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Calcium in PDB 3hz2: Crystal Structure of A Betagamma-Crystallin From An Archaea

Protein crystallography data

The structure of Crystal Structure of A Betagamma-Crystallin From An Archaea, PDB code: 3hz2 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 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 29.300, 54.202, 54.179, 85.81, 74.31, 74.32
R / Rfree (%) 17.2 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Betagamma-Crystallin From An Archaea (pdb code 3hz2). 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 Betagamma-Crystallin From An Archaea, PDB code: 3hz2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3hz2

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Calcium binding site 1 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:9.3
occ:1.00
 OD1 A:ASN76 2.4 6.0 1.0
OG A:SER36 2.5 8.4 1.0
O A:GLU9 2.5 8.4 1.0
O A:LYS34 2.5 8.2 1.0
O A:HOH230 2.6 8.3 1.0
O A:HOH237 2.7 16.1 1.0
O A:HOH96 2.7 13.9 1.0
CG A:ASN76 3.5 8.3 1.0
C A:LYS34 3.6 9.9 1.0
CB A:SER36 3.6 8.3 1.0
C A:GLU9 3.7 10.0 1.0
ND2 A:ASN76 3.9 6.3 1.0
CA A:LYS34 4.1 11.0 1.0
OD1 A:ASP75 4.2 9.3 1.0
O A:HOH242 4.2 10.5 1.0
N A:SER36 4.3 7.5 1.0
OD2 A:ASP75 4.4 12.6 1.0
C A:ILE35 4.5 9.5 1.0
CA A:HIS10 4.5 9.6 1.0
CA A:SER36 4.5 8.7 1.0
N A:HIS10 4.6 9.4 1.0
CA A:GLU9 4.6 9.6 1.0
O A:HOH261 4.6 18.8 1.0
CG A:GLU9 4.6 12.4 1.0
O A:HOH86 4.6 7.0 1.0
ND1 A:HIS10 4.7 13.5 1.0
N A:ILE35 4.7 9.4 1.0
CB A:LYS34 4.7 12.4 1.0
CG A:ASP75 4.7 11.8 1.0
CB A:ASN76 4.7 8.5 1.0
O A:ILE35 4.8 11.2 1.0
CA A:ILE35 5.0 7.9 1.0
CA A:ASN76 5.0 9.6 1.0

Calcium binding site 2 out of 8 in 3hz2

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Calcium binding site 2 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:14.2
occ:1.00
 O A:GLU49 2.4 10.2 1.0
OD1 A:ASP33 2.5 12.0 1.0
O A:SER77 2.5 10.4 1.0
OG A:SER79 2.6 10.6 1.0
O A:HOH272 2.8 41.4 1.0
O A:HOH90 2.8 21.9 1.0
C A:SER77 3.4 10.5 1.0
CG A:ASP33 3.5 16.3 1.0
C A:GLU49 3.6 9.7 1.0
CB A:SER79 3.7 9.9 1.0
OD2 A:ASP33 3.9 20.4 1.0
CA A:SER77 3.9 10.4 1.0
CA A:GLU49 4.3 10.7 1.0
N A:SER79 4.3 9.6 1.0
C A:ILE78 4.3 8.8 1.0
O A:HOH103 4.4 33.9 1.0
CD2 A:TYR50 4.4 17.3 1.0
N A:ILE78 4.5 8.9 1.0
O A:ILE78 4.5 10.6 1.0
CB A:SER77 4.5 12.6 1.0
CA A:SER79 4.5 8.3 1.0
OD1 A:ASN32 4.6 16.1 1.0
N A:TYR50 4.6 10.1 1.0
CA A:TYR50 4.7 10.6 1.0
CB A:GLU49 4.7 12.6 1.0
CB A:ASP33 4.8 13.7 1.0
CA A:ILE78 4.8 9.4 1.0
O A:HOH93 4.9 16.1 1.0
CE2 A:TYR50 4.9 18.7 1.0
O B:HOH100 5.0 15.1 1.0

Calcium binding site 3 out of 8 in 3hz2

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Calcium binding site 3 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:9.9
occ:1.00
 OD1 B:ASN76 2.4 6.8 1.0
O B:GLU9 2.5 8.7 1.0
OG B:SER36 2.5 8.9 1.0
O B:LYS34 2.5 6.5 1.0
O B:HOH85 2.5 8.4 1.0
O B:HOH88 2.6 10.8 1.0
O B:HOH110 2.7 13.6 1.0
CG B:ASN76 3.5 8.2 1.0
C B:LYS34 3.6 8.1 1.0
CB B:SER36 3.6 8.6 1.0
C B:GLU9 3.7 10.5 1.0
ND2 B:ASN76 4.0 7.9 1.0
CA B:LYS34 4.1 9.5 1.0
O B:HOH106 4.2 10.4 1.0
OD1 B:ASP75 4.3 11.5 1.0
N B:SER36 4.3 6.5 1.0
OD2 B:ASP75 4.5 11.7 1.0
O B:HOH108 4.5 16.4 1.0
C B:ILE35 4.5 7.9 1.0
CA B:SER36 4.5 7.6 1.0
CA B:GLU9 4.5 10.0 1.0
CG B:GLU9 4.5 11.5 1.0
CA B:HIS10 4.6 9.4 1.0
N B:HIS10 4.6 9.7 1.0
CB B:LYS34 4.6 10.8 1.0
N B:ILE35 4.7 7.3 1.0
O B:HOH89 4.7 9.0 1.0
ND1 B:HIS10 4.7 12.3 1.0
CG B:ASP75 4.7 11.1 1.0
CB B:ASN76 4.8 8.9 1.0
O B:ILE35 4.8 10.5 1.0
CA B:ILE35 4.9 7.9 1.0
CA B:ASN76 5.0 9.9 1.0
N B:ASN76 5.0 9.9 1.0

Calcium binding site 4 out of 8 in 3hz2

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Calcium binding site 4 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca104

b:12.2
occ:1.00
 O B:GLU49 2.4 11.3 1.0
O B:SER77 2.5 10.4 1.0
OD1 B:ASP33 2.5 13.9 1.0
OG B:SER79 2.6 10.9 1.0
O B:HOH93 2.7 18.2 1.0
O B:HOH254 2.7 34.3 1.0
C B:SER77 3.4 11.0 1.0
CG B:ASP33 3.5 16.6 1.0
C B:GLU49 3.6 9.7 1.0
CB B:SER79 3.7 9.3 1.0
CA B:SER77 3.9 10.7 1.0
OD2 B:ASP33 3.9 18.6 1.0
CA B:GLU49 4.3 10.2 1.0
N B:SER79 4.3 9.2 1.0
C B:ILE78 4.3 8.2 1.0
N B:ILE78 4.4 9.0 1.0
CD2 B:TYR50 4.5 17.2 1.0
CB B:SER77 4.5 13.1 1.0
CA B:SER79 4.5 8.0 1.0
O B:ILE78 4.5 9.3 1.0
OD1 B:ASN32 4.6 15.8 1.0
O B:HOH444 4.6 37.3 1.0
N B:TYR50 4.6 10.9 1.0
CB B:GLU49 4.7 12.7 1.0
CA B:TYR50 4.7 10.2 1.0
CA B:ILE78 4.8 8.9 1.0
CB B:ASP33 4.8 13.7 1.0
CE2 B:TYR50 4.9 19.1 1.0
O B:HOH102 4.9 15.5 1.0
CA B:ASP33 5.0 10.7 1.0

Calcium binding site 5 out of 8 in 3hz2

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Calcium binding site 5 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca105

b:10.3
occ:1.00
 OD1 C:ASN76 2.4 6.5 1.0
O C:GLU9 2.5 9.7 1.0
OG C:SER36 2.5 8.0 1.0
O C:LYS34 2.6 8.9 1.0
O C:HOH85 2.6 9.0 1.0
O C:HOH231 2.6 12.9 1.0
O C:HOH241 2.8 12.1 1.0
CG C:ASN76 3.5 7.0 1.0
CB C:SER36 3.6 7.5 1.0
C C:LYS34 3.6 9.8 1.0
C C:GLU9 3.7 9.9 1.0
O D:TYR53 3.9 9.6 1.0
ND2 C:ASN76 3.9 5.0 1.0
CA C:LYS34 4.2 11.2 1.0
O C:HOH93 4.2 9.2 1.0
OD1 C:ASP75 4.2 9.6 1.0
N C:SER36 4.3 6.6 1.0
OD2 C:ASP75 4.4 11.9 1.0
CA C:HIS10 4.5 9.3 1.0
C C:ILE35 4.5 8.3 1.0
CA C:SER36 4.5 7.5 1.0
CG C:GLU9 4.5 11.6 1.0
N C:HIS10 4.5 8.9 1.0
CA C:GLU9 4.6 9.8 1.0
O C:HOH94 4.6 18.6 1.0
ND1 C:HIS10 4.6 11.7 1.0
O C:HOH233 4.6 8.0 1.0
CB C:LYS34 4.7 12.6 1.0
N C:ILE35 4.7 9.3 1.0
CG C:ASP75 4.7 10.2 1.0
CB C:ASN76 4.8 8.6 1.0
O C:ILE35 4.8 10.6 1.0
C D:TYR53 4.9 9.7 1.0
CA C:ILE35 5.0 8.0 1.0

Calcium binding site 6 out of 8 in 3hz2

Go back to Calcium Binding Sites List in 3hz2
Calcium binding site 6 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca106

