Atomistry » Magnesium » PDB 7k06-7ked » 7kct
Atomistry »
  Magnesium »
    PDB 7k06-7ked »
      7kct »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy