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Magnesium in PDB 6r29: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate:
1.2.4.2; 2.2.1.5; 2.3.1.61; 4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate, PDB code: 6r29 was solved by T.Wagner, P.M.Alzari, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.98 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.470, 108.170, 120.540, 90.00, 103.78, 90.00
R / Rfree (%) 15.3 / 16.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate (pdb code 6r29). 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 Kgd Cocrystallized with Succinylphosphonate, PDB code: 6r29:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6r29

Go back to Magnesium Binding Sites List in 6r29
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate


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 Kgd Cocrystallized with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:19.4
occ:1.00
 O2B A:QSP2001 2.1 17.3 1.0
O1A A:QSP2001 2.1 17.5 1.0
OD1 A:ASP645 2.1 19.8 1.0
OD1 A:ASN678 2.1 18.3 1.0
O A:ILE680 2.1 18.4 1.0
O A:HOH2288 2.2 16.7 1.0
CG A:ASN678 3.1 19.4 1.0
CG A:ASP645 3.2 21.3 1.0
PB A:QSP2001 3.2 18.1 1.0
PA A:QSP2001 3.2 18.0 1.0
O3A A:QSP2001 3.3 16.8 1.0
C A:ILE680 3.4 19.9 1.0
ND2 A:ASN678 3.5 19.0 1.0
OD2 A:ASP645 3.7 23.6 1.0
O1B A:QSP2001 3.8 18.0 1.0
N A:ASP645 4.0 18.0 1.0
O7 A:QSP2001 4.1 17.9 1.0
N A:ILE680 4.1 17.6 1.0
CA A:GLY681 4.2 17.0 1.0
N A:GLY681 4.2 17.9 1.0
N A:ASN678 4.3 17.9 1.0
O2A A:QSP2001 4.4 17.5 1.0
CA A:ILE680 4.4 17.8 1.0
O A:HOH2433 4.4 17.9 1.0
CB A:ASP645 4.4 17.9 1.0
O A:VAL676 4.4 20.5 1.0
N A:ALA646 4.4 16.6 1.0
CB A:ASN678 4.4 18.3 1.0
O3B A:QSP2001 4.5 18.6 1.0
CG2 A:ILE680 4.5 20.5 1.0
CA A:ASP645 4.6 17.2 1.0
CA A:ASN678 4.7 17.8 1.0
N A:GLN679 4.8 18.0 1.0
C A:ASN678 4.8 21.6 1.0
C A:GLY644 4.8 20.5 1.0
CA A:GLY644 4.9 16.9 1.0

Magnesium binding site 2 out of 4 in 6r29

Go back to Magnesium Binding Sites List in 6r29
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate


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 Kgd Cocrystallized with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:26.9
occ:1.00
 O A:ILE1060 2.3 31.4 1.0
OD2 A:ASP1004 2.4 36.0 1.0
O A:HIS1055 2.4 25.6 1.0
O A:HOH2656 2.5 39.8 1.0
OD1 A:ASP1058 2.5 31.7 1.0
OD1 A:ASP1004 2.7 33.2 1.0
CG A:ASP1004 2.8 34.5 1.0
O A:HOH2493 2.9 39.8 1.0
C A:ILE1060 3.5 31.8 1.0
CG A:ASP1058 3.5 33.8 1.0
C A:HIS1055 3.6 26.0 1.0
OD2 A:ASP1058 3.8 40.9 1.0
N A:ILE1060 4.0 32.4 1.0
ND1 A:HIS1055 4.1 26.4 1.0
CE1 A:HIS1055 4.1 25.9 1.0
CA A:ILE1060 4.2 32.2 1.0
CA A:HIS1055 4.2 21.7 1.0
NE2 A:HIS1055 4.3 25.5 1.0
CG A:HIS1055 4.3 24.0 1.0
O A:HOH2177 4.3 35.1 1.0
CB A:ASP1004 4.3 23.7 1.0
CD2 A:HIS1055 4.4 26.1 1.0
CB A:ILE1060 4.5 36.2 1.0
N A:GLN1061 4.5 23.8 1.0
NE2 A:GLN1061 4.5 47.9 1.0
CA A:GLN1061 4.6 24.2 1.0
N A:GLY1059 4.7 30.2 1.0
N A:GLY1056 4.7 23.5 1.0
O A:HOH2533 4.7 39.9 1.0
N A:ASP1058 4.9 27.6 1.0
CB A:ASP1058 4.9 29.6 1.0
C A:GLY1059 4.9 37.5 1.0
CA A:GLY1056 4.9 24.8 1.0
CB A:HIS1055 4.9 21.5 1.0
O A:HOH2591 4.9 40.2 1.0
CD A:GLN1061 5.0 53.5 1.0
N A:ARG1062 5.0 21.2 1.0

