Atomistry » Magnesium » PDB 2ybb-2yni » 2yic
Atomistry »
  Magnesium »
    PDB 2ybb-2yni »
      2yic »

Magnesium in PDB 2yic: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form):
4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form), PDB code: 2yic was solved by T.Wagner, M.Bellinzoni, A.M.Wehenkel, H.M.O'hare, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.20 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.539, 83.244, 158.610, 99.48, 99.06, 101.25
R / Rfree (%) 18.84 / 21.08

Other elements in 2yic:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) (pdb code 2yic). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form), PDB code: 2yic:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)


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 Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:10.3
occ:1.00
 O2A A:TPP2001 2.0 13.6 1.0
O A:HOH3083 2.1 17.8 1.0
OD1 A:ASP645 2.1 25.6 1.0
OD1 A:ASN678 2.1 22.0 1.0
O A:ILE680 2.2 19.2 1.0
O2B A:TPP2001 2.2 15.5 1.0
CG A:ASP645 3.1 24.4 1.0
CG A:ASN678 3.2 25.4 1.0
PA A:TPP2001 3.2 16.1 1.0
PB A:TPP2001 3.3 17.3 1.0
O3A A:TPP2001 3.4 16.1 1.0
C A:ILE680 3.4 18.8 1.0
OD2 A:ASP645 3.5 31.2 1.0
ND2 A:ASN678 3.7 16.0 1.0
O3B A:TPP2001 3.9 14.5 1.0
N A:ASP645 3.9 13.1 1.0
O7 A:TPP2001 4.0 17.0 1.0
N A:ILE680 4.1 17.2 1.0
N A:ASN678 4.2 17.3 1.0
N A:GLY681 4.3 12.2 1.0
O A:VAL676 4.3 18.6 1.0
CA A:GLY681 4.4 11.2 1.0
CB A:ASP645 4.4 12.4 1.0
N A:ALA646 4.4 11.4 1.0
CA A:ILE680 4.4 17.1 1.0
O1A A:TPP2001 4.4 16.5 1.0
O A:HOH3048 4.4 17.8 1.0
CB A:ASN678 4.5 8.8 1.0
O1B A:TPP2001 4.6 20.2 1.0
CA A:ASP645 4.6 11.6 1.0
N A:GLN679 4.6 17.9 1.0
CG2 A:ILE680 4.7 20.8 1.0
CA A:ASN678 4.7 15.7 1.0
C A:GLY644 4.7 19.0 1.0
CA A:GLY644 4.7 17.6 1.0
C A:ASN678 4.8 21.5 1.0

Magnesium binding site 2 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)


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 Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:11.8
occ:1.00
 O2A B:TPP2001 2.1 10.4 1.0
OD1 B:ASP645 2.1 22.5 1.0
OD1 B:ASN678 2.1 21.6 1.0
O2B B:TPP2001 2.2 15.3 1.0
O B:HOH3084 2.2 10.7 1.0
O B:ILE680 2.2 21.3 1.0
CG B:ASP645 3.1 22.5 1.0
PA B:TPP2001 3.2 12.3 1.0
CG B:ASN678 3.2 26.3 1.0
PB B:TPP2001 3.3 16.2 1.0
O3A B:TPP2001 3.3 15.6 1.0
C B:ILE680 3.4 21.2 1.0
OD2 B:ASP645 3.6 23.2 1.0
ND2 B:ASN678 3.6 11.9 1.0
N B:ASP645 3.9 13.8 1.0
O3B B:TPP2001 3.9 16.4 1.0
O7 B:TPP2001 4.0 15.8 1.0
N B:ILE680 4.1 17.9 1.0
N B:ASN678 4.2 15.3 1.0
N B:GLY681 4.3 18.3 1.0
CA B:GLY681 4.3 17.9 1.0
CB B:ASP645 4.3 13.5 1.0
O B:VAL676 4.4 17.1 1.0
N B:ALA646 4.4 14.3 1.0
O1A B:TPP2001 4.4 10.9 1.0
CA B:ILE680 4.4 16.5 1.0
O B:HOH3104 4.4 15.7 1.0
CB B:ASN678 4.5 16.1 1.0
O1B B:TPP2001 4.6 14.1 1.0
CA B:ASP645 4.6 13.1 1.0
N B:GLN679 4.6 19.8 1.0
CG2 B:ILE680 4.7 17.1 1.0
C B:GLY644 4.7 15.6 1.0
CA B:ASN678 4.7 16.3 1.0
CA B:GLY644 4.7 16.1 1.0
C B:ASN678 4.8 22.9 1.0

