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Calcium in PDB 3aka: Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein

Protein crystallography data

The structure of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein, PDB code: 3aka was solved by X.Zhao, H.Pang, S.Wang, W.Zhou, K.Yang, M.Bartlam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.22 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.876, 51.044, 86.998, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein (pdb code 3aka). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein, PDB code: 3aka:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3aka

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Calcium binding site 1 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:8.4
occ:1.00
 OE1 A:GLU135 2.0 22.6 1.0
CD A:GLU135 2.8 23.0 1.0
OE2 A:GLU135 3.0 27.8 1.0
CG A:GLU135 4.2 19.7 1.0
CB A:GLU135 4.7 14.1 1.0
NH2 A:ARG139 5.0 31.0 1.0

Calcium binding site 2 out of 9 in 3aka

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Calcium binding site 2 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:13.2
occ:1.00
 NE2 A:GLN51 2.0 11.4 1.0
CD A:GLN51 3.0 13.8 1.0
OE1 A:GLN51 3.3 15.5 1.0
CG A:GLN51 4.4 8.1 1.0
CB A:GLN51 4.9 10.3 1.0

Calcium binding site 3 out of 9 in 3aka

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Calcium binding site 3 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:10.7
occ:1.00
 OD2 A:ASP148 1.9 17.8 1.0
OD2 A:ASP150 1.9 20.4 1.0
CG A:ASP148 2.8 20.1 1.0
CG A:ASP150 2.9 18.9 1.0
OD1 A:ASP148 3.0 15.1 1.0
OD1 A:ASP150 3.3 16.1 1.0
CA A:CA173 3.6 16.5 1.0
CB A:ASP148 4.2 20.7 1.0
CB A:ASP150 4.2 19.6 1.0
O A:HOH234 4.4 25.6 1.0
OE2 A:GLU157 4.5 18.1 1.0
O A:LYS152 4.9 18.7 1.0

Calcium binding site 4 out of 9 in 3aka

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Calcium binding site 4 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:16.1
occ:1.00
 OD2 A:ASP136 2.0 22.4 1.0
OD1 A:ASP136 2.5 18.6 1.0
CG A:ASP136 2.6 18.3 1.0
O A:HOH233 3.8 38.5 1.0
O A:HOH238 3.9 49.7 1.0
O A:HOH227 4.0 23.2 1.0
CB A:ASP136 4.1 15.7 1.0
O A:HOH317 4.7 39.0 1.0

Calcium binding site 5 out of 9 in 3aka

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Calcium binding site 5 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca171

b:12.8
occ:1.00
 OD2 A:ASP29 2.4 14.0 1.0
OD1 A:ASP18 2.4 12.0 1.0
OD1 A:ASP20 2.4 13.4 1.0
OD1 A:ASN22 2.4 13.1 1.0
O A:HOH200 2.4 14.9 1.0
O A:HIS24 2.5 11.4 1.0
OD1 A:ASP29 2.6 11.3 1.0
CG A:ASP29 2.8 12.8 1.0
CG A:ASP20 3.2 15.6 1.0
CG A:ASN22 3.3 14.6 1.0
OD2 A:ASP20 3.6 19.3 1.0
CG A:ASP18 3.6 14.2 1.0
C A:HIS24 3.7 12.0 1.0
ND2 A:ASN22 3.8 17.6 1.0
N A:ASN22 4.1 12.9 1.0
CA A:ASP18 4.2 14.1 1.0
CB A:ASP29 4.3 10.8 1.0
CA A:ILE25 4.4 12.3 1.0
N A:ASP20 4.4 14.3 1.0
N A:HIS24 4.4 12.6 1.0
CB A:ASP18 4.5 13.8 1.0
OD2 A:ASP18 4.5 12.8 1.0
CB A:ASN22 4.5 14.7 1.0
CB A:ASP20 4.5 15.1 1.0
N A:ILE25 4.5 11.8 1.0
N A:GLY21 4.5 13.5 1.0
N A:ASP26 4.5 13.5 1.0
C A:ASP18 4.5 14.6 1.0
CA A:ASN22 4.6 14.7 1.0
CA A:HIS24 4.7 12.1 1.0
CA A:ASP20 4.7 14.6 1.0
N A:GLY23 4.7 13.2 1.0
C A:ASP20 4.8 14.2 1.0
ND1 A:HIS24 4.8 16.4 1.0
N A:GLN19 4.8 14.3 1.0
OD2 A:ASP26 4.9 18.0 1.0
C A:ILE25 4.9 13.2 1.0
C A:ASN22 4.9 13.9 1.0
CB A:ASP26 5.0 15.1 1.0
CE1 A:HIS24 5.0 15.1 1.0
O A:ASP18 5.0 15.3 1.0

