Atomistry » Magnesium » PDB 6qux-6r5i » 6r2a
Atomistry »
  Magnesium »
    PDB 6qux-6r5i »
      6r2a »

Magnesium in PDB 6r2a: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp):
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 Phosphonoethyl Ester (Pesp), PDB code: 6r2a 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) 40.37 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.480, 108.020, 120.530, 90.00, 103.55, 90.00
R / Rfree (%) 15.1 / 16.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp) (pdb code 6r2a). 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 Phosphonoethyl Ester (Pesp), PDB code: 6r2a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6r2a

Go back to Magnesium Binding Sites List in 6r2a
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp)


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 Phosphonoethyl Ester (Pesp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:16.2
occ:1.00
 O1A A:ZP12001 2.1 13.1 1.0
OD1 A:ASP645 2.1 16.1 1.0
O2B A:ZP12001 2.1 14.7 1.0
O A:ILE680 2.1 14.6 1.0
OD1 A:ASN678 2.1 15.6 1.0
O A:HOH2338 2.3 12.3 1.0
CG A:ASN678 3.1 14.9 1.0
CG A:ASP645 3.2 15.6 1.0
PA A:ZP12001 3.2 15.6 1.0
PB A:ZP12001 3.2 15.4 1.0
O3A A:ZP12001 3.3 14.4 1.0
C A:ILE680 3.3 17.3 1.0
ND2 A:ASN678 3.5 16.4 1.0
OD2 A:ASP645 3.7 17.9 1.0
O1B A:ZP12001 3.8 15.3 1.0
N A:ASP645 3.9 14.8 1.0
O7 A:ZP12001 4.1 15.2 1.0
N A:ILE680 4.1 14.5 1.0
N A:GLY681 4.2 14.8 1.0
CA A:GLY681 4.2 15.2 1.0
N A:ASN678 4.3 15.0 1.0
CA A:ILE680 4.4 15.1 1.0
O A:HOH2376 4.4 15.5 1.0
O2A A:ZP12001 4.4 15.0 1.0
CB A:ASP645 4.4 14.7 1.0
N A:ALA646 4.4 13.9 1.0
O A:VAL676 4.4 16.1 1.0
CB A:ASN678 4.5 16.2 1.0
CG2 A:ILE680 4.5 17.2 1.0
O3B A:ZP12001 4.5 14.8 1.0
CA A:ASP645 4.6 13.5 1.0
CA A:ASN678 4.7 15.7 1.0
N A:GLN679 4.8 15.5 1.0
C A:ASN678 4.8 18.4 1.0
C A:GLY644 4.8 17.9 1.0
CA A:GLY644 4.9 13.8 1.0

Magnesium binding site 2 out of 4 in 6r2a

Go back to Magnesium Binding Sites List in 6r2a
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp)


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 Phosphonoethyl Ester (Pesp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:23.0
occ:1.00
 O A:ILE1060 2.3 27.8 1.0
OD2 A:ASP1004 2.4 32.2 1.0
O A:HIS1055 2.4 22.6 1.0
O A:HOH2657 2.5 35.8 1.0
OD1 A:ASP1058 2.5 26.9 1.0
OD1 A:ASP1004 2.7 26.5 1.0
CG A:ASP1004 2.9 29.2 1.0
O A:HOH2453 3.0 35.2 1.0
C A:ILE1060 3.5 29.4 1.0
CG A:ASP1058 3.5 28.7 1.0
C A:HIS1055 3.6 22.9 1.0
OD2 A:ASP1058 3.9 36.6 1.0
N A:ILE1060 3.9 29.4 1.0
CE1 A:HIS1055 4.2 22.1 1.0
CA A:ILE1060 4.2 29.4 1.0
ND1 A:HIS1055 4.2 22.4 1.0
CA A:HIS1055 4.3 19.1 1.0
O A:HOH2127 4.3 32.6 1.0
CB A:ASP1004 4.3 20.2 1.0
NE2 A:HIS1055 4.3 21.9 1.0
CG A:HIS1055 4.3 20.9 1.0
CD2 A:HIS1055 4.4 22.6 1.0
NE2 A:GLN1061 4.5 44.3 1.0
N A:GLN1061 4.5 22.6 1.0
CB A:ILE1060 4.5 33.1 1.0
N A:GLY1059 4.6 27.6 1.0
CA A:GLN1061 4.7 22.5 1.0
N A:GLY1056 4.7 20.7 1.0
O A:HOH2513 4.7 33.1 1.0
N A:ASP1058 4.8 25.2 1.0
C A:GLY1059 4.9 34.6 1.0
O A:HOH2526 4.9 33.7 1.0
CB A:ASP1058 4.9 27.6 1.0
CA A:GLY1056 4.9 21.9 1.0
CB A:HIS1055 5.0 19.0 1.0
CD A:GLN1061 5.0 51.7 1.0
C A:GLY1056 5.0 26.9 1.0

