 O E:TRP38 2.6 20.4 1.0 O E:HOH102 2.7 23.7 1.0 O E:HOH104 2.7 31.1 1.0 O E:HOH97 2.7 27.0 1.0 CG E:ASP78 3.4 22.4 1.0 OD2 E:ASP78 3.6 21.7 1.0 C E:TRP38 3.7 21.7 1.0 C E:GLU8 3.7 27.4 1.0 CB E:THR40 3.8 22.9 1.0 OD1 E:ASN77 4.2 25.8 1.0 N E:THR40 4.3 21.0 1.0 CA E:TRP38 4.4 20.4 1.0 O E:HOH404 4.4 24.8 1.0 C E:MET39 4.4 20.3 1.0 CA E:GLU8 4.5 26.6 1.0 OD1 E:ASP9 4.6 28.1 1.0 CA E:THR40 4.6 22.4 1.0 CG E:GLU8 4.6 27.3 1.0 N E:MET39 4.7 20.6 1.0 N E:ASP9 4.7 28.9 1.0 O E:HOH752 4.7 35.9 1.0 CA E:ASP9 4.7 29.5 1.0 O E:MET39 4.7 18.4 1.0 CB E:ASP78 4.8 20.7 1.0 ND2 E:ASN77 4.8 27.1 1.0 CA E:MET39 4.9 19.8 1.0 CG2 E:THR40 4.9 23.9 1.0 CG E:ASN77 4.9 24.9 1.0

Calcium binding site 10 out of 16 in the Crystal Structure 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 Betagamma-Crystallin Domain From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca110 b:27.2 occ:1.00 O E:GLU54 2.5 17.2 1.0 OG1 E:THR81 2.5 21.0 1.0 OD1 E:ASP37 2.5 26.0 1.0 O E:HOH89 2.6 20.7 1.0 O E:LYS79 2.6 21.9 1.0 O E:HOH123 2.9 34.2 1.0 O E:HOH99 3.0 30.8 1.0 C E:LYS79 3.5 22.1 1.0 CG E:ASP37 3.6 25.4 1.0 CB E:THR81 3.7 21.8 1.0 C E:GLU54 3.7 20.0 1.0 OD2 E:ASP37 3.9 20.8 1.0 OD1 E:ASN36 4.0 19.6 1.0 CA E:LYS79 4.0 22.8 1.0 N E:THR81 4.3 19.2 1.0 O E:HOH421 4.4 34.6 1.0 C E:MET80 4.4 19.6 1.0 CA E:GLU54 4.4 20.8 1.0 O E:HOH290 4.5 35.8 1.0 CA E:THR81 4.5 18.9 1.0 N E:MET80 4.6 20.2 1.0 CB E:LYS79 4.6 25.3 1.0 CG E:GLU54 4.6 28.9 1.0 O E:MET80 4.7 18.1 1.0 N E:ASN55 4.7 18.7 1.0 OD1 E:ASN55 4.7 24.4 1.0 CG2 E:THR81 4.8 20.9 1.0 CA E:ASN55 4.8 19.2 1.0 CB E:ASP37 4.9 22.7 1.0 CG E:ASN36 4.9 22.0 1.0 CA E:MET80 4.9 18.6 1.0

P.Aravind, A.Mishra, S.K.Suman, M.K.Jobby, R.Sankaranarayanan, Y.Sharma. Betagamma-Crystallin Superfamily Contains A Universal Motif For Binding Calcium. Biochemistry 2009.
ISSN: ISSN 0006-2960
PubMed: 19921810
DOI: 10.1021/BI9017076