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Magnesium in PDB 4d7m: Tetr(D) in Complex with Anhydrotetracycline and Magnesium

Protein crystallography data

The structure of Tetr(D) in Complex with Anhydrotetracycline and Magnesium, PDB code: 4d7m was solved by S.Werten, D.Dalm, G.J.Palm, W.Hinrichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.60 / 1.55
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.628, 65.628, 178.598, 90.00, 90.00, 90.00
R / Rfree (%) 17.627 / 21.669

Other elements in 4d7m:

The structure of Tetr(D) in Complex with Anhydrotetracycline and Magnesium also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium (pdb code 4d7m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium, PDB code: 4d7m:

Magnesium binding site 1 out of 1 in 4d7m

Go back to Magnesium Binding Sites List in 4d7m
Magnesium binding site 1 out of 1 in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetr(D) in Complex with Anhydrotetracycline and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:18.2
occ:1.00
O12 A:TDC222 2.0 19.1 1.0
O11 A:TDC222 2.0 19.7 1.0
O A:HOH2100 2.1 19.4 1.0
O A:HOH2101 2.1 20.5 1.0
NE2 A:HIS100 2.2 18.7 1.0
C12 A:TDC222 3.0 18.4 1.0
C11 A:TDC222 3.1 18.9 1.0
CE1 A:HIS100 3.1 20.2 1.0
CD2 A:HIS100 3.2 21.2 1.0
C1B A:TDC222 3.5 16.2 1.0
O A:HOH2112 4.0 24.6 1.0
OG1 A:THR103 4.0 21.9 1.0
O A:THR103 4.0 20.8 1.0
O10 A:TDC222 4.1 23.0 1.0
O A:HOH2134 4.2 27.7 1.0
ND1 A:HIS100 4.2 20.3 1.0
C1C A:TDC222 4.3 16.6 1.0
CG A:HIS100 4.3 19.8 1.0
O1C A:TDC222 4.4 18.7 1.0
C1A A:TDC222 4.4 19.8 1.0
C A:THR103 4.7 21.9 1.0
C10 A:TDC222 4.7 22.0 1.0
O1 A:TDC222 4.9 19.5 1.0
O A:HIS100 4.9 19.1 1.0
C51 A:TDC222 5.0 16.9 1.0

Reference:

S.Werten, D.Dalm, G.J.Palm, C.C.Grimm, W.Hinrichs. Tetracycline Repressor Allostery Does Not Depend on Divalent Metal Recognition. Biochemistry 2014.
ISSN: ESSN 1520-4995
PubMed: 25432019
DOI: 10.1021/BI5012805
Page generated: Mon Dec 14 12:01:40 2020

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