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Magnesium in PDB 4prv: E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp

Enzymatic activity of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp

All present enzymatic activity of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp:
5.99.1.3;

Protein crystallography data

The structure of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp, PDB code: 4prv was solved by F.V.Stanger, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.03 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.250, 142.520, 79.090, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp (pdb code 4prv). 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 E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp, PDB code: 4prv:

Magnesium binding site 1 out of 1 in 4prv

Go back to Magnesium Binding Sites List in 4prv
Magnesium binding site 1 out of 1 in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:20.0
occ:1.00
OD1 A:ASN46 2.2 20.5 1.0
O3B A:ADP401 2.2 18.5 1.0
O2A A:ADP401 2.3 17.7 1.0
O A:HOH527 2.3 21.2 1.0
CG A:ASN46 3.1 20.9 1.0
PA A:ADP401 3.2 24.3 1.0
PB A:ADP401 3.2 21.2 1.0
O3A A:ADP401 3.3 22.7 1.0
ND2 A:ASN46 3.3 21.6 1.0
O1B A:ADP401 3.6 17.3 1.0
O A:HOH574 3.7 26.8 1.0
O5' A:ADP401 4.0 20.5 1.0
NZ A:LYS103 4.1 22.0 1.0
CA A:GLY119 4.2 19.2 1.0
N A:GLY119 4.3 18.2 1.0
CA A:GLY114 4.4 25.6 1.0
O A:GLU42 4.4 18.7 1.0
O A:HOH515 4.5 13.7 1.0
CB A:ASN46 4.5 21.7 1.0
OE2 A:GLU42 4.5 19.6 1.0
O1A A:ADP401 4.5 16.3 1.0
N A:VAL120 4.6 19.4 1.0
O2B A:ADP401 4.6 23.0 1.0
C A:GLY119 4.9 20.6 1.0
CA A:ASN46 4.9 19.3 1.0
O A:HOH529 5.0 22.5 1.0
N A:ASN46 5.0 18.4 1.0

Reference:

F.V.Stanger, C.Dehio, T.Schirmer. Structure of the N-Terminal Gyrase B Fragment in Complex with Adppi Reveals Rigid-Body Motion Induced By Atp Hydrolysis Plos One V. 9 07289 2014.
ISSN: ESSN 1932-6203
PubMed: 25202966
DOI: 10.1371/JOURNAL.PONE.0107289
Page generated: Mon Dec 14 19:20:54 2020

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