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Magnesium in PDB 3ccv: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A

Protein crystallography data

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A, PDB code: 3ccv was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.752, 299.012, 574.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.5

Other elements in 3ccv:

The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A also contains other interesting chemical elements:

Strontium (Sr) 108 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 93;

Binding sites:

The binding sites of Magnesium atom in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A (pdb code 3ccv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 93 binding sites of Magnesium where determined in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A, PDB code: 3ccv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 93 in 3ccv

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Magnesium binding site 1 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8051

b:60.5
occ:1.00
 O 0:HOH4373 2.5 71.4 1.0
N A:LEU27 2.5 58.2 1.0
O A:LEU27 2.6 62.9 1.0
C A:ASP26 2.8 58.5 1.0
OP2 0:G1873 2.9 39.8 1.0
NH2 A:ARG120 2.9 39.3 1.0
C A:LEU27 3.0 61.5 1.0
OP1 0:G1873 3.0 43.2 1.0
CA A:LEU27 3.1 59.3 1.0
OD2 A:ASP26 3.1 67.4 1.0
P 0:G1873 3.3 41.1 1.0
CA A:ASP26 3.3 59.0 1.0
O A:ASP26 3.4 59.0 1.0
CG A:ASP26 3.6 65.8 1.0
CB A:LEU27 3.7 56.3 1.0
CZ A:ARG120 3.8 39.7 1.0
O3' 0:C1872 3.9 39.1 1.0
CG A:GLU28 4.0 71.4 1.0
NH1 A:ARG120 4.0 40.5 1.0
CB A:ASP26 4.0 62.2 1.0
N A:GLU28 4.0 63.9 1.0
O 0:HOH5213 4.3 75.6 1.0
OD1 A:ASP26 4.3 66.3 1.0
SR A:SR8930 4.3 0.2 1.0
O 0:HOH7912 4.5 49.3 1.0
CG A:LEU27 4.5 54.5 1.0
N A:ASP26 4.5 57.6 1.0
O A:ALA25 4.5 57.1 1.0
O5' 0:G1873 4.8 40.4 1.0
CA A:GLU28 4.8 66.5 1.0
O A:HOH9001 4.9 56.5 1.0
CB A:GLU28 4.9 68.1 1.0
NE A:ARG120 5.0 38.4 1.0
C A:ALA25 5.0 56.1 1.0

Magnesium binding site 2 out of 93 in 3ccv

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Magnesium binding site 2 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg8042

b:44.6
occ:1.00
 O B:HOH9134 2.3 33.5 1.0
O B:HOH9133 2.5 77.7 1.0
O U:HOH2221 2.5 44.8 1.0
O 0:HOH6443 2.5 42.8 1.0
O B:HOH9022 2.7 31.5 1.0
OXT B:GLY337 3.2 59.0 1.0
O B:HOH9135 3.4 63.1 1.0
C B:GLY337 4.1 56.8 1.0
O B:GLY337 4.4 57.1 1.0
OP2 0:U2721 4.5 44.5 1.0
O 0:HOH4274 4.5 73.7 1.0
OP1 0:C2720 4.6 45.8 1.0
CG2 U:THR17 4.7 45.7 1.0
OE2 B:GLU333 4.7 49.6 1.0
O U:CYS32 4.8 49.6 1.0
CB U:SER33 4.8 51.6 1.0
O 0:HOH3710 4.8 53.6 1.0
OP1 0:U2721 4.8 43.9 1.0
OE1 B:GLU333 4.8 52.0 1.0

Magnesium binding site 3 out of 93 in 3ccv

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Magnesium binding site 3 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg8054

b:37.5
occ:1.00
 O K:HOH7871 2.3 59.0 1.0
O 0:HOH4258 2.4 49.0 1.0
O 0:HOH6070 2.5 24.8 1.0
O K:HOH2121 2.5 19.4 1.0
O 0:HOH3429 2.6 49.8 1.0
OD1 K:ASN42 2.7 35.2 1.0
O 0:HOH4712 3.5 43.9 1.0
CG K:ASN42 3.8 34.7 1.0
OP1 0:U2546 4.1 38.9 1.0
O 0:HOH5562 4.1 65.4 1.0
ND2 K:ASN42 4.3 34.5 1.0
OP1 0:U1749 4.5 37.9 1.0
C5' 0:U2545 4.5 37.5 1.0
CE K:LYS41 4.5 45.7 1.0
O 0:HOH7774 4.5 32.9 1.0
OP1 0:U2545 4.7 40.1 1.0
OP1 0:A2583 4.8 38.2 1.0
O 0:HOH3845 4.9 41.1 1.0
P 0:U2546 4.9 38.8 1.0
OP2 0:U2546 5.0 38.2 1.0
O3' 0:U2545 5.0 36.6 1.0

