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Magnesium in PDB 6c5u: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form

Enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form

All present enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form:
2.7.1.190;

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form, PDB code: 6c5u was solved by S.J.Caldwell, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.71 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.249, 100.280, 94.040, 90.00, 105.29, 90.00
R / Rfree (%) 18 / 22.7

Other elements in 6c5u:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form (pdb code 6c5u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form, PDB code: 6c5u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6c5u

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:88.0
occ:1.00
 O A:HOH901 1.3 69.8 1.0
O A:HOH900 1.8 73.7 1.0
O2B A:GNP500 1.9 78.3 1.0
O2A A:GNP500 2.1 68.9 1.0
NE2 A:HIS379 2.2 54.7 1.0
OD2 A:ASP393 2.3 51.1 1.0
CE1 A:HIS379 3.2 52.7 1.0
CD2 A:HIS379 3.2 54.5 1.0
CG A:ASP393 3.4 47.8 1.0
PB A:GNP500 3.4 70.6 1.0
PA A:GNP500 3.5 66.4 1.0
O3A A:GNP500 3.7 66.7 1.0
CB A:ASP393 3.8 45.6 1.0
O A:HOH972 3.9 62.5 1.0
O A:HOH1221 4.0 57.6 1.0
MG A:MG702 4.0 75.1 1.0
O1B A:GNP500 4.1 74.8 1.0
O A:HOH904 4.2 73.7 1.0
ND1 A:HIS379 4.3 55.3 1.0
O1A A:GNP500 4.3 63.8 1.0
CG A:HIS379 4.3 50.4 1.0
O5' A:GNP500 4.4 66.3 1.0
OD1 A:ASP393 4.5 50.0 1.0
O3G A:GNP500 4.5 76.9 1.0
O A:HOH921 4.5 66.2 1.0
ND2 A:ASN378 4.5 72.9 1.0
C5' A:GNP500 4.7 66.2 1.0
N3B A:GNP500 4.7 72.2 1.0
O3' A:GNP500 4.8 73.2 1.0
O A:HOH902 4.8 68.3 1.0
OD2 A:ASP374 4.8 60.2 1.0
O A:HOH1287 4.8 79.9 1.0
C3' A:GNP500 5.0 69.0 1.0

Magnesium binding site 2 out of 8 in 6c5u

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:75.1
occ:1.00
 O A:HOH902 1.8 68.3 1.0
O3G A:GNP500 1.9 76.9 1.0
O A:HOH904 2.0 73.7 1.0
OD2 A:ASP393 2.1 51.1 1.0
O A:HOH903 2.2 80.8 1.0
OD1 A:ASP393 2.3 50.0 1.0
CG A:ASP393 2.5 47.8 1.0
PG A:GNP500 3.2 80.7 1.0
O2B A:GNP500 3.4 78.3 1.0
O2G A:GNP500 3.4 83.2 1.0
O A:HOH901 3.5 69.8 1.0
OD2 A:ASP374 3.9 60.2 1.0
MG A:MG700 4.0 88.0 1.0
CB A:ASP393 4.0 45.6 1.0
N3B A:GNP500 4.2 72.2 1.0
PB A:GNP500 4.3 70.6 1.0
O1G A:GNP500 4.3 77.3 1.0
NZ A:LYS226 4.4 59.8 1.0
CA A:GLY395 4.5 57.4 1.0
O3A A:GNP500 4.5 66.7 1.0
N A:GLY395 4.5 54.9 1.0
O A:HOH951 4.7 48.3 1.0
O A:ASP393 4.7 46.6 1.0
OD2 A:ASP396 4.7 64.0 1.0
O A:HOH911 4.7 73.6 1.0
CG A:ASP396 4.8 63.6 1.0
CA A:ASP393 4.8 47.4 1.0
O2A A:GNP500 4.9 68.9 1.0
CE1 A:HIS379 4.9 52.7 1.0
OD1 A:ASP396 4.9 65.7 1.0
C A:GLY395 4.9 59.3 1.0
O A:HOH921 4.9 66.2 1.0
C A:ASP393 4.9 47.6 1.0
N A:ASP396 5.0 55.2 1.0
NE2 A:HIS379 5.0 54.7 1.0

