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Magnesium in PDB 7kct: Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-)

Enzymatic activity of Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-)

All present enzymatic activity of Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-):
6.4.1.7;

Protein crystallography data

The structure of Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-), PDB code: 7kct was solved by G.K.Buhrman, R.B.Rose, P.Enriquez, V.Truong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.10 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.282, 86.878, 86.105, 90, 113.65, 90
R / Rfree (%) 17.4 / 21.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-) (pdb code 7kct). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-), PDB code: 7kct:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7kct

Go back to Magnesium Binding Sites List in 7kct
Magnesium binding site 1 out of 2 in the Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:47.5
occ:1.00
 O2B A:ADP501 1.8 36.1 1.0
O A:HOH617 1.9 49.7 1.0
OE2 A:GLU287 2.1 56.0 1.0
OE2 A:GLU274 2.2 43.6 1.0
O1A A:ADP501 2.3 34.4 1.0
O A:HOH658 2.4 48.6 1.0
CD A:GLU287 3.1 53.2 1.0
PB A:ADP501 3.1 42.4 1.0
CD A:GLU274 3.3 46.4 1.0
PA A:ADP501 3.3 40.4 1.0
HG2 A:GLU287 3.4 51.5 1.0
O3B A:ADP501 3.5 56.0 1.0
HE1 A:HIS207 3.6 51.3 1.0
OE1 A:GLU274 3.6 51.8 1.0
CG A:GLU287 3.8 42.9 1.0
O3A A:ADP501 3.8 43.4 1.0
OE1 A:GLU287 3.9 55.7 1.0
H5'1 A:ADP501 4.1 53.8 1.0
HZ3 A:LYS236 4.1 50.6 1.0
HG3 A:GLU287 4.2 51.5 1.0
HD21 A:ASN289 4.2 58.0 1.0
OD1 A:ASN289 4.3 53.7 1.0
O5' A:ADP501 4.4 42.3 1.0
O1B A:ADP501 4.4 48.1 1.0
CE1 A:HIS207 4.5 42.7 1.0
O2A A:ADP501 4.6 45.8 1.0
CG A:GLU274 4.6 39.9 1.0
HE3 A:LYS236 4.6 48.0 1.0
C5' A:ADP501 4.7 44.8 1.0
HB2 A:GLU274 4.8 37.2 1.0
HE2 A:LYS115 4.8 59.7 1.0
HD12 A:ILE286 4.8 38.8 1.0
ND2 A:ASN289 4.8 48.4 1.0
HG3 A:GLU274 4.8 47.9 1.0
NZ A:LYS236 4.8 42.1 1.0
HZ1 A:LYS236 4.9 50.6 1.0
HB3 A:GLU274 4.9 37.2 1.0
H3' A:ADP501 5.0 49.9 1.0
CG A:ASN289 5.0 44.3 1.0

Magnesium binding site 2 out of 2 in 7kct

Go back to Magnesium Binding Sites List in 7kct
Magnesium binding site 2 out of 2 in the Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase (Ogc) Biotin Carboxylase (Bc) Domain Dimer in Complex with Adenosine 5'-Diphosphate Magnesium Salt (Mgadp), Adenosine 5'- Diphosphate (Adp, and Bicarbonate Anion (Hydrogen Carbonate/HCO3-) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:48.3
occ:1.00
 O2B B:ADP502 2.0 49.0 1.0
OE2 B:GLU287 2.1 51.8 1.0
O B:HOH723 2.1 48.5 1.0
O B:HOH640 2.2 52.5 1.0
O2A B:ADP502 2.2 45.7 1.0
OE1 B:GLU274 2.4 52.5 1.0
CD B:GLU287 3.2 55.3 1.0
CD B:GLU274 3.2 42.4 1.0
OE2 B:GLU274 3.2 47.5 1.0
PB B:ADP502 3.4 54.1 1.0
HE1 B:HIS207 3.4 47.2 1.0
PA B:ADP502 3.4 46.5 1.0
HG2 B:GLU287 3.6 56.7 1.0
H5'2 B:ADP502 3.7 55.1 1.0
O3B B:ADP502 3.9 54.1 1.0
CG B:GLU287 4.0 47.2 1.0
OE1 B:GLU287 4.0 63.7 1.0
O B:HOH610 4.1 50.5 1.0
O3A B:ADP502 4.1 55.5 1.0
HZ2 B:LYS236 4.2 57.2 1.0
HE3 B:LYS236 4.3 46.1 1.0
HG3 B:GLU287 4.3 56.7 1.0
CE1 B:HIS207 4.3 39.3 1.0
C5' B:ADP502 4.4 45.9 1.0
OD1 B:ASN289 4.4 49.9 1.0
HO3' B:ADP502 4.4 55.1 1.0
HD21 B:ASN289 4.6 55.4 1.0
H5'1 B:ADP502 4.6 55.1 1.0
CG B:GLU274 4.6 41.8 1.0
O5' B:ADP502 4.6 50.1 1.0
O1A B:ADP502 4.7 51.2 1.0
O1B B:ADP502 4.7 53.4 1.0
HZ3 B:LYS236 4.8 57.2 1.0
NZ B:LYS236 4.8 47.6 1.0
HG3 B:GLU274 4.9 50.1 1.0
HB3 B:GLU274 4.9 43.9 1.0
CE B:LYS236 5.0 38.4 1.0
H3' B:ADP502 5.0 58.0 1.0

Reference:

G.Buhrman, P.Enriquez, L.Dillard, H.Baer, V.Truong, A.M.Grunden, R.B.Rose. Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer From Hydrogenobacter Thermophilus 2-Oxoglutarate Carboxylase. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33464881
DOI: 10.1021/ACS.BIOCHEM.0C00815
Page generated: Wed Oct 2 22:13:18 2024

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