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Calcium in PDB 3tkk: Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis

Protein crystallography data

The structure of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis, PDB code: 3tkk was solved by M.Qian, Q.Huang, G.Wu, L.Lai, Y.Tang, J.Pei, M.Kusunoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.230, 152.882, 100.255, 90.00, 99.49, 90.00
R / Rfree (%) 17.4 / 23.7

Other elements in 3tkk:

The structure of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis (pdb code 3tkk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis, PDB code: 3tkk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3tkk

Go back to Calcium Binding Sites List in 3tkk
Calcium binding site 1 out of 5 in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca300

b:5.8
occ:1.00
O A:HOH517 2.0 2.0 1.0
O A:HOH717 2.2 5.5 1.0
O A:THR254 2.2 40.0 1.0
O A:LYS251 2.3 39.8 1.0
C A:THR254 3.4 40.3 1.0
C A:LYS251 3.4 40.7 1.0
CA A:ASP255 4.0 44.2 1.0
N A:ASP255 4.2 41.7 1.0
O A:HOH818 4.3 19.0 1.0
CA A:LYS251 4.3 37.1 1.0
N A:THR254 4.3 38.9 1.0
N A:LYS252 4.4 40.3 1.0
CA A:THR254 4.5 39.3 1.0
CA A:LYS252 4.5 44.0 1.0
CG A:LYS251 4.7 43.2 1.0
O A:PHE250 4.7 37.7 1.0
C A:LYS252 4.7 44.7 1.0
N A:HIS253 4.9 41.7 1.0
C A:ASP255 4.9 42.8 1.0

Calcium binding site 2 out of 5 in 3tkk

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Calcium binding site 2 out of 5 in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:6.9
occ:1.00
OD1 A:ASN155 2.3 17.4 1.0
OD2 A:ASP182 2.3 17.9 1.0
OD1 A:ASP157 2.3 19.8 1.0
O A:HOH340 2.5 15.6 1.0
O A:HOH368 2.5 13.8 1.0
O A:HOH343 2.5 4.2 1.0
OD2 A:ASP157 2.6 20.4 1.0
CG A:ASP157 2.8 17.1 1.0
CG A:ASN155 3.2 21.0 1.0
CG A:ASP182 3.3 17.0 1.0
ND2 A:ASN155 3.4 20.2 1.0
OD2 A:CSD37 3.5 38.4 0.7
ZN A:ZN301 3.5 7.4 0.7
OD1 A:ASP182 3.7 22.1 1.0
NE2 A:HIS184 4.3 20.2 1.0
OE2 A:GLU191 4.3 18.1 1.0
CE1 A:HIS184 4.3 17.1 1.0
OD2 A:ASP278 4.4 20.8 1.0
CB A:ASP157 4.4 16.1 1.0
ND2 A:ASN58 4.4 43.0 1.0
O A:HOH707 4.5 23.3 1.0
OE1 A:GLU191 4.6 16.0 1.0
CB A:ASP182 4.6 17.2 1.0
CB A:ASN155 4.6 19.4 1.0
CG2 A:VAL134 4.6 17.2 1.0
OD1 A:ASP278 4.6 29.9 1.0
SG A:CSD37 4.8 46.4 0.7
CD A:GLU191 4.9 20.7 1.0
O A:HOH445 4.9 17.5 1.0
CA A:GLY133 4.9 15.9 1.0
CG A:ASP278 4.9 27.8 1.0
O A:GLY133 4.9 15.7 1.0
C A:GLY133 4.9 16.8 1.0

Calcium binding site 3 out of 5 in 3tkk

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Calcium binding site 3 out of 5 in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:5.8
occ:1.00
OD2 B:ASP182 2.3 36.7 1.0
ND2 B:ASN155 2.3 33.5 1.0
OD2 B:ASP157 2.4 37.8 1.0
O B:HOH708 2.4 6.5 1.0
OD1 B:ASP157 2.5 37.7 1.0
O B:HOH709 2.6 4.3 1.0
CG B:ASP157 2.8 36.6 1.0
CG B:ASN155 3.3 35.6 1.0
CG B:ASP182 3.4 35.4 1.0
OD1 B:ASN155 3.5 37.8 1.0
ZN B:ZN303 3.7 8.6 1.0
OD2 B:CSD37 4.0 54.2 1.0
OD1 B:ASP182 4.1 35.9 1.0
OE1 B:GLU191 4.2 36.7 1.0
NE2 B:HIS184 4.4 38.1 1.0
CE1 B:HIS184 4.4 37.2 1.0
CB B:ASP157 4.4 34.5 1.0
OE2 B:GLU191 4.4 37.1 1.0
CB B:ASP182 4.5 35.2 1.0
ND2 B:ASN58 4.5 61.5 1.0
OD2 B:ASP278 4.5 51.1 1.0
CG2 B:VAL134 4.6 34.2 1.0
CB B:ASN155 4.7 37.0 1.0
CD B:GLU191 4.8 36.1 1.0
O B:GLY133 4.8 36.9 1.0
C B:GLY133 4.9 34.5 1.0
CA B:GLY133 4.9 33.8 1.0