Magnesium binding site 3 out of 8 in 6c5u

Go back to Magnesium Binding Sites List in 6c5u
Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:58.0
occ:1.00
 O B:HOH900 1.7 55.4 1.0
O2A B:GNP500 1.9 55.6 1.0
O B:HOH901 2.0 56.7 1.0
OD2 B:ASP393 2.2 61.1 1.0
NE2 B:HIS379 2.4 50.0 1.0
O2B B:GNP500 2.5 64.8 1.0
PA B:GNP500 3.1 59.9 1.0
CG B:ASP393 3.2 57.8 1.0
CD2 B:HIS379 3.3 51.4 1.0
CE1 B:HIS379 3.4 49.4 1.0
PB B:GNP500 3.4 62.9 1.0
O3A B:GNP500 3.5 63.5 1.0
CB B:ASP393 3.7 55.4 1.0
MG B:MG702 3.9 73.2 1.0
O1B B:GNP500 3.9 74.9 1.0
O B:HOH904 4.0 80.9 1.0
O1A B:GNP500 4.1 58.8 1.0
OD1 B:ASP393 4.3 57.4 1.0
O5' B:GNP500 4.3 56.9 1.0
O B:HOH921 4.4 69.9 0.8
O B:HOH1260 4.4 61.2 1.0
CG B:HIS379 4.4 48.8 1.0
ND1 B:HIS379 4.4 46.2 1.0
C5' B:GNP500 4.4 55.9 1.0
O3G B:GNP500 4.5 74.9 1.0
O3' B:GNP500 4.5 54.9 1.0
O B:HOH902 4.7 70.2 1.0
C3' B:GNP500 4.8 53.4 1.0
N3B B:GNP500 4.8 71.7 1.0
ND2 B:ASN378 4.8 58.8 1.0

Magnesium binding site 4 out of 8 in 6c5u

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:73.2
occ:1.00
 O3G B:GNP500 2.0 74.9 1.0
O B:HOH902 2.0 70.2 1.0
O B:HOH904 2.0 80.9 1.0
OD2 B:ASP393 2.1 61.1 1.0
O B:HOH903 2.2 64.9 1.0
OD1 B:ASP393 2.4 57.4 1.0
CG B:ASP393 2.6 57.8 1.0
O2B B:GNP500 3.2 64.8 1.0
PG B:GNP500 3.2 87.7 1.0
O2G B:GNP500 3.4 79.4 1.0
O B:HOH901 3.5 56.7 1.0
MG B:MG700 3.9 58.0 1.0
PB B:GNP500 3.9 62.9 1.0
N3B B:GNP500 4.0 71.7 1.0
CB B:ASP393 4.1 55.4 1.0
OD2 B:ASP374 4.1 70.4 1.0
O3A B:GNP500 4.4 63.5 1.0
NZ B:LYS226 4.5 69.7 1.0
O1G B:GNP500 4.5 83.8 1.0
CA B:GLY395 4.5 53.9 1.0
OD2 B:ASP396 4.6 70.7 1.0
N B:GLY395 4.6 52.9 1.0
O2A B:GNP500 4.8 55.6 1.0
O B:ASP393 4.8 55.2 1.0
O B:HOH921 4.8 69.9 0.8
CG B:ASP396 4.8 66.5 1.0
C B:GLY395 4.9 56.7 1.0
CE1 B:HIS379 4.9 49.4 1.0
OD1 B:ASP396 4.9 71.1 1.0
O B:HOH951 4.9 55.2 1.0
CA B:ASP393 5.0 53.6 1.0
N B:ASP396 5.0 56.5 1.0
NE2 B:HIS379 5.0 50.0 1.0

Magnesium binding site 5 out of 8 in 6c5u

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:76.9
occ:1.00
 O C:HOH900 1.6 70.1 1.0
O C:HOH901 1.9 71.7 1.0
O2A C:GNP500 2.0 75.3 1.0
O2B C:GNP500 2.2 81.4 1.0
OD2 C:ASP393 2.3 60.2 1.0
NE2 C:HIS379 2.4 60.8 1.0
CE1 C:HIS379 3.3 60.0 1.0
CD2 C:HIS379 3.4 61.2 1.0
PA C:GNP500 3.4 70.8 1.0
CG C:ASP393 3.4 59.5 1.0
PB C:GNP500 3.5 79.4 1.0
O3A C:GNP500 3.7 74.5 1.0
O C:HOH1260 3.8 71.5 1.0
O C:HOH904 3.9 69.9 1.0
CB C:ASP393 3.9 55.9 1.0
O C:HOH921 4.0 65.1 1.0
O1B C:GNP500 4.1 82.3 1.0
O1A C:GNP500 4.2 66.3 1.0
MG C:MG702 4.2 85.3 1.0
O3G C:GNP500 4.2 86.1 1.0
O5' C:GNP500 4.4 69.4 1.0
ND1 C:HIS379 4.4 58.6 1.0
CG C:HIS379 4.5 59.2 1.0
OD1 C:ASP393 4.5 64.0 1.0
ND2 C:ASN378 4.6 68.7 1.0
C5' C:GNP500 4.7 69.2 1.0
O3' C:GNP500 4.7 73.7 1.0
N3B C:GNP500 4.7 82.5 1.0
OD2 C:ASP374 4.8 66.0 1.0
O C:HOH902 4.9 70.0 1.0

Magnesium binding site 6 out of 8 in 6c5u

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:85.3
occ:1.00
 O C:HOH904 1.9 69.9 1.0
O C:HOH903 2.0 64.8 1.0
O C:HOH902 2.1 70.0 1.0
O3G C:GNP500 2.1 86.1 1.0
OD1 C:ASP393 2.3 64.0 1.0
OD2 C:ASP393 2.3 60.2 1.0
CG C:ASP393 2.6 59.5 1.0
PG C:GNP500 3.3 90.1 1.0
O C:HOH901 3.3 71.7 1.0
O2G C:GNP500 3.4 93.7 1.0
O2B C:GNP500 3.6 81.4 1.0
OD2 C:ASP374 4.0 66.0 1.0
CB C:ASP393 4.1 55.9 1.0
MG C:MG700 4.2 76.9 1.0
O C:HOH1083 4.2 76.3 1.0
OD2 C:ASP396 4.3 68.1 1.0
CA C:GLY395 4.3 65.1 1.0
O1G C:GNP500 4.3 87.9 1.0
O C:HOH911 4.4 72.9 1.0
N3B C:GNP500 4.4 82.5 1.0
N C:GLY395 4.4 63.5 1.0
NZ C:LYS226 4.5 69.8 1.0
CG C:ASP396 4.5 70.4 1.0
O C:HOH951 4.5 58.1 1.0
PB C:GNP500 4.5 79.4 1.0
OD1 C:ASP396 4.6 74.8 1.0
O C:ASP393 4.6 56.0 1.0
C C:GLY395 4.7 65.5 1.0
N C:ASP396 4.7 64.7 1.0
CA C:ASP393 4.9 57.4 1.0
C C:ASP393 4.9 57.5 1.0
O3A C:GNP500 4.9 74.5 1.0

Magnesium binding site 7 out of 8 in 6c5u

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:62.4
occ:1.00
 O2A D:GNP500 2.0 72.2 1.0
O D:HOH900 2.2 65.5 1.0
OD2 D:ASP393 2.2 84.5 1.0
NE2 D:HIS379 2.3 72.8 1.0
O2G D:GNP500 2.4 0.3 1.0
N3B D:GNP500 2.4 99.6 1.0
PG D:GNP500 2.8 0.6 1.0
CD2 D:HIS379 3.2 70.7 1.0
CG D:ASP393 3.2 79.6 1.0
CE1 D:HIS379 3.3 68.4 1.0
PA D:GNP500 3.4 76.1 1.0
PB D:GNP500 3.5 89.0 1.0
CB D:ASP393 3.6 79.0 1.0
O3A D:GNP500 3.6 81.8 1.0
O3G D:GNP500 3.9 0.4 1.0
O1G D:GNP500 4.0 0.5 1.0
MG D:MG702 4.1 90.6 1.0
O3' D:GNP500 4.2 71.1 1.0
O1A D:GNP500 4.3 71.4 1.0
ND1 D:HIS379 4.3 68.6 1.0
OD1 D:ASP393 4.3 78.6 1.0
CG D:HIS379 4.3 69.3 1.0
O5' D:GNP500 4.5 74.4 1.0
C5' D:GNP500 4.5 75.3 1.0
O1B D:GNP500 4.6 98.8 1.0
O D:HOH902 4.6 68.2 1.0
O2B D:GNP500 4.6 89.9 1.0
C3' D:GNP500 4.6 71.6 1.0
ND2 D:ASN378 4.7 85.9 1.0
OD2 D:ASP374 5.0 66.2 1.0

Magnesium binding site 8 out of 8 in 6c5u

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Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:90.6
occ:1.00
 OD1 D:ASP393 2.0 78.6 1.0
OD2 D:ASP393 2.3 84.5 1.0
O3G D:GNP500 2.3 0.4 1.0
CG D:ASP393 2.5 79.6 1.0
O D:HOH903 2.5 99.0 1.0
O D:HOH902 2.6 68.2 1.0
O2B D:GNP500 2.6 89.9 1.0
O D:HOH911 3.2 72.0 1.0
PB D:GNP500 3.4 89.0 1.0
PG D:GNP500 3.5 0.6 1.0
N3B D:GNP500 3.6 99.6 1.0
NZ D:LYS226 3.7 78.7 1.0
O3A D:GNP500 3.9 81.8 1.0
CB D:ASP393 4.0 79.0 1.0
MG D:MG700 4.1 62.4 1.0
O D:HOH1299 4.2 71.3 0.7
CA D:GLY395 4.2 76.8 1.0
O2G D:GNP500 4.2 0.3 1.0
N D:GLY395 4.3 76.0 1.0
O2A D:GNP500 4.6 72.2 1.0
CA D:ASP393 4.7 74.5 1.0
PA D:GNP500 4.7 76.1 1.0
O1G D:GNP500 4.7 0.5 1.0
C D:GLY395 4.8 75.2 1.0
O1A D:GNP500 4.8 71.4 1.0
O1B D:GNP500 4.8 98.8 1.0
O D:ASP393 4.8 69.2 1.0
CE D:LYS226 4.8 76.5 1.0
C D:ASP393 4.9 73.2 1.0
OD2 D:ASP374 4.9 66.2 1.0

Reference:

S.J.Caldwell, A.M.Berghuis. Plasticity of Aminoglycoside Binding to Antibiotic Kinase Aph(2′′)-Ia. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 29661878
DOI: 10.1128/AAC.00202-18
Page generated: Mon Sep 30 20:11:25 2024

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