Magnesium binding site 4 out of 93 in 3ccv

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Magnesium binding site 4 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg8057

b:66.9
occ:1.00
 O T:SER114 2.5 94.1 1.0
O T:LEU112 2.8 72.3 1.0
O T:ASP117 2.9 0.8 1.0
O T:HOH2868 2.9 52.2 1.0
OE1 T:GLN37 3.3 64.7 1.0
C T:SER114 3.5 93.8 1.0
C T:LEU112 3.6 72.7 1.0
O T:ARG111 3.6 67.1 1.0
O T:TYR35 3.7 60.5 1.0
CG T:GLN37 4.0 60.2 1.0
C T:ASP117 4.1 0.3 1.0
CD T:GLN37 4.1 61.7 1.0
C T:GLU113 4.1 82.6 1.0
O T:GLU113 4.2 83.1 1.0
N T:SER114 4.2 86.1 1.0
CA T:GLU115 4.3 0.8 1.0
CA T:LEU112 4.3 70.5 1.0
N T:GLU115 4.3 97.6 1.0
N T:GLU113 4.4 76.2 1.0
CA T:SER118 4.5 0.8 1.0
CA T:SER114 4.5 90.9 1.0
CA T:GLU113 4.6 80.4 1.0
C T:ARG111 4.6 66.7 1.0
OG T:SER114 4.6 93.5 1.0
N T:SER118 4.7 0.2 1.0
C T:GLU115 4.8 0.0 1.0
C T:TYR35 4.9 59.5 1.0
N T:LEU112 4.9 68.5 1.0

Magnesium binding site 5 out of 93 in 3ccv

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Magnesium binding site 5 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg8086

b:36.0
occ:1.00
 O Y:HOH9065 2.5 41.7 1.0
O Y:HIS133 2.5 31.2 1.0
O Y:HOH9100 2.6 42.5 1.0
O Y:VAL139 2.6 31.9 1.0
O Y:HOH9045 2.6 40.8 1.0
O Y:LYS136 2.6 32.9 1.0
O Y:LYS137 3.4 31.0 1.0
CA Y:LYS137 3.4 31.8 1.0
C Y:LYS136 3.5 30.9 1.0
C Y:LYS137 3.6 31.2 1.0
C Y:VAL139 3.6 31.8 1.0
C Y:HIS133 3.6 32.1 1.0
N Y:LYS137 3.8 31.0 1.0
N Y:VAL139 4.2 30.1 1.0
CA Y:HIS133 4.4 32.7 1.0
CA Y:VAL139 4.4 30.8 1.0
N Y:SER140 4.5 32.4 1.0
N Y:ARG138 4.6 31.2 1.0
CA Y:SER140 4.6 32.6 1.0
CB Y:HIS133 4.6 33.3 1.0
N Y:HIS134 4.7 32.0 1.0
CB Y:LYS137 4.7 31.8 1.0
O Y:HOH9021 4.7 31.7 1.0
CA Y:LYS136 4.7 30.3 1.0
N Y:LYS136 4.8 30.4 1.0
CD2 Y:HIS133 4.8 33.7 1.0
CB Y:VAL139 4.8 29.4 1.0
CA Y:HIS134 4.9 33.3 1.0