Magnesium binding site 3 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:10.4
occ:1.00
 OD1 C:ASN678 2.1 17.6 1.0
O C:ILE680 2.1 20.6 1.0
O2A C:TPP2001 2.1 13.4 1.0
OD1 C:ASP645 2.2 20.3 1.0
O2B C:TPP2001 2.2 20.5 1.0
O C:HOH3073 2.2 17.8 1.0
CG C:ASN678 3.1 24.7 1.0
CG C:ASP645 3.1 24.7 1.0
PA C:TPP2001 3.3 15.3 1.0
PB C:TPP2001 3.3 17.6 1.0
C C:ILE680 3.3 20.2 1.0
O3A C:TPP2001 3.4 17.3 1.0
OD2 C:ASP645 3.6 29.2 1.0
ND2 C:ASN678 3.6 15.9 1.0
O3B C:TPP2001 3.9 18.6 1.0
N C:ASP645 4.0 12.7 1.0
O7 C:TPP2001 4.1 18.2 1.0
N C:ILE680 4.1 15.6 1.0
N C:ASN678 4.2 17.8 1.0
N C:GLY681 4.2 16.4 1.0
CA C:GLY681 4.3 15.9 1.0
CA C:ILE680 4.3 15.5 1.0
O C:HOH3100 4.3 24.9 1.0
O C:VAL676 4.4 22.8 1.0
CB C:ASP645 4.4 12.8 1.0
N C:ALA646 4.4 12.7 1.0
CB C:ASN678 4.4 14.9 1.0
O1A C:TPP2001 4.5 14.8 1.0
CG2 C:ILE680 4.6 16.4 1.0
O1B C:TPP2001 4.6 19.9 1.0
N C:GLN679 4.6 16.0 1.0
CA C:ASN678 4.7 17.2 1.0
CA C:ASP645 4.7 11.6 1.0
C C:ASN678 4.7 19.9 1.0
C C:GLY644 4.8 16.0 1.0
CA C:GLY644 4.8 14.4 1.0

Magnesium binding site 4 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:12.5
occ:1.00
 O2A D:TPP2001 2.1 15.2 1.0
O2B D:TPP2001 2.1 15.7 1.0
O D:ILE680 2.1 18.1 1.0
OD1 D:ASN678 2.1 17.8 1.0
OD1 D:ASP645 2.2 21.7 1.0
O D:HOH3067 2.3 19.2 1.0
CG D:ASP645 3.2 22.5 1.0
PA D:TPP2001 3.2 15.2 1.0
CG D:ASN678 3.2 24.1 1.0
PB D:TPP2001 3.2 16.0 1.0
O3A D:TPP2001 3.3 19.7 1.0
C D:ILE680 3.3 19.1 1.0
OD2 D:ASP645 3.6 21.4 1.0
ND2 D:ASN678 3.6 16.4 1.0
O3B D:TPP2001 3.9 16.6 1.0
O7 D:TPP2001 4.0 16.7 1.0
N D:ASP645 4.0 14.0 1.0
N D:ILE680 4.1 14.2 1.0
O D:HOH3084 4.2 20.0 1.0
N D:GLY681 4.2 17.4 1.0
CA D:GLY681 4.2 17.4 1.0
N D:ASN678 4.3 15.6 1.0
CA D:ILE680 4.3 13.6 1.0
N D:ALA646 4.4 12.7 1.0
O1A D:TPP2001 4.4 12.4 1.0
O D:VAL676 4.4 22.8 1.0
CB D:ASP645 4.4 15.5 1.0
CB D:ASN678 4.5 20.1 1.0
O1B D:TPP2001 4.5 17.0 1.0
CG2 D:ILE680 4.6 14.4 1.0
N D:GLN679 4.7 15.2 1.0
CA D:ASP645 4.7 14.2 1.0
CA D:ASN678 4.7 15.6 1.0
C D:GLY644 4.8 16.9 1.0
CA D:GLY644 4.8 15.5 1.0
C D:ASN678 4.8 18.4 1.0

Reference:

T.Wagner, M.Bellinzoni, A.M.Wehenkel, H.M.O'hare, P.M.Alzari. Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism. Chem.Biol. V. 18 1011 2011.
ISSN: ISSN 1074-5521
PubMed: 21867916
DOI: 10.1016/J.CHEMBIOL.2011.06.004
Page generated: Wed Aug 14 07:32:19 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy