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Magnesium in PDB 2bkk: Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A

Enzymatic activity of Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A

All present enzymatic activity of Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A:
2.7.1.95;

Protein crystallography data

The structure of Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A, PDB code: 2bkk was solved by A.Kohl, P.Amstutz, P.Parizek, H.K.Binz, C.Briand, G.Capitani, P.Forrer, A.Pluckthun, M.G.Grutter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.670, 98.082, 81.300, 90.00, 110.01, 90.00
R / Rfree (%) 19.9 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A (pdb code 2bkk). 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 Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A, PDB code: 2bkk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2bkk

Go back to Magnesium Binding Sites List in 2bkk
Magnesium binding site 1 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A


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 Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1266

b:50.3
occ:1.00
 OD1 A:ASN195 1.9 48.8 1.0
O2A A:ADP1265 2.0 43.1 1.0
O A:HOH2114 2.2 52.8 1.0
OD2 A:ASP208 2.3 56.5 1.0
O1B A:ADP1265 2.5 45.4 1.0
CG A:ASN195 2.8 49.3 1.0
CG A:ASP208 2.9 46.0 1.0
CB A:ASP208 3.0 39.5 1.0
ND2 A:ASN195 3.2 47.9 1.0
PA A:ADP1265 3.3 47.0 1.0
PB A:ADP1265 3.5 53.1 1.0
O3A A:ADP1265 3.8 48.3 1.0
O3B A:ADP1265 4.0 37.1 1.0
OD1 A:ASP208 4.0 44.1 1.0
O1A A:ADP1265 4.1 45.6 1.0
OD2 A:ASP190 4.2 55.6 1.0
CB A:ASN195 4.2 52.0 1.0
O5' A:ADP1265 4.4 45.7 1.0
O A:SER194 4.5 53.5 1.0
CA A:ASP208 4.5 37.8 1.0
C5' A:ADP1265 4.5 44.2 1.0
OG A:SER194 4.6 69.8 1.0
O3' A:ADP1265 4.6 43.0 1.0
CA A:ASN195 4.7 50.6 1.0
C A:SER194 4.8 60.5 1.0
O2B A:ADP1265 4.8 51.9 1.0
N A:ASN195 4.9 53.9 1.0
CG1 A:ILE207 4.9 37.9 1.0
C3' A:ADP1265 5.0 38.6 1.0
CD1 A:ILE207 5.0 42.1 1.0
N A:ASP208 5.0 40.3 1.0
CB A:SER194 5.0 67.6 1.0

Magnesium binding site 2 out of 4 in 2bkk

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Magnesium binding site 2 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A


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 Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1267

b:60.7
occ:1.00
 O3B A:ADP1265 2.2 37.1 1.0
OD1 A:ASP208 2.7 44.1 1.0
NH2 A:ARG211 2.8 70.6 1.0
OD2 A:ASP208 3.0 56.5 1.0
CG A:ASP208 3.3 46.0 1.0
O A:HOH2088 3.4 40.9 1.0
CZ A:ARG211 3.4 75.5 1.0
PB A:ADP1265 3.6 53.1 1.0
CB A:SER27 3.6 49.9 1.0
OG A:SER27 3.8 51.2 1.0
NH1 A:ARG211 3.9 77.8 1.0
O1B A:ADP1265 4.0 45.4 1.0
NE A:ARG211 4.2 73.1 1.0
O2B A:ADP1265 4.2 51.9 1.0
NZ A:LYS44 4.4 45.5 1.0
CD2 A:TYR55 4.5 60.6 1.0
CE2 A:TYR55 4.5 60.8 1.0
CB A:ASP208 4.8 39.5 1.0
O3A A:ADP1265 4.8 48.3 1.0
OD2 A:ASP190 5.0 55.6 1.0

Magnesium binding site 3 out of 4 in 2bkk

Go back to Magnesium Binding Sites List in 2bkk
Magnesium binding site 3 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A