Magnesium binding site 6 out of 93 in 3ccv

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Magnesium binding site 6 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8001

b:30.9
occ:1.00
 OP2 0:C2534 2.1 38.0 1.0
OP2 0:C2533 2.1 37.0 1.0
O 0:HOH9183 2.2 36.0 1.0
O 0:HOH7787 2.2 30.1 1.0
O 0:HOH3624 2.3 31.8 1.0
OP2 0:A2483 2.4 40.0 1.0
O3' 0:G2482 3.1 38.4 1.0
P 0:A2483 3.3 38.3 1.0
O 0:HOH9647 3.6 38.8 1.0
P 0:C2534 3.6 39.7 1.0
P 0:C2533 3.6 39.6 1.0
O2' 0:A2532 3.9 38.4 1.0
OP2 0:U2484 4.1 40.1 1.0
O2' 0:G2482 4.1 35.0 1.0
O3' 0:A2532 4.1 39.6 1.0
O 0:HOH4345 4.3 46.4 1.0
O 0:HOH6395 4.3 72.8 1.0
OP1 0:A2483 4.3 39.8 1.0
OP1 0:C2534 4.3 38.0 1.0
C3' 0:G2482 4.4 36.5 1.0
O3' 0:C2533 4.4 36.8 1.0
O5' 0:A2483 4.5 38.5 1.0
O5' 0:C2534 4.5 38.4 1.0
OP1 0:C2533 4.5 42.2 1.0
O5' 0:C2533 4.5 37.0 1.0
C5' 0:A2483 4.6 34.8 1.0
C3' 0:C2533 4.7 33.7 1.0
C2' 0:G2482 4.7 36.6 1.0
C1' 0:G2482 4.8 37.8 1.0
C5 0:C2534 4.9 50.0 1.0
O 0:HOH7494 5.0 37.3 1.0
C2' 0:A2532 5.0 39.3 1.0

Magnesium binding site 7 out of 93 in 3ccv

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Magnesium binding site 7 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8002

b:30.5
occ:1.00
 O6 0:G627 2.0 35.0 1.0
OP1 0:A2483 2.1 39.8 1.0
O 0:HOH7765 2.2 48.8 1.0
O 0:HOH4345 2.3 46.4 1.0
OP1 0:C2534 2.4 38.0 1.0
O 0:HOH7766 2.4 28.6 1.0
P 0:A2483 3.2 38.3 1.0
C6 0:G627 3.2 34.3 1.0
OP2 0:A2483 3.5 40.0 1.0
O4 0:U626 3.6 38.4 1.0
P 0:C2534 3.6 39.7 1.0
O 0:HOH7122 3.8 37.9 1.0
N1 0:G627 4.0 34.4 1.0
O2' 0:U625 4.1 29.2 1.0
C5 0:U626 4.1 36.1 1.0
O 0:HOH9270 4.2 25.0 1.0
OP2 0:C2534 4.2 38.0 1.0
C4 0:U626 4.2 37.5 1.0
O5' 0:A2483 4.2 38.5 1.0
O 0:HOH5896 4.2 70.1 1.0
O3' 0:C2533 4.3 36.8 1.0
C5 0:G627 4.4 32.3 1.0
O3' 0:G2482 4.4 38.4 1.0
O 0:HOH3539 4.6 52.8 1.0
OP2 0:U2535 4.7 41.8 1.0
N7 0:G627 4.8 31.9 1.0
O5' 0:C2534 4.8 38.4 1.0
C3' 0:G2482 5.0 36.5 1.0

Magnesium binding site 8 out of 93 in 3ccv

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Magnesium binding site 8 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8003

b:26.7
occ:1.00
 OP1 0:A2624 2.1 29.1 1.0
OP2 0:G877 2.1 24.2 1.0
O 0:HOH3675 2.3 33.3 1.0
O A:HOH8980 2.3 22.9 1.0
OP2 0:A876 2.4 30.8 1.0
O 0:HOH9836 2.7 44.0 1.0
P 0:G877 3.4 25.8 1.0
P 0:A2624 3.5 31.6 1.0
OD1 A:ASN195 3.7 33.6 1.0
P 0:A876 3.8 31.5 1.0
OP1 0:G877 3.8 25.9 1.0
O A:HOH9010 4.0 48.1 1.0
O3' 0:G2623 4.1 31.3 1.0
OP2 0:A2624 4.2 33.6 1.0
O A:ALA193 4.3 31.6 1.0
O3' 0:A875 4.3 30.5 1.0
O3' 0:A876 4.3 25.9 1.0
O 0:HOH6301 4.4 30.9 1.0
O A:HOH9079 4.5 50.1 1.0
O5' 0:A876 4.5 29.1 1.0
O5' 0:G877 4.5 24.7 1.0
O5' 0:A2624 4.6 31.9 1.0
CG A:ASN195 4.7 30.9 1.0
O A:HOH9028 4.7 38.9 1.0
C5' 0:A876 4.8 29.1 1.0
MG 0:MG8009 4.8 28.5 1.0
C5' 0:A2624 4.9 32.3 1.0
O A:HOH9086 4.9 35.2 1.0
C3' 0:A876 4.9 27.6 1.0
OP1 0:A876 4.9 30.7 1.0

