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Magnesium in PDB 4ork: Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia

Protein crystallography data

The structure of Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia, PDB code: 4ork was solved by C.A.Smith, M.Toth, M.Bhattacharya, H.Frase, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.20 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.685, 95.697, 91.149, 90.00, 104.88, 90.00
R / Rfree (%) 18.5 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia (pdb code 4ork). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia, PDB code: 4ork:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ork

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


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 the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:54.7
occ:1.00
 O A:HOH601 1.9 83.8 1.0
O A:HOH602 1.9 62.5 1.0
O2B A:GDP500 1.9 72.1 1.0
O1A A:GDP500 2.1 55.8 1.0
OD2 A:ASP219 2.1 46.5 1.0
NE2 A:HIS205 2.3 54.1 1.0
PB A:GDP500 3.1 73.0 1.0
CE1 A:HIS205 3.2 55.7 1.0
CD2 A:HIS205 3.3 49.6 1.0
CG A:ASP219 3.3 56.1 1.0
PA A:GDP500 3.4 59.1 1.0
O1B A:GDP500 3.7 47.5 1.0
O3A A:GDP500 3.7 43.7 1.0
CB A:ASP219 3.9 52.5 1.0
MG A:MG502 4.0 73.9 1.0
O3' A:GDP500 4.0 49.8 1.0
O3B A:GDP500 4.3 58.1 1.0
O5' A:GDP500 4.3 53.1 1.0
OD1 A:ASP219 4.3 51.7 1.0
OD2 A:ASP200 4.3 49.4 1.0
ND1 A:HIS205 4.3 48.4 1.0
C5' A:GDP500 4.4 45.2 1.0
ND2 A:ASN204 4.4 61.8 1.0
CG A:HIS205 4.4 53.5 1.0
O A:HOH605 4.4 49.7 1.0
O2A A:GDP500 4.5 52.1 1.0
C3' A:GDP500 4.6 49.7 1.0
O A:HOH604 4.7 48.1 1.0
CA A:GLY37 4.7 82.5 1.0

Magnesium binding site 2 out of 8 in 4ork

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


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 the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:73.9
occ:1.00
 O A:HOH604 1.8 48.1 1.0
O A:HOH603 2.0 56.0 1.0
O1B A:GDP500 2.1 47.5 1.0
O A:HOH605 2.1 49.7 1.0
OD1 A:ASP219 2.3 51.7 1.0
OD2 A:ASP219 2.5 46.5 1.0
CG A:ASP219 2.7 56.1 1.0
PB A:GDP500 3.4 73.0 1.0
O2B A:GDP500 3.5 72.1 1.0
OD2 A:ASP200 3.7 49.4 1.0
O A:HOH602 3.7 62.5 1.0
OD1 A:ASP222 3.9 65.3 1.0
MG A:MG501 4.0 54.7 1.0
OD2 A:ASP39 4.1 70.5 1.0
OD2 A:ASP222 4.2 78.6 1.0
CG A:ASP222 4.2 64.2 1.0
CB A:ASP219 4.2 52.5 1.0
O3A A:GDP500 4.3 43.7 1.0
CA A:GLY221 4.3 50.7 1.0
O3B A:GDP500 4.4 58.1 1.0
O1A A:GDP500 4.4 55.8 1.0
N A:GLY221 4.5 43.3 1.0
O A:ASP219 4.6 47.5 1.0
C A:GLY221 4.6 52.4 1.0
N A:ASP222 4.7 57.3 1.0
CG A:ASP200 4.7 53.0 1.0
PA A:GDP500 4.8 59.1 1.0
CE1 A:HIS205 4.8 55.7 1.0
CB A:ASP39 4.8 70.5 1.0
O A:HOH610 4.8 54.1 1.0
CG A:ASP39 4.8 76.8 1.0
NE2 A:HIS205 4.9 54.1 1.0
CB A:ASP200 4.9 51.9 1.0

Magnesium binding site 3 out of 8 in 4ork

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


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 the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:53.5
occ:1.00
 O2B B:GDP500 1.9 69.7 1.0
O1A B:GDP500 1.9 52.9 1.0
O B:HOH602 2.0 79.3 1.0
NE2 B:HIS205 2.0 59.3 1.0
O B:HOH601 2.0 51.2 1.0
OD2 B:ASP219 2.4 48.1 1.0
CE1 B:HIS205 2.8 68.9 1.0
PB B:GDP500 3.2 66.9 1.0
CD2 B:HIS205 3.2 59.0 1.0
PA B:GDP500 3.3 60.2 1.0
CG B:ASP219 3.3 50.1 1.0
CB B:ASP219 3.7 44.2 1.0
O3A B:GDP500 3.7 62.4 1.0
MG B:MG502 3.8 66.6 1.0
O1B B:GDP500 3.8 55.0 1.0
ND1 B:HIS205 4.0 63.9 1.0
O B:HOH605 4.0 51.8 1.0
O3' B:GDP500 4.1 61.1 1.0
O2A B:GDP500 4.2 53.0 1.0
CG B:HIS205 4.2 56.1 1.0
O3B B:GDP500 4.3 62.6 1.0
ND2 B:ASN204 4.3 62.8 1.0
O5' B:GDP500 4.4 73.9 1.0
OD1 B:ASP219 4.4 67.4 1.0
OD2 B:ASP200 4.5 54.6 1.0
C3' B:GDP500 4.6 61.0 1.0
C5' B:GDP500 4.6 62.1 1.0
O B:HOH604 4.6 57.2 1.0