Magnesium binding site 3 out of 4 in 6r2a

Go back to Magnesium Binding Sites List in 6r2a
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp)


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 Phosphonoethyl Ester (Pesp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:18.9
occ:1.00
 OD1 B:ASP645 2.1 18.0 1.0
O1A B:ZP12001 2.1 16.8 1.0
O B:ILE680 2.1 18.0 1.0
O2B B:ZP12001 2.1 17.4 1.0
OD1 B:ASN678 2.1 19.4 1.0
O B:HOH2325 2.2 17.0 1.0
CG B:ASN678 3.1 21.8 1.0
CG B:ASP645 3.1 17.9 1.0
PA B:ZP12001 3.2 17.9 1.0
PB B:ZP12001 3.2 18.3 1.0
C B:ILE680 3.3 19.8 1.0
O3A B:ZP12001 3.4 18.6 1.0
ND2 B:ASN678 3.5 19.5 1.0
OD2 B:ASP645 3.7 19.5 1.0
O1B B:ZP12001 3.8 19.2 1.0
N B:ASP645 3.9 16.3 1.0
O7 B:ZP12001 4.1 17.2 1.0
N B:ILE680 4.1 17.6 1.0
N B:GLY681 4.2 17.8 1.0
CA B:GLY681 4.2 17.2 1.0
CA B:ILE680 4.3 17.6 1.0
N B:ASN678 4.3 19.7 1.0
O B:HOH2322 4.3 18.6 1.0
CB B:ASP645 4.4 16.4 1.0
O2A B:ZP12001 4.4 16.2 1.0
N B:ALA646 4.4 16.5 1.0
CB B:ASN678 4.5 19.2 1.0
CG2 B:ILE680 4.5 19.8 1.0
O B:VAL676 4.5 20.3 1.0
O3B B:ZP12001 4.5 18.2 1.0
CA B:ASP645 4.6 15.1 1.0
CA B:ASN678 4.7 19.1 1.0
N B:GLN679 4.8 18.5 1.0
C B:ASN678 4.8 21.3 1.0
C B:GLY644 4.8 19.5 1.0
CA B:GLY644 4.9 15.7 1.0

Magnesium binding site 4 out of 4 in 6r2a

Go back to Magnesium Binding Sites List in 6r2a
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd Cocrystallized with Succinylphosphonate Phosphonoethyl Ester (Pesp)


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 Phosphonoethyl Ester (Pesp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:29.7
occ:1.00
 O B:ILE1060 2.3 35.6 1.0
OD2 B:ASP1004 2.3 39.4 1.0
O B:HIS1055 2.4 26.4 1.0
OD1 B:ASP1058 2.6 32.6 1.0
OD1 B:ASP1004 2.6 35.1 1.0
O B:HOH2464 2.6 47.0 1.0
CG B:ASP1004 2.8 34.4 1.0
O B:HOH2553 2.8 43.4 1.0
C B:ILE1060 3.5 33.9 1.0
C B:HIS1055 3.6 25.6 1.0
CG B:ASP1058 3.6 33.2 1.0
N B:ILE1060 3.9 31.7 1.0
OD2 B:ASP1058 4.0 40.6 1.0
CE1 B:HIS1055 4.0 24.3 1.0
ND1 B:HIS1055 4.0 24.8 1.0
NE2 B:HIS1055 4.2 24.2 1.0
O B:HOH2114 4.2 35.4 1.0
CA B:HIS1055 4.2 22.2 1.0
CG B:HIS1055 4.2 23.4 1.0
CA B:ILE1060 4.2 31.1 1.0
CB B:ASP1004 4.2 24.1 1.0
CD2 B:HIS1055 4.3 24.6 1.0
NE2 B:GLN1061 4.4 40.6 1.0
N B:GLY1059 4.5 31.4 1.0
N B:GLN1061 4.6 26.5 1.0
CB B:ILE1060 4.6 34.6 1.0
N B:GLY1056 4.7 23.8 1.0
C B:GLY1059 4.7 37.5 1.0
CA B:GLN1061 4.7 25.2 1.0
O B:HOH2278 4.8 35.8 1.0
CB B:HIS1055 4.9 21.2 1.0
N B:ASP1058 4.9 27.1 1.0
CA B:GLY1056 4.9 24.9 1.0
CB B:ASP1058 4.9 29.3 1.0
CA B:GLY1059 5.0 32.9 1.0
O B:ARG1054 5.0 26.6 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 16:29:58 2024

Last articles

Na in 2F81
Na in 2FAD
Na in 2F8G
Na in 2F6P
Na in 2EZT
Na in 2EZU
Na in 2F53
Na in 2EZ4
Na in 2EZ9
Na in 2EZ8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy