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Magnesium in PDB 5d1r: Crystal Structure of Mycobacterium Tuberculosis RV1816 Transcriptional Regulator.

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis RV1816 Transcriptional Regulator., PDB code: 5d1r was solved by T.-H.Chou, J.Delmar, C.-C.Su, E.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.05 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.444, 86.533, 129.870, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.2

Other elements in 5d1r:

The structure of Crystal Structure of Mycobacterium Tuberculosis RV1816 Transcriptional Regulator. also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis RV1816 Transcriptional Regulator. (pdb code 5d1r). 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 Mycobacterium Tuberculosis RV1816 Transcriptional Regulator., PDB code: 5d1r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5d1r

Go back to Magnesium Binding Sites List in 5d1r
Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis RV1816 Transcriptional Regulator.


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 Mycobacterium Tuberculosis RV1816 Transcriptional Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:16.6
occ:1.00
H A:ALA111 2.6 23.5 1.0
HA A:ASN109 2.8 18.5 1.0
H A:ARG112 2.8 19.7 1.0
HB1 A:ALA111 2.8 30.4 1.0
O A:HOH475 3.0 40.7 1.0
HD2 A:PRO110 3.0 29.1 1.0
HG3 A:ARG112 3.0 22.4 1.0
O A:HOH506 3.1 39.3 1.0
HG A:LEU30 3.1 52.7 1.0
N A:ALA111 3.3 19.6 1.0
C A:ASN109 3.3 14.7 1.0
CA A:ASN109 3.4 15.4 1.0
N A:ARG112 3.5 16.4 1.0
HB3 A:ASN109 3.6 21.9 1.0
N A:PRO110 3.6 16.4 1.0
CB A:ALA111 3.6 25.4 1.0
O A:ASN109 3.7 17.4 1.0
CD A:PRO110 3.7 24.2 1.0
HD3 A:ARG112 3.7 26.3 1.0
HD2 A:ARG112 3.8 26.3 1.0
CG A:ARG112 3.8 18.6 1.0
CA A:ALA111 3.9 21.6 1.0
HB3 A:ALA111 3.9 30.4 1.0
CD A:ARG112 4.0 21.9 1.0
HB2 A:ARG112 4.0 17.2 1.0
CB A:ASN109 4.0 18.3 1.0
HG2 A:PRO110 4.0 21.7 1.0
CG A:LEU30 4.1 43.9 1.0
C A:ALA111 4.2 16.0 1.0
HD22 A:LEU30 4.2 56.3 1.0
C A:PRO110 4.3 19.6 1.0
CB A:ARG112 4.3 14.3 1.0
HD13 A:LEU30 4.4 65.1 1.0
HB2 A:ALA111 4.4 30.4 1.0
CG A:PRO110 4.4 18.1 1.0
CA A:PRO110 4.5 17.1 1.0
HD21 A:LEU30 4.5 56.3 1.0
HD3 A:PRO110 4.5 29.1 1.0
OD1 A:ASN109 4.5 22.7 1.0
CD2 A:LEU30 4.5 46.9 1.0
CA A:ARG112 4.5 16.8 1.0
HG2 A:ARG112 4.6 22.4 1.0
CD1 A:LEU30 4.7 54.3 1.0
HD11 A:LEU30 4.7 65.1 1.0
N A:ASN109 4.7 18.6 1.0
O A:THR108 4.7 19.9 1.0
CG A:ASN109 4.7 18.2 1.0
HA A:ALA111 4.8 25.9 1.0
HB2 A:ASN109 4.8 21.9 1.0
HA A:LEU30 4.9 50.5 1.0
H A:TRP113 5.0 19.6 1.0

Magnesium binding site 2 out of 2 in 5d1r

Go back to Magnesium Binding Sites List in 5d1r
Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis RV1816 Transcriptional Regulator.


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 Mycobacterium Tuberculosis RV1816 Transcriptional Regulator. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:27.5
occ:1.00
HG3 B:ARG112 2.7 35.0 1.0
H B:ARG112 2.7 23.1 1.0
H B:ALA111 2.7 26.3 1.0
HA B:ASN109 2.8 24.8 1.0
HB3 B:ALA111 2.8 29.9 1.0
HD22 B:LEU30 3.0 98.2 1.0
HB3 B:ASN109 3.3 28.8 1.0
N B:ALA111 3.4 21.9 1.0
C B:ASN109 3.4 23.1 1.0
CA B:ASN109 3.4 20.6 1.0
N B:ARG112 3.4 19.2 1.0
HD2 B:ARG112 3.5 42.2 1.0
CG B:ARG112 3.5 29.1 1.0
HD2 B:PRO110 3.5 33.5 1.0
HD3 B:ARG112 3.5 42.2 1.0
CB B:ALA111 3.7 24.9 1.0
HD21 B:LEU30 3.7 98.2 1.0
CD B:ARG112 3.7 35.1 1.0
CD2 B:LEU30 3.7 81.8 1.0
N B:PRO110 3.7 24.5 1.0
HG B:LEU30 3.8 87.1 1.0
CB B:ASN109 3.8 24.0 1.0
O B:ASN109 3.9 18.8 1.0
CA B:ALA111 3.9 21.2 1.0
HB2 B:ARG112 3.9 26.6 1.0
HB2 B:ALA111 4.0 29.9 1.0
CD B:PRO110 4.1 27.9 1.0
C B:ALA111 4.1 17.8 1.0
CB B:ARG112 4.2 22.1 1.0
HD13 B:LEU30 4.2 91.5 1.0
HG2 B:ARG112 4.2 35.0 1.0
CG B:LEU30 4.2 72.6 1.0
OD1 B:ASN109 4.4 35.5 1.0
HB1 B:ALA111 4.4 29.9 1.0
C B:PRO110 4.4 23.1 1.0
CA B:ARG112 4.4 19.5 1.0
HG2 B:PRO110 4.4 34.5 1.0
HD23 B:LEU30 4.5 98.2 1.0
CG B:ASN109 4.6 32.8 1.0
HB2 B:ASN109 4.6 28.8 1.0
CA B:PRO110 4.6 24.3 1.0
O B:THR108 4.8 26.3 1.0
N B:ASN109 4.8 22.4 1.0
CD1 B:LEU30 4.8 76.3 1.0
CG B:PRO110 4.8 28.7 1.0
HA B:ALA111 4.8 25.5 1.0
HD3 B:PRO110 4.9 33.5 1.0
HA B:ARG112 4.9 23.4 1.0

Reference:

J.A.Delmar, T.H.Chou, C.C.Wright, M.H.Licon, J.K.Doh, A.Radhakrishnan, N.Kumar, H.T.Lei, J.R.Bolla, K.R.Rajashankar, C.C.Su, G.E.Purdy, E.W.Yu. Structural Basis For the Regulation of the Mmpl Transporters of Mycobacterium Tuberculosis. J.Biol.Chem. V. 290 28559 2015.
ISSN: ESSN 1083-351X
PubMed: 26396194
DOI: 10.1074/JBC.M115.683797
Page generated: Mon Dec 14 20:09:47 2020

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