Magnesium binding site 4 out of 8 in 4ork

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


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 the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:66.6
occ:1.00
 O B:HOH603 1.8 66.4 1.0
O B:HOH605 1.8 51.8 1.0
O B:HOH604 1.9 57.2 1.0
O1B B:GDP500 2.0 55.0 1.0
OD2 B:ASP219 2.0 48.1 1.0
CG B:ASP219 2.7 50.1 1.0
OD1 B:ASP219 2.7 67.4 1.0
PB B:GDP500 3.1 66.9 1.0
O2B B:GDP500 3.2 69.7 1.0
OD2 B:ASP39 3.7 78.5 1.0
OD2 B:ASP200 3.8 54.6 1.0
MG B:MG501 3.8 53.5 1.0
O B:HOH602 3.8 79.3 1.0
OD1 B:ASP222 4.0 78.5 1.0
O3B B:GDP500 4.0 62.6 1.0
CB B:ASP219 4.2 44.2 1.0
O3A B:GDP500 4.3 62.4 1.0
CG B:ASP222 4.4 71.5 1.0
O1A B:GDP500 4.4 52.9 1.0
O B:HOH638 4.5 55.7 1.0
OD2 B:ASP222 4.6 70.2 1.0
CG B:ASP39 4.7 79.8 1.0
CA B:GLY221 4.7 58.6 1.0
O B:HOH607 4.8 54.5 1.0
CE1 B:HIS205 4.8 68.9 1.0
PA B:GDP500 4.8 60.2 1.0
N B:ASP222 4.8 62.7 1.0
C B:GLY221 4.8 56.7 1.0
N B:GLY221 4.9 58.9 1.0
O B:ASP219 4.9 53.7 1.0
CG B:ASP200 4.9 59.1 1.0
NE2 B:HIS205 4.9 59.3 1.0
CB B:ASP39 4.9 69.5 1.0
O2A B:GDP500 5.0 53.0 1.0

Magnesium binding site 5 out of 8 in 4ork

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:53.6
occ:1.00
 O C:HOH602 1.9 53.8 1.0
O C:HOH601 2.0 57.8 1.0
O2B C:GDP500 2.0 79.7 1.0
O2A C:GDP500 2.0 69.6 1.0
NE2 C:HIS205 2.2 51.0 1.0
OD2 C:ASP219 2.2 48.9 1.0
CE1 C:HIS205 3.0 46.8 1.0
PB C:GDP500 3.2 85.8 1.0
PA C:GDP500 3.3 57.7 1.0
CD2 C:HIS205 3.3 52.2 1.0
CG C:ASP219 3.3 49.4 1.0
O3A C:GDP500 3.5 71.0 1.0
O C:HOH623 3.6 56.9 1.0
O3B C:GDP500 3.8 58.6 1.0
O3' C:GDP500 3.9 59.5 1.0
O C:HOH605 3.9 67.1 1.0
CB C:ASP219 4.0 58.2 1.0
ND1 C:HIS205 4.2 49.1 1.0
MG C:MG502 4.3 52.8 1.0
ND2 C:ASN204 4.3 50.5 1.0
OD1 C:ASP219 4.3 46.4 1.0
O5' C:GDP500 4.3 61.6 1.0
CG C:HIS205 4.4 49.6 1.0
O1A C:GDP500 4.4 50.9 1.0
C5' C:GDP500 4.4 59.0 1.0
O1B C:GDP500 4.4 56.7 1.0
C3' C:GDP500 4.5 56.2 1.0
O C:HOH604 4.8 45.2 1.0
OD2 C:ASP200 4.9 45.2 1.0
CA C:GLY37 5.0 90.8 1.0