Calcium binding site 6 out of 9 in 3aka

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Calcium binding site 6 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca172

b:17.6
occ:1.00
 OD1 A:ASP69 2.3 17.9 1.0
O A:HOH176 2.3 20.8 1.0
O A:ARG75 2.4 16.3 1.0
OD1 A:ASP71 2.4 21.5 1.0
OE1 A:GLU80 2.4 17.9 1.0
OD1 A:ASP73 2.5 17.4 1.0
OE2 A:GLU80 2.5 18.1 1.0
CD A:GLU80 2.8 19.2 1.0
CG A:ASP71 3.4 24.5 1.0
CG A:ASP73 3.4 18.1 1.0
CG A:ASP69 3.5 19.4 1.0
C A:ARG75 3.6 16.3 1.0
OD2 A:ASP71 3.8 25.1 1.0
OD2 A:ASP73 3.9 19.5 1.0
CA A:ASP69 4.3 20.2 1.0
OD2 A:ASP69 4.3 19.6 1.0
N A:ASP71 4.3 24.6 1.0
N A:ASP73 4.3 17.3 1.0
N A:ARG75 4.3 15.6 1.0
CG A:GLU80 4.3 21.0 1.0
CB A:ASP69 4.4 19.4 1.0
O A:HOH309 4.4 35.5 1.0
CA A:ILE76 4.4 15.1 1.0
N A:ILE76 4.5 14.5 1.0
C A:ASP69 4.5 20.8 1.0
N A:GLY72 4.6 22.2 1.0
CA A:ARG75 4.6 16.4 1.0
N A:ARG70 4.6 22.6 1.0
CB A:ASP73 4.6 16.9 1.0
CB A:ASP71 4.6 24.2 1.0
O A:HOH239 4.7 33.9 1.0
CA A:ASP71 4.8 23.9 1.0
N A:THR77 4.8 16.7 1.0
N A:GLN74 4.8 14.2 1.0
CA A:ASP73 4.8 16.6 1.0
C A:ASP71 4.9 23.9 1.0
CB A:ARG75 4.9 16.8 1.0
CG2 A:THR77 5.0 18.0 1.0

Calcium binding site 7 out of 9 in 3aka

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Calcium binding site 7 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca173

b:16.5
occ:1.00
 O A:LYS152 2.2 18.7 1.0
OD1 A:ASP146 2.2 18.2 1.0
OD1 A:ASP148 2.4 15.1 1.0
OE2 A:GLU157 2.5 18.1 1.0
OD1 A:ASP150 2.5 16.1 1.0
OE1 A:GLU157 2.7 22.5 1.0
CD A:GLU157 2.9 19.5 1.0
CG A:ASP146 3.4 19.1 1.0
CG A:ASP148 3.4 20.1 1.0
CG A:ASP150 3.4 18.9 1.0
C A:LYS152 3.5 19.7 1.0
CA A:CA3 3.6 10.7 1.0
OD2 A:ASP150 3.7 20.4 1.0
OD2 A:ASP148 3.9 17.8 1.0
CA A:ASP146 4.1 19.3 1.0
N A:LYS152 4.2 20.0 1.0
CB A:ASP146 4.2 18.2 1.0
N A:ASP150 4.3 19.7 1.0
OD2 A:ASP146 4.3 20.5 1.0
CA A:LYS152 4.3 20.0 1.0
N A:ASP148 4.3 21.3 1.0
C A:ASP146 4.4 20.2 1.0
N A:VAL153 4.4 18.6 1.0
CG A:GLU157 4.4 18.3 1.0
CA A:VAL153 4.5 18.6 1.0
O A:HOH234 4.5 25.6 1.0
N A:GLY149 4.5 21.1 1.0
N A:THR147 4.6 21.4 1.0
CB A:ASP148 4.6 20.7 1.0
CB A:ASP150 4.7 19.6 1.0
CB A:LYS152 4.7 20.0 1.0
CA A:ASP148 4.8 21.2 1.0
CA A:ASP150 4.8 19.6 1.0
C A:ASP148 4.9 21.6 1.0
N A:GLY151 4.9 19.1 1.0
O A:ASP146 5.0 20.4 1.0

