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Calcium in PDB 4jcm: Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution

Enzymatic activity of Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution, PDB code: 4jcm was solved by L.Wu, D.Yang, J.Zhou, J.Wu, J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.65 / 1.65
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 205.736, 205.736, 43.504, 90.00, 90.00, 120.00
R / Rfree (%) 12.7 / 13.4

Other elements in 4jcm:

The structure of Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution (pdb code 4jcm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution, PDB code: 4jcm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4jcm

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Calcium binding site 1 out of 6 in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution


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 Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:29.6
occ:1.00
 OD1 A:ASN33 2.4 31.7 1.0
OD2 A:ASP53 2.4 27.5 1.0
OD1 A:ASN32 2.5 26.5 0.8
O A:GLY51 2.5 26.5 1.0
OD1 A:ASP27 2.6 30.2 1.0
O A:HOH909 2.7 30.6 1.0
O A:ASP29 2.7 29.8 1.0
CG A:ASP53 3.4 24.2 1.0
CG A:ASP27 3.4 32.9 1.0
C A:ASP29 3.5 32.0 1.0
CG A:ASN33 3.6 29.5 1.0
CG A:ASN32 3.6 24.4 0.8
C A:GLY51 3.6 26.1 1.0
CB A:ASP53 3.8 23.3 1.0
N A:ASN33 4.0 28.7 1.0
OD2 A:ASP27 4.0 38.2 1.0
CA A:GLY51 4.0 22.1 1.0
N A:PRO30 4.2 31.6 1.0
ND2 A:ASN32 4.2 24.3 0.8
CA A:PRO30 4.2 31.2 1.0
O A:PHE108 4.2 24.3 1.0
N A:ASP29 4.2 31.9 1.0
CA A:ASN33 4.3 27.0 1.0
C A:ASN32 4.3 29.3 1.0
CA A:ASP29 4.3 32.6 1.0
ND2 A:ASN33 4.4 31.3 1.0
CB A:ASN32 4.4 27.9 0.2
CB A:ASP27 4.4 31.2 1.0
OD1 A:ASP53 4.5 25.5 1.0
CA A:ASP27 4.5 28.6 1.0
CB A:ASN33 4.5 30.8 1.0
C A:PRO30 4.6 37.7 1.0
N A:ASN32 4.7 29.5 1.0
CB A:ASP29 4.7 38.5 1.0
CA A:ASN32 4.7 28.9 0.2
O A:HOH856 4.8 22.4 1.0
N A:GLY52 4.8 21.6 1.0
O A:PRO30 4.8 38.6 1.0
CB A:ASN32 4.8 23.6 0.8
C A:GLY52 4.8 22.1 1.0
CA A:ASN32 4.8 27.1 0.8
O A:ASN32 4.8 28.5 1.0
N A:ASP53 4.8 20.8 1.0
C A:ASP27 4.9 28.7 1.0
N A:GLY28 4.9 24.3 1.0
O A:GLY52 5.0 23.1 1.0
CA A:ASP53 5.0 20.6 1.0

Calcium binding site 2 out of 6 in 4jcm

Go back to Calcium Binding Sites List in 4jcm
Calcium binding site 2 out of 6 in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution


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 Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:76.2
occ:1.00
 OE2 A:GLU62 3.4 40.4 1.0
NE2 A:GLN55 4.0 30.1 1.0
O A:HOH1012 4.1 50.8 1.0
CD A:GLU62 4.3 41.9 1.0
CG2 A:ILE58 4.4 23.7 1.0
OE1 A:GLU62 4.4 44.9 1.0
NE A:ARG117 4.4 49.2 1.0
OE1 A:GLN55 4.4 35.3 1.0
CD A:GLN55 4.6 31.2 1.0

Calcium binding site 3 out of 6 in 4jcm

Go back to Calcium Binding Sites List in 4jcm
Calcium binding site 3 out of 6 in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution


