Magnesium in PDB 6r2d: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase:
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 After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase, PDB code: 6r2d 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) 33.44 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.840, 83.730, 160.570, 99.52, 98.94, 100.81
R / Rfree (%) 21.7 / 24.2

Other elements in 6r2d:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase 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 Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase (pdb code 6r2d). 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 After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase, PDB code: 6r2d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6r2d

Go back to Magnesium Binding Sites List in 6r2d
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:37.3
occ:1.00
 O1B A:ZP12001 2.1 38.5 1.0
O A:ILE680 2.1 39.1 1.0
O A:HOH2164 2.1 33.5 1.0
OD1 A:ASP645 2.2 42.0 1.0
O2A A:ZP12001 2.2 37.7 1.0
OD1 A:ASN678 2.2 48.0 1.0
CG A:ASN678 3.2 55.0 1.0
CG A:ASP645 3.2 43.1 1.0
PB A:ZP12001 3.2 43.2 1.0
PA A:ZP12001 3.2 37.6 1.0
C A:ILE680 3.3 40.1 1.0
O3A A:ZP12001 3.4 43.3 1.0
ND2 A:ASN678 3.6 45.0 1.0
OD2 A:ASP645 3.7 41.4 1.0
O3B A:ZP12001 3.9 42.0 1.0
N A:ILE680 4.0 39.5 1.0
N A:ASP645 4.1 37.2 1.0
O7 A:ZP12001 4.2 34.5 1.0
CA A:ILE680 4.2 38.6 1.0
N A:GLY681 4.3 36.7 1.0
N A:ASN678 4.4 41.4 1.0
O A:HOH2235 4.4 43.6 1.0
N A:ALA646 4.4 36.5 1.0
O A:VAL676 4.4 42.0 1.0
CA A:GLY681 4.4 37.5 1.0
CB A:ASP645 4.5 38.0 1.0
O2B A:ZP12001 4.5 44.0 1.0
CB A:ASN678 4.5 42.6 1.0
O1A A:ZP12001 4.5 43.0 1.0
CG2 A:ILE680 4.6 40.8 1.0
N A:GLN679 4.7 38.8 1.0
C A:ASN678 4.7 42.5 1.0
CA A:ASP645 4.7 36.4 1.0
CA A:ASN678 4.8 40.8 1.0
CA A:GLY644 4.8 40.5 1.0
C A:GLY644 4.9 42.8 1.0

Magnesium binding site 2 out of 4 in 6r2d

Go back to Magnesium Binding Sites List in 6r2d
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:36.7
occ:1.00
 O1B B:ZP12001 2.0 34.0 1.0
O B:HOH2217 2.0 34.4 1.0
OD1 B:ASN678 2.1 48.9 1.0
O B:ILE680 2.1 36.9 1.0
O2A B:ZP12001 2.2 38.4 1.0
OD1 B:ASP645 2.2 36.3 1.0
CG B:ASN678 3.1 45.7 1.0
PB B:ZP12001 3.1 37.7 1.0
PA B:ZP12001 3.2 40.8 1.0
CG B:ASP645 3.3 39.7 1.0
C B:ILE680 3.3 38.6 1.0
O3A B:ZP12001 3.4 43.0 1.0
ND2 B:ASN678 3.4 32.4 1.0
O3B B:ZP12001 3.8 38.9 1.0
OD2 B:ASP645 3.9 46.5 1.0
N B:ASP645 4.0 34.5 1.0
O7 B:ZP12001 4.1 35.8 1.0
N B:GLY681 4.2 36.2 1.0
N B:ILE680 4.2 36.4 1.0
CA B:GLY681 4.3 35.8 1.0
N B:ASN678 4.3 34.9 1.0
O B:HOH2245 4.3 41.8 1.0
O B:VAL676 4.3 44.0 1.0
CA B:ILE680 4.4 34.9 1.0
O2B B:ZP12001 4.4 39.6 1.0
CB B:ASN678 4.4 33.5 1.0
N B:ALA646 4.5 35.1 1.0
O1A B:ZP12001 4.5 41.1 1.0
CB B:ASP645 4.5 37.9 1.0
CG2 B:ILE680 4.6 34.3 1.0
CA B:GLY644 4.7 34.5 1.0
CA B:ASN678 4.7 35.4 1.0
CA B:ASP645 4.7 35.1 1.0
C B:GLY644 4.8 36.4 1.0
N B:GLN679 4.9 38.8 1.0
C B:ASN678 4.9 41.6 1.0