b:12.4
occ:1.00
 O C:GLU49 2.4 11.9 1.0
OD1 C:ASP33 2.5 13.0 1.0
O C:SER77 2.5 9.9 1.0
OG C:SER79 2.6 8.9 1.0
O C:HOH239 2.7 18.4 1.0
O C:HOH249 2.7 31.2 1.0
C C:SER77 3.4 11.0 1.0
CG C:ASP33 3.5 15.9 1.0
C C:GLU49 3.6 10.3 1.0
CB C:SER79 3.7 8.8 1.0
OD2 C:ASP33 3.9 17.9 1.0
CA C:SER77 3.9 10.8 1.0
CA C:GLU49 4.3 10.8 1.0
N C:SER79 4.3 9.7 1.0
C C:ILE78 4.3 9.2 1.0
N C:ILE78 4.5 9.0 1.0
O C:ILE78 4.5 11.3 1.0
CD2 C:TYR50 4.5 17.1 1.0
CA C:SER79 4.5 7.9 1.0
CB C:SER77 4.5 12.9 1.0
N C:TYR50 4.6 10.5 1.0
OD1 C:ASN32 4.6 17.0 1.0
CB C:GLU49 4.7 11.6 1.0
CA C:TYR50 4.7 11.2 1.0
CA C:ILE78 4.8 9.1 1.0
CB C:ASP33 4.8 13.2 1.0
O C:HOH277 4.9 19.3 1.0
CE2 C:TYR50 4.9 18.8 1.0
O C:HOH90 5.0 12.5 1.0
CA C:ASP33 5.0 10.4 1.0

Calcium binding site 7 out of 8 in 3hz2

Go back to Calcium Binding Sites List in 3hz2
Calcium binding site 7 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca107

b:9.5
occ:1.00
 OD1 D:ASN76 2.4 7.8 1.0
OG D:SER36 2.5 8.7 1.0
O D:GLU9 2.5 9.7 1.0
O D:LYS34 2.5 9.0 1.0
O D:HOH87 2.6 9.7 1.0
O D:HOH85 2.7 13.0 1.0
O D:HOH97 2.7 11.8 1.0
CG D:ASN76 3.5 8.6 1.0
C D:LYS34 3.6 9.7 1.0
CB D:SER36 3.6 8.1 1.0
C D:GLU9 3.7 10.6 1.0
O B:TYR53 3.9 9.5 1.0
ND2 D:ASN76 3.9 6.5 1.0
CA D:LYS34 4.1 10.7 1.0
OD2 D:ASP75 4.2 9.9 1.0
O B:HOH191 4.2 10.6 1.0
N D:SER36 4.3 6.4 1.0
C D:ILE35 4.5 8.4 1.0
O D:HOH99 4.5 20.0 1.0
CA D:SER36 4.5 8.6 1.0
OD1 D:ASP75 4.5 13.1 1.0
CA D:HIS10 4.6 9.9 1.0
CA D:GLU9 4.6 10.8 1.0
CG D:GLU9 4.6 13.3 1.0
N D:HIS10 4.6 10.3 1.0
ND1 D:HIS10 4.6 12.4 1.0
CB D:LYS34 4.6 12.4 1.0
O D:HOH89 4.7 7.2 1.0
N D:ILE35 4.7 9.5 1.0
CG D:ASP75 4.7 11.1 1.0
CB D:ASN76 4.8 9.9 1.0
O D:ILE35 4.8 9.2 1.0
C B:TYR53 5.0 10.1 1.0
CA D:ILE35 5.0 7.7 1.0

Calcium binding site 8 out of 8 in 3hz2

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Calcium binding site 8 out of 8 in the Crystal Structure of A Betagamma-Crystallin From An Archaea


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 From An Archaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca108

b:12.1
occ:1.00
 O D:GLU49 2.4 11.3 1.0
O D:SER77 2.5 9.7 1.0
OD2 D:ASP33 2.5 11.6 1.0
OG D:SER79 2.6 9.0 1.0
O D:HOH98 2.7 20.1 1.0
O D:HOH257 2.7 33.6 1.0
C D:SER77 3.4 10.2 1.0
CG D:ASP33 3.5 16.2 1.0
C D:GLU49 3.5 9.5 1.0
CB D:SER79 3.7 8.4 1.0
OD1 D:ASP33 3.8 20.6 1.0
CA D:SER77 3.9 10.1 1.0
CA D:GLU49 4.2 10.2 1.0
N D:SER79 4.3 9.4 1.0
C D:ILE78 4.3 9.1 1.0
CD2 D:TYR50 4.4 16.7 1.0
N D:ILE78 4.5 8.5 1.0
CA D:SER79 4.5 8.9 1.0
O D:HOH91 4.5 36.1 1.0
OD1 D:ASN32 4.5 16.9 1.0
N D:TYR50 4.5 10.5 1.0
O D:ILE78 4.5 10.6 1.0
CB D:SER77 4.5 12.2 1.0
CA D:TYR50 4.6 11.8 1.0
CB D:GLU49 4.7 13.0 1.0
CA D:ILE78 4.8 9.4 1.0
CB D:ASP33 4.8 13.4 1.0
CE2 D:TYR50 4.9 18.4 1.0
O D:HOH100 4.9 17.7 1.0
CA D:ASP33 5.0 10.1 1.0

Reference:

P.Aravind, A.Mishra, S.K.Suman, M.K.Jobby, R.Sankaranarayanan, Y.Sharma. The Betagamma-Crystallin Superfamily Contains A Universal Motif For Binding Calcium Biochemistry V. 48 12180 2009.
ISSN: ISSN 0006-2960
PubMed: 19921810
DOI: 10.1021/BI9017076
Page generated: Sat Jul 13 11:19:14 2024

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