Calcium binding site 4 out of 5 in 3tkk

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Calcium binding site 4 out of 5 in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca306

b:4.2
occ:1.00
O C:HOH628 2.3 8.2 1.0
OD2 C:ASP182 2.3 28.4 1.0
ND2 C:ASN155 2.3 24.8 1.0
OD2 C:ASP157 2.4 26.6 1.0
OD1 C:ASP157 2.4 28.1 1.0
O C:HOH710 2.5 12.3 1.0
O C:HOH832 2.7 5.7 1.0
CG C:ASP157 2.8 27.4 1.0
CG C:ASN155 3.2 27.5 1.0
OD1 C:ASN155 3.4 34.5 1.0
CG C:ASP182 3.4 29.1 1.0
ZN C:ZN305 3.7 2.0 0.7
OD2 C:CSD37 3.9 42.6 0.7
OD1 C:ASP182 4.0 30.9 1.0
OE2 C:GLU191 4.2 27.9 1.0
O C:HOH454 4.2 9.3 1.0
CB C:ASP157 4.3 24.6 1.0
OE1 C:GLU191 4.4 27.4 1.0
CE1 C:HIS184 4.4 29.6 1.0
OD2 C:ASP278 4.5 40.2 1.0
NE2 C:HIS184 4.5 30.6 1.0
CB C:ASP182 4.6 27.4 1.0
CG2 C:VAL134 4.6 25.4 1.0
OD1 C:ASN58 4.6 55.5 1.0
CB C:ASN155 4.7 24.4 1.0
CD C:GLU191 4.8 26.5 1.0
O C:GLY133 4.8 24.0 1.0
CA C:GLY133 4.9 24.3 1.0
C C:GLY133 4.9 25.7 1.0

Calcium binding site 5 out of 5 in 3tkk

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Calcium binding site 5 out of 5 in the Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of A Recombinant Predicted Acetamidase/ Formamidase From the Thermophile Thermoanaerobacter Tengcongensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca308

b:7.1
occ:1.00
O D:HOH345 2.2 2.0 1.0
O D:HOH835 2.2 14.7 1.0
OD2 D:ASP182 2.3 36.2 1.0
OD1 D:ASN155 2.3 35.2 1.0
OD1 D:ASP157 2.3 38.5 1.0
O D:HOH337 2.5 16.3 1.0
OD2 D:ASP157 2.6 35.6 1.0
CG D:ASP157 2.8 36.4 1.0
CG D:ASP182 3.3 36.0 1.0
CG D:ASN155 3.3 37.3 1.0
OD2 D:CSD37 3.4 58.0 1.0
ZN D:ZN307 3.7 12.9 1.0
ND2 D:ASN155 3.7 39.2 1.0
OD1 D:ASP182 3.7 36.9 1.0
OE2 D:GLU191 4.2 34.2 1.0
CE1 D:HIS184 4.3 34.6 1.0
NE2 D:HIS184 4.3 35.4 1.0
CB D:ASP157 4.4 34.4 1.0
CB D:ASP182 4.5 35.9 1.0
OE1 D:GLU191 4.5 32.4 1.0
CG2 D:VAL134 4.5 36.3 1.0
CB D:ASN155 4.7 37.8 1.0
OD1 D:ASN58 4.7 67.3 1.0
CD D:GLU191 4.8 33.5 1.0
OD2 D:ASP278 4.8 50.8 1.0
CA D:GLY133 4.8 35.2 1.0
ND2 D:ASN58 4.9 65.3 1.0
C D:GLY133 4.9 34.2 1.0
SG D:CSD37 5.0 67.2 1.0
O D:GLY133 5.0 34.1 1.0

Reference:

M.Qian, Q.Huang, G.Wu, L.Lai, Y.Tang, J.Pei, M.Kusunoki. Crystal Structure Analysis of A Recombinant Predicted Acetamidase/Formamidase From the Thermophile Thermoanaerobacter Tengcongensis. Protein J. V. 31 166 2012.
ISSN: ISSN 1572-3887
PubMed: 22207484
DOI: 10.1007/S10930-011-9387-0
Page generated: Sat Dec 12 04:31:47 2020

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