Magnesium in PDB 6x3j: Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)

Protein crystallography data

The structure of Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46), PDB code: 6x3j was solved by H.A.Chaires, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.51 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.800, 109.220, 173.030, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 27.1

Other elements in 6x3j:

The structure of Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) also contains other interesting chemical elements:

Fluorine (F) 7 atoms
Chlorine (Cl) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) (pdb code 6x3j). 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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46), PDB code: 6x3j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6x3j

Go back to Magnesium Binding Sites List in 6x3j
Magnesium binding site 1 out of 2 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:45.7
occ:1.00
O F:HOH514 2.0 50.8 1.0
O C:ASN164 2.0 49.3 1.0
O F:HOH522 2.1 41.2 1.0
O E:HOH521 2.1 42.9 1.0
O E:ASN164 2.4 43.5 1.0
O F:ASN164 2.5 57.1 1.0
H E:ASN164 2.8 45.7 1.0
C C:ASN164 2.9 48.7 1.0
HD2 C:PRO165 2.9 58.5 1.0
H C:ASN164 3.0 50.7 1.0
C E:ASN164 3.2 41.8 1.0
H F:ASN164 3.3 54.5 1.0
C F:ASN164 3.5 56.4 1.0
N C:PRO165 3.5 53.8 1.0
N E:ASN164 3.6 41.7 1.0
CD C:PRO165 3.6 54.2 1.0
N C:ASN164 3.7 48.5 1.0
HD2 F:PRO165 3.7 47.4 1.0
HD2 E:PRO165 3.8 48.8 1.0
CA C:ASN164 3.8 48.4 1.0
HB3 E:ASN164 3.9 44.4 1.0
CA E:ASN164 3.9 40.6 1.0
HE3 C:LYS167 3.9 71.1 1.0
HD3 C:PRO165 4.0 58.5 1.0
HB3 C:ASN164 4.1 51.1 1.0
N E:PRO165 4.1 47.5 1.0
N F:ASN164 4.1 55.9 1.0
HB3 F:ASN164 4.2 54.2 1.0
N F:PRO165 4.3 47.5 1.0
CA F:ASN164 4.3 55.3 1.0
CD F:PRO165 4.4 48.6 1.0
CD E:PRO165 4.4 48.5 1.0
O C:PRO165 4.4 53.0 1.0
CB C:ASN164 4.5 49.0 1.0
CB E:ASN164 4.5 40.9 1.0
HE3 E:LYS167 4.5 83.5 1.0
HZ2 C:LYS167 4.5 71.6 1.0
HA3 E:GLY163 4.6 43.9 1.0
O E:PRO165 4.6 47.2 1.0
HA2 E:GLY163 4.6 43.9 1.0
HA C:ASN164 4.6 51.0 1.0
HZ2 E:LYS167 4.6 83.1 1.0
C E:GLY163 4.7 39.4 1.0
HD3 F:PRO165 4.7 47.4 1.0
HZ1 C:LYS167 4.7 71.6 1.0
CB F:ASN164 4.8 54.4 1.0
HG2 C:PRO165 4.8 58.5 1.0
HA E:ASN164 4.8 44.8 1.0
CE C:LYS167 4.8 63.4 1.0
CG C:PRO165 4.8 53.8 1.0
CA C:PRO165 4.8 53.0 1.0
HA3 C:GLY163 4.9 41.8 1.0
CA E:GLY163 4.9 41.0 1.0
HD3 E:PRO165 4.9 48.8 1.0
C C:GLY163 4.9 39.7 1.0
NZ C:LYS167 4.9 62.7 1.0
HD2 E:LYS167 4.9 82.3 1.0

Magnesium binding site 2 out of 2 in 6x3j

Go back to Magnesium Binding Sites List in 6x3j
Magnesium binding site 2 out of 2 in the Crystal Structure of Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46)


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 Streptogramin A Acetyltransferase Vata From Staphylococcus Aureus in Complex with Streptogramin Analog F0224 (46) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:60.5
occ:1.00
O B:HOH509 2.1 51.7 1.0
O A:HOH520 2.1 41.1 1.0
O D:HOH424 2.1 63.9 1.0
O D:ASN164 2.6 51.1 1.0
O B:ASN164 2.8 44.5 1.0
O A:ASN164 2.9 49.5 1.0
HD2 D:PRO165 3.0 50.9 1.0
HD2 B:PRO165 3.3 38.8 1.0
H B:ASN164 3.3 43.8 1.0
C D:ASN164 3.4 50.1 1.0
HD2 A:PRO165 3.5 55.6 1.0
C B:ASN164 3.5 43.6 1.0
H D:ASN164 3.6 48.7 1.0
HE3 B:LYS167 3.6 67.2 1.0
H A:ASN164 3.7 50.5 1.0
HZ2 A:LYS167 3.7 71.7 1.0
C A:ASN164 3.8 48.9 1.0
CD D:PRO165 3.8 53.6 1.0
N D:PRO165 3.9 53.1 1.0
HZ2 B:LYS167 3.9 69.5 1.0
CD B:PRO165 4.0 40.9 1.0
N B:PRO165 4.1 40.1 1.0
HE3 A:LYS167 4.1 73.8 1.0
N B:ASN164 4.1 43.6 1.0
HZ1 B:LYS167 4.2 69.5 1.0
N D:ASN164 4.3 49.6 1.0
CD A:PRO165 4.3 52.9 1.0
HD3 D:PRO165 4.3 50.9 1.0
HZ1 A:LYS167 4.3 71.7 1.0
NZ B:LYS167 4.4 74.1 1.0
NZ A:LYS167 4.4 81.2 1.0
N A:PRO165 4.4 51.0 1.0
CE B:LYS167 4.4 72.8 1.0
CA B:ASN164 4.4 42.8 1.0
CA D:ASN164 4.4 49.0 1.0
N A:ASN164 4.5 46.1 1.0
O B:PRO165 4.5 40.7 1.0
HD3 B:PRO165 4.5 38.8 1.0
O D:PRO165 4.6 53.0 1.0
HD2 A:LYS167 4.7 73.0 1.0
CE A:LYS167 4.7 77.5 1.0
HG2 D:PRO165 4.7 50.5 1.0
HD3 A:PRO165 4.7 55.6 1.0
CA A:ASN164 4.7 47.0 1.0
HB3 B:ASN164 4.8 42.6 1.0
HD2 B:LYS167 4.8 67.4 1.0
HA3 B:GLY163 4.8 47.3 1.0
HB3 D:ASN164 4.8 48.1 1.0
HB3 A:ASN164 4.9 49.5 1.0
CG D:PRO165 4.9 53.1 1.0
HG2 B:PRO165 5.0 39.0 1.0
O A:PRO165 5.0 48.6 1.0

Reference:

Q.Li, J.Pellegrino, D.J.Lee, A.A.Tran, H.A.Chaires, R.Wang, J.E.Park, K.Ji, D.Chow, N.Zhang, A.F.Brilot, J.T.Biel, G.Van Zundert, K.Borrelli, D.Shinabarger, C.Wolfe, B.Murray, M.P.Jacobson, E.Muhle, O.Chesneau, J.S.Fraser, I.B.Seiple. Synthetic Group A Streptogramin Antibiotics That Overcome Vat Resistance. Nature V. 586 145 2020.
ISSN: ESSN 1476-4687
PubMed: 32968273
DOI: 10.1038/S41586-020-2761-3
Page generated: Tue Dec 15 01:40:08 2020

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