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Calcium in PDB 3rup: Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions

Enzymatic activity of Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions

All present enzymatic activity of Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions:
6.3.4.14; 6.4.1.2;

Protein crystallography data

The structure of Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions, PDB code: 3rup was solved by C.Y.Chou, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.180, 58.843, 85.083, 90.00, 94.24, 90.00
R / Rfree (%) 17.1 / 22.7

Other elements in 3rup:

The structure of Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions (pdb code 3rup). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions, PDB code: 3rup:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3rup

Go back to Calcium Binding Sites List in 3rup
Calcium binding site 1 out of 4 in the Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions


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 E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:12.1
occ:1.00
 O2A A:ADP1002 2.2 13.4 1.0
O3B A:ADP1002 2.3 13.3 1.0
O A:HOH619 2.3 30.2 1.0
OE1 A:GLU288 2.3 19.4 1.0
OE1 A:GLU276 2.3 14.7 1.0
O A:HOH530 2.4 8.8 1.0
CD A:GLU276 3.3 13.5 1.0
PB A:ADP1002 3.5 14.9 1.0
PA A:ADP1002 3.5 13.7 1.0
CD A:GLU288 3.5 18.6 1.0
OE2 A:GLU276 3.5 15.2 1.0
O3A A:ADP1002 3.8 13.6 1.0
O A:HOH553 3.9 19.3 1.0
O2B A:ADP1002 4.0 15.8 1.0
O A:HOH459 4.1 13.8 1.0
OE2 A:GLU288 4.3 22.4 1.0
CE1 A:HIS209 4.4 12.7 1.0
NZ A:LYS238 4.4 13.1 1.0
C5' A:ADP1002 4.5 14.1 1.0
O5' A:ADP1002 4.5 13.7 1.0
CB A:GLU288 4.6 15.2 1.0
CG A:GLU288 4.6 17.2 1.0
O1A A:ADP1002 4.6 14.2 1.0
CG A:GLU276 4.6 11.6 1.0
O3' A:ADP1002 4.7 15.4 1.0
O1B A:ADP1000 4.8 18.5 1.0
CE A:LYS238 4.8 12.3 1.0
O1B A:ADP1002 4.8 12.6 1.0
ND2 A:ASN290 4.8 17.4 1.0
CB A:GLU276 5.0 12.9 1.0

Calcium binding site 2 out of 4 in 3rup

Go back to Calcium Binding Sites List in 3rup
Calcium binding site 2 out of 4 in the Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions


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 E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:17.3
occ:1.00
 OE2 A:GLU288 2.3 22.4 1.0
O A:HOH538 2.3 23.3 1.0
OD1 A:ASN290 2.4 14.4 1.0
O A:HOH531 2.4 14.4 1.0
O A:HOH486 2.6 12.8 1.0
OE2 A:GLU87 2.7 20.4 1.0
OE1 A:GLU87 2.8 16.6 1.0
CD A:GLU87 3.1 17.1 1.0
CD A:GLU288 3.3 18.6 1.0
CG A:ASN290 3.6 14.3 1.0
CG A:GLU288 4.0 17.2 1.0
O A:HOH899 4.0 35.3 1.0
OE1 A:GLU288 4.2 19.4 1.0
CA A:ASN290 4.4 13.7 1.0
O A:MET289 4.4 15.1 1.0
NH2 A:ARG292 4.4 12.1 1.0
ND2 A:ASN290 4.4 17.4 1.0
CB A:ASN290 4.5 13.6 1.0
O A:HOH718 4.5 22.5 1.0
CG A:GLU87 4.5 12.8 1.0
N7 A:ADP1000 4.6 22.6 1.0
O A:GLY163 4.6 17.2 1.0
O2B A:ADP1002 4.6 15.8 1.0
N6 A:ADP1000 4.8 23.0 1.0
O A:HOH459 4.8 13.8 1.0
O A:GLY114 4.8 18.5 1.0
NE A:ARG292 4.8 12.6 1.0
N A:ASN290 4.8 14.4 1.0
C A:MET289 4.9 14.9 1.0