Magnesium binding site 9 out of 93 in 3ccv

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Magnesium binding site 9 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8004

b:25.0
occ:1.00
 OP1 0:A459 2.1 25.9 1.0
O6 0:G456 2.1 33.2 1.0
O 0:HOH9052 2.2 30.1 1.0
O 0:HOH3796 2.2 23.8 1.0
O 0:HOH9787 2.2 19.5 1.0
O 0:HOH7772 2.2 32.6 1.0
C6 0:G456 3.2 34.4 1.0
P 0:A459 3.4 29.3 1.0
C5 0:G456 3.9 32.7 1.0
N7 0:G456 3.9 31.7 1.0
O5' 0:A459 4.1 27.2 1.0
OP2 0:A459 4.1 31.1 1.0
OP2 0:A455 4.2 28.4 1.0
C5' 0:A459 4.2 27.8 1.0
O 0:HOH3712 4.2 33.4 1.0
N1 0:G456 4.3 35.0 1.0
N7 0:A455 4.3 32.8 1.0
O 0:HOH3525 4.3 44.1 1.0
CE C:LYS85 4.3 26.9 1.0
O 0:HOH5981 4.4 58.8 1.0
NZ C:LYS85 4.5 25.2 1.0
O3' 0:G458 4.5 27.3 1.0
O 0:HOH9344 4.6 27.7 1.0
OP1 0:A460 4.6 31.4 1.0
CD C:LYS85 4.6 27.9 1.0
O 0:HOH5424 4.7 39.1 1.0
OP1 0:A477 4.7 29.8 1.0
O 0:HOH7773 4.8 15.9 1.0
C5' 0:U454 4.9 25.9 1.0
N6 0:A455 4.9 32.3 1.0

Magnesium binding site 10 out of 93 in 3ccv

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Magnesium binding site 10 out of 93 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8005

b:31.2
occ:1.00
 OP2 0:A1839 2.1 35.9 1.0
OP1 0:A1836 2.1 31.1 1.0
O 0:HOH3620 2.2 23.3 1.0
OP1 0:U1838 2.3 27.9 1.0
O 0:HOH7788 2.3 38.3 1.0
O 0:HOH7789 2.3 20.8 1.0
P 0:A1839 3.5 35.5 1.0
P 0:A1836 3.6 29.4 1.0
P 0:U1838 3.7 29.4 1.0
O 0:HOH5521 4.0 49.9 1.0
O5' 0:A1839 4.1 31.0 1.0
C2' 0:U1835 4.1 31.1 1.0
O 0:HOH9524 4.2 32.0 1.0
N7 0:A1839 4.2 31.3 1.0
O5' 0:A1836 4.3 32.2 1.0
C8 0:A1839 4.3 31.3 1.0
OP1 0:A1839 4.4 34.8 1.0
O5' 0:U1838 4.4 29.9 1.0
O 0:HOH9644 4.4 42.0 1.0
C3' 0:U1835 4.4 29.9 1.0
OP2 0:A1836 4.4 30.8 1.0
O3' 0:U1835 4.5 28.4 1.0
O3' 0:U1838 4.5 33.9 1.0
OP2 0:U1838 4.5 27.7 1.0
O2' 0:U1835 4.5 33.1 1.0
C3' 0:U1838 4.6 30.8 1.0
C3' 0:G1837 4.6 31.0 1.0
C5' 0:U1838 4.7 27.8 1.0
O3' 0:G1837 4.7 30.4 1.0
O 0:HOH9013 4.8 1.0 1.0
O 0:HOH5578 4.8 65.8 1.0
OP2 0:G1837 4.8 32.5 1.0
O 0:HOH7862 4.9 18.3 1.0

Reference:

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Wed Aug 14 10:34:29 2024

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