Magnesium binding site 3 out of 4 in 6r29

Go back to Magnesium Binding Sites List in 6r29
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate


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 Kgd Cocrystallized with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:19.9
occ:1.00
 OD1 B:ASP645 2.1 21.2 1.0
O1A B:QSP2001 2.1 18.9 1.0
OD1 B:ASN678 2.1 19.7 1.0
O B:ILE680 2.1 20.6 1.0
O2B B:QSP2001 2.1 18.8 1.0
O B:HOH2298 2.2 19.3 1.0
CG B:ASN678 3.1 22.7 1.0
CG B:ASP645 3.2 21.8 1.0
PB B:QSP2001 3.2 20.3 1.0
PA B:QSP2001 3.2 19.7 1.0
C B:ILE680 3.3 21.8 1.0
O3A B:QSP2001 3.4 19.7 1.0
ND2 B:ASN678 3.5 21.2 1.0
OD2 B:ASP645 3.7 22.3 1.0
O1B B:QSP2001 3.8 20.6 1.0
N B:ASP645 4.0 18.6 1.0
O7 B:QSP2001 4.1 19.2 1.0
N B:ILE680 4.1 20.5 1.0
CA B:GLY681 4.2 19.6 1.0
N B:GLY681 4.2 19.6 1.0
N B:ASN678 4.3 20.1 1.0
CA B:ILE680 4.3 19.5 1.0
CB B:ASP645 4.4 18.8 1.0
O2A B:QSP2001 4.4 18.6 1.0
O B:HOH2424 4.4 20.7 1.0
N B:ALA646 4.4 18.9 1.0
CB B:ASN678 4.4 21.0 1.0
O B:VAL676 4.4 22.4 1.0
CG2 B:ILE680 4.5 22.3 1.0
O3B B:QSP2001 4.5 20.4 1.0
CA B:ASP645 4.6 16.9 1.0
CA B:ASN678 4.7 20.2 1.0
N B:GLN679 4.7 20.1 1.0
C B:ASN678 4.8 22.7 1.0
C B:GLY644 4.9 21.1 1.0
CA B:GLY644 4.9 18.8 1.0

Magnesium binding site 4 out of 4 in 6r29

Go back to Magnesium Binding Sites List in 6r29
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate


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 Kgd Cocrystallized with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:29.7
occ:1.00
 O B:ILE1060 2.3 36.8 1.0
OD2 B:ASP1004 2.3 40.9 1.0
O B:HIS1055 2.5 28.2 1.0
OD1 B:ASP1058 2.5 36.0 1.0
OD1 B:ASP1004 2.6 38.4 1.0
O B:HOH2553 2.6 47.1 1.0
O B:HOH2523 2.7 42.5 1.0
CG B:ASP1004 2.8 36.9 1.0
C B:ILE1060 3.5 34.0 1.0
CG B:ASP1058 3.6 35.8 1.0
C B:HIS1055 3.6 27.2 1.0
N B:ILE1060 3.9 32.4 1.0
OD2 B:ASP1058 3.9 42.3 1.0
CE1 B:HIS1055 4.0 26.4 1.0
ND1 B:HIS1055 4.0 26.5 1.0
NE2 B:HIS1055 4.1 26.7 1.0
CA B:ILE1060 4.2 31.4 1.0
CG B:HIS1055 4.2 24.4 1.0
CA B:HIS1055 4.2 23.2 1.0
CB B:ASP1004 4.3 26.9 1.0
O B:HOH2231 4.3 38.7 1.0
CD2 B:HIS1055 4.3 26.4 1.0
NE2 B:GLN1061 4.4 42.6 1.0
N B:GLY1059 4.5 31.6 1.0
CB B:ILE1060 4.5 34.9 1.0
N B:GLN1061 4.5 26.5 1.0
CA B:GLN1061 4.7 25.4 1.0
N B:GLY1056 4.7 25.0 1.0
C B:GLY1059 4.7 38.4 1.0
O B:HOH2448 4.8 37.9 1.0
CB B:HIS1055 4.8 22.5 1.0
CB B:ASP1058 4.9 29.9 1.0
N B:ASP1058 4.9 26.6 1.0
N B:ARG1062 4.9 22.7 1.0
CA B:GLY1056 5.0 26.4 1.0
CA B:GLY1059 5.0 33.4 1.0

Reference:

T.Wagner, A.Boyko, P.M.Alzari, V.I.Bunik, M.Bellinzoni. Conformational Transitions in the Active Site of Mycobacterial 2-Oxoglutarate Dehydrogenase Upon Binding Phosphonate Analogues of 2-Oxoglutarate: From A Michaelis-Like Complex to Thdp Adducts. J.Struct.Biol. V. 208 182 2019.
ISSN: ESSN 1095-8657
PubMed: 31476368
DOI: 10.1016/J.JSB.2019.08.012
Page generated: Tue Oct 1 16:29:56 2024

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