Calcium binding site 3 out of 4 in 3rup

Go back to Calcium Binding Sites List in 3rup
Calcium binding site 3 out of 4 in the Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions


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 E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1005

b:13.0
occ:1.00
 O B:HOH623 2.2 32.0 1.0
O2B B:ADP1001 2.2 17.6 1.0
O2A B:ADP1001 2.2 17.6 1.0
OE1 B:GLU276 2.3 12.7 1.0
O B:HOH545 2.3 19.2 1.0
OE1 B:GLU288 2.3 21.4 1.0
CD B:GLU276 3.2 13.4 1.0
PB B:ADP1001 3.4 16.9 1.0
OE2 B:GLU276 3.5 14.1 1.0
PA B:ADP1001 3.5 16.4 1.0
CD B:GLU288 3.6 17.3 1.0
O3A B:ADP1001 3.8 15.7 1.0
O3B B:ADP1001 4.0 17.4 1.0
O B:HOH665 4.1 21.0 1.0
O B:HOH536 4.2 20.6 1.0
OE2 B:GLU288 4.3 18.5 1.0
NZ B:LYS238 4.4 14.1 1.0
CE1 B:HIS209 4.4 13.2 1.0
C5' B:ADP1001 4.4 15.7 1.0
O5' B:ADP1001 4.4 15.9 1.0
CB B:GLU288 4.6 16.6 1.0
CG B:GLU276 4.6 11.0 1.0
O1A B:ADP1001 4.6 16.1 1.0
CG B:GLU288 4.6 16.9 1.0
O1B B:ADP1001 4.7 17.7 1.0
O3' B:ADP1001 4.7 19.1 1.0
CE B:LYS238 4.7 12.8 1.0
O1B B:ADP1003 4.7 19.5 1.0
ND2 B:ASN290 4.9 19.6 1.0
CB B:GLU276 4.9 11.4 1.0

Calcium binding site 4 out of 4 in 3rup

Go back to Calcium Binding Sites List in 3rup
Calcium binding site 4 out of 4 in the Crystal Structure of E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions


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 E.Coli Biotin Carboxylase in Complex with Two Adp and Two Ca Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1007

b:25.1
occ:1.00
 OE2 B:GLU288 2.3 18.5 1.0
O B:HOH492 2.5 14.2 1.0
OD1 B:ASN290 2.5 19.8 1.0
O B:HOH622 2.6 16.0 1.0
O B:HOH540 2.6 28.2 1.0
OE2 B:GLU87 2.9 23.1 1.0
OE1 B:GLU87 2.9 20.6 1.0
CD B:GLU87 3.2 19.5 1.0
CD B:GLU288 3.3 17.3 1.0
CG B:ASN290 3.7 17.5 1.0
CG B:GLU288 4.0 16.9 1.0
O B:HOH758 4.0 47.4 1.0
OE1 B:GLU288 4.2 21.4 1.0
O B:MET289 4.3 16.5 1.0
O B:GLY163 4.4 20.3 1.0
CA B:ASN290 4.4 15.4 1.0
N7 B:ADP1003 4.5 25.2 1.0
O3B B:ADP1001 4.5 17.4 1.0
ND2 B:ASN290 4.5 19.6 1.0
NH2 B:ARG292 4.6 14.1 1.0
CB B:ASN290 4.6 15.5 1.0
O B:HOH635 4.6 17.8 1.0
N6 B:ADP1003 4.7 25.1 1.0
CG B:GLU87 4.7 18.2 1.0
O B:GLY114 4.8 22.7 1.0
O B:HOH536 4.8 20.6 1.0
C B:MET289 4.9 16.3 1.0
N B:ASN290 4.9 15.7 1.0
NE B:ARG292 5.0 13.0 1.0

Reference:

C.Y.Chou, L.Tong. Structural and Biochemical Studies on the Regulation of Biotin Carboxylase By Substrate Inhibition and Dimerization. J.Biol.Chem. V. 286 24417 2011.
ISSN: ISSN 0021-9258
PubMed: 21592965
DOI: 10.1074/JBC.M111.220517
Page generated: Sat Jul 13 18:13:05 2024

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