Magnesium binding site 6 out of 8 in 4ork

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:52.8
occ:1.00
 O C:HOH603 1.8 64.4 1.0
O C:HOH605 1.8 67.1 1.0
OD1 C:ASP219 1.9 46.4 1.0
O3B C:GDP500 1.9 58.6 1.0
O C:HOH604 1.9 45.2 1.0
CG C:ASP219 2.6 49.4 1.0
OD2 C:ASP219 2.6 48.9 1.0
PB C:GDP500 3.1 85.8 1.0
O2B C:GDP500 3.4 79.7 1.0
O1B C:GDP500 4.0 56.7 1.0
CB C:ASP219 4.1 58.2 1.0
O C:HOH601 4.1 57.8 1.0
MG C:MG501 4.3 53.6 1.0
OD2 C:ASP200 4.3 45.2 1.0
OD2 C:ASP222 4.3 64.5 1.0
O3A C:GDP500 4.4 71.0 1.0
CA C:GLY221 4.4 42.4 1.0
N C:GLY221 4.4 43.7 1.0
OD1 C:ASP222 4.4 70.5 1.0
CG C:ASP222 4.5 50.9 1.0
O C:ASP219 4.6 53.5 1.0
O2A C:GDP500 4.6 69.6 1.0
C C:GLY221 4.7 55.5 1.0
O C:HOH607 4.7 53.1 1.0
NZ C:LYS52 4.7 56.6 1.0
CA C:ASP219 4.7 53.5 1.0
N C:ASP222 4.8 52.6 1.0
O1A C:GDP500 4.8 50.9 1.0
C C:ASP219 4.8 53.4 1.0
PA C:GDP500 4.8 57.7 1.0

Magnesium binding site 7 out of 8 in 4ork

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:96.6
occ:1.00
 O D:HOH602 1.8 60.9 1.0
O D:HOH601 2.0 63.1 1.0
O2A D:GDP500 2.0 63.2 1.0
O2B D:GDP500 2.0 62.7 1.0
NE2 D:HIS205 2.0 76.3 1.0
OD2 D:ASP219 2.1 75.9 1.0
CE1 D:HIS205 2.8 74.0 1.0
CG D:ASP219 3.1 69.0 1.0
CD2 D:HIS205 3.1 73.1 1.0
PB D:GDP500 3.3 65.4 1.0
PA D:GDP500 3.4 60.6 1.0
CB D:ASP219 3.6 52.2 1.0
O3A D:GDP500 3.8 70.8 1.0
O D:HOH605 4.0 63.3 1.0
O3B D:GDP500 4.0 75.0 1.0
MG D:MG502 4.0 60.3 1.0
ND1 D:HIS205 4.0 77.0 1.0
OD1 D:ASP219 4.1 70.2 1.0
CG D:HIS205 4.2 73.1 1.0
O3' D:GDP500 4.3 67.0 1.0
O1A D:GDP500 4.3 66.7 1.0
O5' D:GDP500 4.4 78.2 1.0
OD2 D:ASP200 4.4 68.2 1.0
C5' D:GDP500 4.5 72.0 1.0
O1B D:GDP500 4.5 68.0 1.0
ND2 D:ASN204 4.6 62.2 1.0
O D:HOH604 4.6 54.7 1.0
C3' D:GDP500 4.7 65.3 1.0

Magnesium binding site 8 out of 8 in 4ork

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:60.3
occ:1.00
 O D:HOH604 1.8 54.7 1.0
O D:HOH603 1.9 55.9 1.0
O3B D:GDP500 1.9 75.0 1.0
O D:HOH605 1.9 63.3 1.0
OD1 D:ASP219 2.1 70.2 1.0
OD2 D:ASP219 2.6 75.9 1.0
CG D:ASP219 2.7 69.0 1.0
PB D:GDP500 3.0 65.4 1.0
O2B D:GDP500 3.1 62.7 1.0
O D:HOH641 3.7 59.2 1.0
O1B D:GDP500 3.9 68.0 1.0
MG D:MG501 4.0 96.6 1.0
NZ D:LYS52 4.1 48.0 1.0
OD2 D:ASP200 4.1 68.2 1.0
O D:HOH602 4.2 60.9 1.0
CB D:ASP219 4.2 52.2 1.0
OD1 D:ASP222 4.2 66.7 1.0
O3A D:GDP500 4.3 70.8 1.0
CA D:GLY221 4.3 62.1 1.0
N D:GLY221 4.4 66.4 1.0
O2A D:GDP500 4.6 63.2 1.0
CG D:ASP222 4.7 61.2 1.0
N D:ASP222 4.8 62.7 1.0
CA D:ASP219 4.9 62.0 1.0
O D:ASP219 4.9 66.3 1.0
C D:GLY221 4.9 66.3 1.0
PA D:GDP500 4.9 60.6 1.0
C D:ASP219 5.0 61.4 1.0
OD2 D:ASP222 5.0 63.7 1.0

Reference:

C.A.Smith, M.Toth, M.Bhattacharya, H.Frase, S.B.Vakulenko. Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside-Resistance Enzyme Aac(6')-Ie-Aph(2'')-Ia. Acta Crystallogr.,Sect.D V. 70 1561 2014.
ISSN: ISSN 0907-4449
PubMed: 24914967
DOI: 10.1107/S1399004714005331
Page generated: Tue Aug 20 00:57:44 2024

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