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 Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:57.5
occ:1.00
 OE2 A:GLU144 2.6 33.7 0.6
NE2 A:HIS157 3.1 18.7 1.0
OH A:TYR149 3.2 36.4 1.0
C1 A:GOL735 3.3 46.5 1.0
CG A:GLU144 3.3 27.5 0.6
CD A:GLU144 3.4 28.0 0.6
O1 A:GOL735 3.6 40.4 1.0
CB A:ALA147 3.9 17.9 1.0
CE1 A:HIS157 3.9 18.2 1.0
CD2 A:HIS157 4.1 17.9 1.0
C2 A:GOL735 4.1 50.1 1.0
C3 A:GOL735 4.1 50.5 1.0
CZ A:TYR149 4.3 28.5 1.0
CE1 A:TYR149 4.5 25.9 1.0
OE1 A:GLU144 4.6 33.9 0.6
CB A:GLU144 4.6 21.1 0.4
O A:GLU144 4.6 17.2 1.0
NH2 A:ARG100 4.7 40.7 1.0
O3 A:GOL735 4.8 55.2 1.0
CB A:GLU144 4.8 23.4 0.6
OE1 A:GLU144 4.9 19.1 0.4

Calcium binding site 4 out of 6 in 4jcm

Go back to Calcium Binding Sites List in 4jcm
Calcium binding site 4 out of 6 in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution


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 Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:69.1
occ:1.00
 O A:HOH1163 3.4 39.3 1.0
N A:THR433 3.6 30.0 1.0
CA A:TYR432 4.1 31.7 1.0
OG1 A:THR433 4.2 31.6 1.0
CB A:THR433 4.2 31.1 1.0
C A:TYR432 4.4 29.6 1.0
CD1 A:TYR432 4.4 30.8 1.0
CA A:THR433 4.5 29.0 1.0
O A:ALA431 4.5 34.3 1.0
CB A:TYR432 4.8 30.3 1.0
O A:THR433 4.8 27.7 1.0

Calcium binding site 5 out of 6 in 4jcm

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Calcium binding site 5 out of 6 in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution


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 Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:58.2
occ:1.00
 O A:HOH1205 3.5 61.7 1.0
NE2 A:HIS195 3.6 22.9 1.0
OH A:TYR165 3.7 22.0 1.0
O A:HOH846 3.7 27.9 1.0
CE1 A:TYR165 3.9 18.5 1.0
CB A:PHE197 4.1 18.6 1.0
CZ A:TYR165 4.3 19.0 1.0
CD2 A:HIS195 4.4 19.1 1.0
CG A:PHE197 4.5 22.2 1.0
CE1 A:HIS195 4.6 23.5 1.0
CB A:ASN163 4.7 17.4 1.0
ND2 A:ASN163 4.7 26.4 1.0
CD2 A:PHE197 4.8 26.7 1.0
CG A:ASN163 4.9 21.6 1.0
O A:ASN163 4.9 21.0 1.0

Calcium binding site 6 out of 6 in 4jcm

Go back to Calcium Binding Sites List in 4jcm
Calcium binding site 6 out of 6 in the Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution


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 Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:33.1
occ:1.00
 O A:HIS224 2.4 15.7 1.0
O A:HOH947 2.4 28.7 1.0
OD1 A:ASN136 2.5 20.1 1.0
O A:HOH828 2.5 21.8 1.0
O A:HOH832 2.5 17.6 1.0
O A:ILE181 2.6 19.5 1.0
CG A:ASN136 3.5 21.9 1.0
C A:HIS224 3.6 18.3 1.0
C A:ILE181 3.7 16.8 1.0
ND2 A:ASN136 4.0 23.0 1.0
CG A:MET225 4.2 16.1 1.0
CA A:ILE181 4.3 17.1 1.0
CB A:HIS224 4.4 17.6 1.0
CA A:MET225 4.4 14.3 1.0
NE2 A:GLN193 4.4 18.6 1.0
N A:MET225 4.4 15.7 1.0
OG A:SER190 4.6 26.4 1.0
O A:ASN136 4.6 15.8 1.0
CA A:HIS224 4.6 19.6 1.0
CG2 A:ILE181 4.6 16.8 1.0
OE1 A:GLN193 4.7 19.4 1.0
CB A:SER190 4.8 21.3 1.0
CB A:ASN136 4.8 17.1 1.0
N A:TYR182 4.8 18.4 1.0
O A:SER180 4.9 19.8 0.6
CB A:MET225 4.9 16.1 1.0
O A:SER180 5.0 24.9 0.4

Reference:

L.Wu, D.Yang, J.Li, J.Zhou, J.Wu. The Crystal Structure of Gamma-Cgtase From Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution. To Be Published.
Page generated: Sun Jul 14 08:27:29 2024

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