Magnesium binding site 3 out of 4 in 6r2d

Go back to Magnesium Binding Sites List in 6r2d
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:35.2
occ:1.00
 O1B C:ZP12001 2.0 39.9 1.0
O2A C:ZP12001 2.2 41.6 1.0
O C:HOH2127 2.2 32.4 1.0
O C:ILE680 2.2 44.7 1.0
OD1 C:ASP645 2.2 47.4 1.0
OD1 C:ASN678 2.2 53.8 1.0
PB C:ZP12001 3.1 44.5 1.0
PA C:ZP12001 3.2 40.9 1.0
CG C:ASN678 3.2 57.1 1.0
CG C:ASP645 3.3 48.6 1.0
O3A C:ZP12001 3.3 41.3 1.0
C C:ILE680 3.4 44.9 1.0
ND2 C:ASN678 3.5 44.3 1.0
OD2 C:ASP645 3.8 48.4 1.0
O3B C:ZP12001 3.8 41.3 1.0
N C:ASP645 4.1 40.3 1.0
N C:ILE680 4.1 44.7 1.0
O7 C:ZP12001 4.1 39.7 1.0
N C:GLY681 4.3 40.9 1.0
CA C:ILE680 4.3 42.9 1.0
N C:ASN678 4.3 44.9 1.0
O2B C:ZP12001 4.4 41.6 1.0
O C:HOH2250 4.4 49.1 1.0
O C:VAL676 4.4 49.9 1.0
CA C:GLY681 4.4 41.5 1.0
N C:ALA646 4.5 36.5 1.0
O1A C:ZP12001 4.5 44.5 1.0
CB C:ASN678 4.5 43.6 1.0
CB C:ASP645 4.5 40.0 1.0
CG2 C:ILE680 4.6 45.5 1.0
CA C:ASN678 4.8 44.6 1.0
N C:GLN679 4.8 43.3 1.0
CA C:ASP645 4.8 39.1 1.0
C C:ASN678 4.8 47.7 1.0
CA C:GLY644 4.8 44.2 1.0
C C:GLY644 4.9 46.9 1.0

Magnesium binding site 4 out of 4 in 6r2d

Go back to Magnesium Binding Sites List in 6r2d
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:40.8
occ:1.00
 O D:HOH2169 1.9 41.0 1.0
OD1 D:ASN678 2.0 52.3 1.0
O1B D:ZP12001 2.0 35.1 1.0
OD1 D:ASP645 2.1 42.9 1.0
O D:ILE680 2.2 39.5 1.0
O2A D:ZP12001 2.2 44.8 1.0
CG D:ASN678 3.0 50.5 1.0
PB D:ZP12001 3.2 40.3 1.0
PA D:ZP12001 3.2 42.7 1.0
CG D:ASP645 3.2 44.0 1.0
C D:ILE680 3.4 39.9 1.0
O3A D:ZP12001 3.4 42.1 1.0
ND2 D:ASN678 3.5 36.9 1.0
OD2 D:ASP645 3.8 50.4 1.0
O3B D:ZP12001 3.8 37.9 1.0
N D:ASP645 4.0 39.9 1.0
N D:ILE680 4.1 39.6 1.0
O7 D:ZP12001 4.2 41.5 1.0
N D:ASN678 4.2 37.9 1.0
N D:GLY681 4.3 35.0 1.0
O D:HOH2131 4.3 36.4 1.0
O D:VAL676 4.3 43.7 1.0
CA D:GLY681 4.3 35.2 1.0
CB D:ASN678 4.4 38.8 1.0
CA D:ILE680 4.4 38.2 1.0
CB D:ASP645 4.4 41.8 1.0
O2B D:ZP12001 4.5 42.6 1.0
N D:ALA646 4.5 38.9 1.0
O1A D:ZP12001 4.5 43.0 1.0
CG2 D:ILE680 4.6 38.6 1.0
CA D:ASN678 4.7 38.2 1.0
CA D:ASP645 4.7 40.4 1.0
N D:GLN679 4.7 39.6 1.0
CA D:GLY644 4.8 37.8 1.0
C D:GLY644 4.8 40.7 1.0
C D:ASN678 4.8 43.5 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: Mon Dec 14 23:55:34 2020

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