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 Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1266

b:65.0
occ:1.00
 O2A C:ADP1265 1.9 71.3 1.0
O C:HOH2127 2.1 65.7 1.0
OD1 C:ASN195 2.1 63.2 1.0
OD1 C:ASP208 2.3 44.2 0.5
O2B C:ADP1265 2.6 71.4 1.0
CG C:ASP208 2.8 39.5 0.5
CB C:ASP208 2.9 33.5 1.0
PA C:ADP1265 3.3 60.3 1.0
CG C:ASN195 3.3 52.0 1.0
O C:HOH2096 3.3 56.4 1.0
PB C:ADP1265 3.6 74.7 1.0
O1A C:ADP1265 3.7 62.9 1.0
O C:SER194 3.8 58.0 1.0
O3A C:ADP1265 3.9 67.8 1.0
OD2 C:ASP208 3.9 41.6 0.5
ND2 C:ASN195 3.9 49.7 1.0
O1B C:ADP1265 4.2 71.0 1.0
CA C:ASP208 4.2 31.3 1.0
MG C:MG1267 4.3 91.8 1.0
CB C:ASN195 4.4 51.8 1.0
O5' C:ADP1265 4.5 59.2 1.0
O3' C:ADP1265 4.5 51.4 1.0
CD1 C:ILE207 4.5 34.1 1.0
OD1 C:ASP190 4.5 61.8 1.0
CG1 C:ILE207 4.6 35.8 1.0
N C:ASP208 4.6 32.9 1.0
CA C:ASN195 4.6 54.0 1.0
C C:SER194 4.6 58.4 1.0
C3' C:ADP1265 4.8 47.7 1.0
O3B C:ADP1265 4.9 74.6 1.0
N C:ASN195 4.9 57.7 1.0
OG C:SER194 5.0 70.9 1.0

Magnesium binding site 4 out of 4 in 2bkk

Go back to Magnesium Binding Sites List in 2bkk
Magnesium binding site 4 out of 4 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A


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 Aminoglycoside Phosphotransferase Aph (3')-Iiia in Complex with the Inhibitor AR_3A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1267

b:91.8
occ:1.00
 O2B C:ADP1265 2.3 71.4 1.0
PB C:ADP1265 3.2 74.7 1.0
OD1 C:ASP208 3.2 44.2 0.5
O C:HOH2096 3.2 56.4 1.0
O3B C:ADP1265 3.2 74.6 1.0
O1B C:ADP1265 3.4 71.0 1.0
CE C:MET26 3.4 99.7 1.0
CB C:SER27 3.8 63.6 1.0
OD1 C:ASP190 4.0 61.8 1.0
CG C:ASP208 4.2 39.5 0.5
CB C:MET26 4.3 92.3 1.0
MG C:MG1266 4.3 65.0 1.0
O C:HOH2104 4.3 54.2 1.0
OD2 C:ASP208 4.3 41.6 0.5
O C:HOH2127 4.4 65.7 1.0
OG C:SER27 4.4 60.1 1.0
N C:SER27 4.5 71.7 1.0
O3A C:ADP1265 4.7 67.8 1.0
CG C:ASP190 4.7 59.3 1.0
SD C:MET26 4.7 99.5 1.0
CG C:MET26 4.7 95.9 1.0
OD2 C:ASP190 4.8 67.8 1.0
CA C:SER27 4.8 63.2 1.0

Reference:

A.Kohl, P.Amstutz, P.Parizek, H.K.Binz, C.Briand, G.Capitani, P.Forrer, A.Pluckthun, M.G.Grutter. Allosteric Inhibition of Aminoglycoside Phosphotransferase By A Designed Ankyrin Repeat Protein Structure V. 13 1131 2005.
ISSN: ISSN 0969-2126
PubMed: 16084385
DOI: 10.1016/J.STR.2005.04.020
Page generated: Mon Dec 14 07:17:06 2020

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