Calcium binding site 8 out of 9 in 3aka

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Calcium binding site 8 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca174

b:21.0
occ:1.00
 OD1 A:ASP112 2.2 13.3 1.0
OD1 A:ASP114 2.3 14.3 1.0
CA A:CA175 2.3 33.0 1.0
O A:ALA118 2.4 13.4 1.0
OD1 A:ASP116 2.4 16.1 1.0
CG A:ASP116 3.2 19.3 1.0
CG A:ASP112 3.3 15.0 1.0
CG A:ASP114 3.3 16.1 1.0
C A:ALA118 3.4 14.6 1.0
OD2 A:ASP116 3.5 19.1 1.0
N A:ALA118 3.8 17.1 1.0
OD2 A:ASP114 3.8 15.5 1.0
N A:ASP116 4.0 17.7 1.0
N A:ASP114 4.0 16.2 1.0
CA A:ALA118 4.1 16.6 1.0
OD2 A:ASP112 4.1 15.5 1.0
CB A:ASP112 4.2 13.1 1.0
CA A:ASP112 4.2 13.5 1.0
N A:THR113 4.3 13.7 1.0
N A:GLY115 4.3 17.0 1.0
CB A:ASP116 4.4 17.9 1.0
O A:HOH179 4.4 11.0 1.0
CB A:ALA118 4.4 16.8 1.0
C A:ASP112 4.4 14.4 1.0
O A:HOH300 4.4 24.8 1.0
N A:VAL119 4.4 13.6 1.0
N A:GLY117 4.5 19.5 1.0
CB A:ASP114 4.5 16.5 1.0
CA A:ASP116 4.5 18.9 1.0
CA A:ASP114 4.6 16.8 1.0
C A:ASP114 4.7 16.8 1.0
CA A:VAL119 4.7 13.1 1.0
C A:ASP116 4.7 19.3 1.0
O A:HOH225 5.0 27.2 1.0
C A:GLY117 5.0 19.6 1.0
C A:GLY115 5.0 17.9 1.0

Calcium binding site 9 out of 9 in 3aka

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Calcium binding site 9 out of 9 in the Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structural Basis For Prokaryotic Calcium-Mediated Regulation By A Streptomyces Coelicolor Calcium-Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca175

b:33.0
occ:1.00
 CA A:CA174 2.3 21.0 1.0
O A:HOH179 2.7 11.0 1.0
O A:HOH300 2.9 24.8 1.0
N A:THR113 3.0 13.7 1.0
OG1 A:THR113 3.2 15.8 1.0
OD1 A:ASP114 3.2 14.3 1.0
OD1 A:ASP112 3.3 13.3 1.0
N A:ASP114 3.4 16.2 1.0
O A:ALA118 3.6 13.4 1.0
C A:ASP112 3.7 14.4 1.0
CG A:ASP114 3.7 16.1 1.0
CA A:THR113 3.8 15.5 1.0
CA A:ASP112 3.8 13.5 1.0
O A:HOH382 3.9 71.8 1.0
CB A:THR113 4.0 15.7 1.0
C A:THR113 4.0 16.1 1.0
O A:ALA111 4.3 11.9 1.0
OD2 A:ASP114 4.3 15.5 1.0
CG A:ASP112 4.4 15.0 1.0
OD2 A:ASP123 4.4 14.8 1.0
CB A:ASP114 4.4 16.5 1.0
CA A:ASP114 4.4 16.8 1.0
CG2 A:THR120 4.6 13.9 1.0
O A:HOH289 4.6 39.1 1.0
CG2 A:THR113 4.6 14.6 1.0
O A:HOH225 4.6 27.2 1.0
CB A:ASP112 4.6 13.1 1.0
C A:ALA118 4.7 14.6 1.0
OD1 A:ASP116 4.7 16.1 1.0
CA A:VAL119 4.7 13.1 1.0
O A:ASP112 4.8 15.6 1.0
N A:THR120 4.8 13.2 1.0
N A:ASP112 4.9 12.4 1.0
N A:GLY115 5.0 17.0 1.0

Reference:

X.Zhao, H.Pang, S.Wang, W.Zhou, K.Yang, M.Bartlam. Structural Basis For Prokaryotic Calciummediated Regulation By A Streptomyces Coelicolor Calcium Binding Protein Protein Cell V. 1 771 2010.
ISSN: ISSN 1674-800X
PubMed: 21203918
DOI: 10.1007/S13238-010-0085-Z
Page generated: Tue Jul 8 10:49:59 2025

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