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Magnesium in PDB 3cd6: Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin

Protein crystallography data

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6 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) 49.95 / 2.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.805, 299.997, 576.002, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 3cd6:

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin also contains other interesting chemical elements:

Strontium (Sr) 107 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 Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin (pdb code 3cd6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 93 binding sites of Magnesium where determined in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 93 in 3cd6

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Magnesium binding site 1 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8050

b:60.4
occ:1.00
 O A:HOH8969 2.6 56.4 1.0
O 0:HOH9952 2.9 58.0 1.0
O A:HOH8942 2.9 60.5 1.0
O A:HOH9015 3.0 64.6 1.0
O A:HOH9044 3.0 36.0 1.0
O A:HOH8973 3.2 70.5 1.0
O A:ARG17 3.2 41.3 1.0
O A:THR15 3.2 45.6 1.0
O A:SER14 3.6 46.2 1.0
O2' 0:G782 3.8 35.1 1.0
C A:THR15 3.9 45.0 1.0
O3' 0:G782 4.2 32.8 1.0
CA A:THR15 4.3 44.4 1.0
O A:ARG182 4.3 56.3 1.0
C A:ARG17 4.4 42.4 1.0
C4' 0:G782 4.6 32.4 1.0
C A:SER14 4.6 45.0 1.0
N A:ARG17 4.7 43.4 1.0
N A:PHE16 4.7 44.2 1.0
O A:THR184 4.8 54.2 1.0
C3' 0:G782 4.8 33.5 1.0
C2' 0:G782 4.9 33.7 1.0
N A:THR15 5.0 44.3 1.0
O 0:HOH9372 5.0 76.5 1.0
C A:PHE16 5.0 43.0 1.0

Magnesium binding site 2 out of 93 in 3cd6

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Magnesium binding site 2 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8051

b:81.8
occ:1.00
 OP2 0:G1873 2.8 44.7 1.0
NH2 A:ARG120 2.9 55.6 1.0
N A:LEU27 3.1 75.1 1.0
O A:LEU27 3.1 80.6 1.0
NH1 A:ARG120 3.2 58.1 1.0
C A:ASP26 3.3 75.4 1.0
OP1 0:G1873 3.3 48.6 1.0
C A:LEU27 3.4 79.3 1.0
O A:HOH8980 3.4 0.3 1.0
CZ A:ARG120 3.4 55.7 1.0
OD2 A:ASP26 3.4 81.0 1.0
P 0:G1873 3.5 45.8 1.0
SR A:SR8930 3.5 0.6 1.0
CA A:LEU27 3.6 76.5 1.0
CG A:ASP26 3.7 79.7 1.0
CA A:ASP26 3.8 75.6 1.0
O A:ASP26 3.9 75.8 1.0
CG A:GLU28 3.9 86.2 1.0
O 0:HOH5238 4.0 76.5 1.0
O 0:HOH3013 4.0 80.2 1.0
OD1 A:ASP26 4.1 80.2 1.0
N A:GLU28 4.1 81.6 1.0
CB A:LEU27 4.3 73.3 1.0
O3' 0:C1872 4.3 47.0 1.0
CB A:ASP26 4.3 77.6 1.0
NE A:ARG120 4.7 55.3 1.0
CA A:GLU28 4.7 84.3 1.0
OE1 A:GLU28 4.8 88.4 1.0
O5' 0:G1873 4.9 45.5 1.0
CD A:GLU28 4.9 88.3 1.0
CB A:GLU28 4.9 84.9 1.0

Magnesium binding site 3 out of 93 in 3cd6

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Magnesium binding site 3 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg8042

b:56.0
occ:1.00
 O B:HOH9084 2.6 43.2 1.0
O U:HOH2221 2.7 63.5 1.0
O 0:HOH6464 2.8 57.2 1.0
O 0:HOH3827 2.8 60.0 1.0
O 0:HOH7767 3.1 86.5 1.0
OXT B:GLY337 3.2 63.5 1.0
C B:GLY337 3.9 61.4 1.0
O 0:HOH7936 3.9 0.5 1.0
O B:GLY337 4.2 61.5 1.0
O B:HOH8985 4.4 65.1 1.0
OP1 0:C2720 4.5 47.5 1.0
OE2 B:GLU333 4.7 55.2 1.0
OP2 0:U2721 4.7 47.0 1.0
O B:HOH8970 4.9 63.6 1.0
CA B:GLY337 4.9 59.1 1.0
CG2 U:THR17 4.9 63.9 1.0

Magnesium binding site 4 out of 93 in 3cd6

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Magnesium binding site 4 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg8054

b:44.6
occ:1.00
 O 0:HOH7939 2.5 85.9 1.0
O 0:HOH6093 2.6 42.6 1.0
O K:HOH2121 2.6 30.6 1.0
O 0:HOH4279 2.6 68.4 1.0
O 0:HOH3445 2.7 58.5 1.0
OD1 K:ASN42 2.9 36.3 1.0
O 0:HOH4731 3.3 62.0 1.0
CG K:ASN42 4.0 36.5 1.0
O 0:HOH5590 4.4 62.8 1.0
O 0:HOH7811 4.4 44.5 1.0
OP1 0:U2546 4.5 34.9 1.0
CE K:LYS41 4.6 48.9 1.0
OP1 0:U1749 4.6 34.5 1.0
OP1 0:A2583 4.6 38.0 1.0
OP1 0:U2545 4.6 41.4 1.0
ND2 K:ASN42 4.6 35.6 1.0
C5' 0:U2545 4.7 38.2 1.0
O 0:HOH5985 4.9 63.6 1.0
O 0:HOH7552 5.0 84.2 1.0

Magnesium binding site 5 out of 93 in 3cd6

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Magnesium binding site 5 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg8057

b:76.5
occ:1.00
 O T:LEU112 2.7 80.3 1.0
O T:SER114 2.7 99.6 1.0
O T:HOH2868 2.8 61.1 1.0
OE1 T:GLN37 3.1 63.7 1.0
O T:ASP117 3.1 0.9 1.0
O T:TYR35 3.3 58.8 1.0
C T:LEU112 3.4 80.0 1.0
O T:ARG111 3.6 75.7 1.0
C T:SER114 3.8 99.7 1.0
CD T:GLN37 3.8 62.2 1.0
CG T:GLN37 3.9 60.2 1.0
CA T:LEU112 4.1 77.7 1.0
N T:SER114 4.2 92.0 1.0
C T:GLU113 4.2 88.7 1.0
N T:GLU113 4.2 82.7 1.0
C T:ASP117 4.2 0.5 1.0
O T:GLU113 4.5 89.6 1.0
CA T:GLU113 4.5 86.0 1.0
C T:TYR35 4.5 58.5 1.0
C T:ARG111 4.6 75.1 1.0
CA T:SER118 4.6 0.7 1.0
CA T:SER114 4.6 96.6 1.0
N T:GLU115 4.7 0.1 1.0
N T:LEU112 4.8 75.7 1.0
CA T:GLU115 4.8 0.9 1.0
N T:SER118 4.9 0.8 1.0
OG T:SER114 4.9 97.7 1.0

Magnesium binding site 6 out of 93 in 3cd6

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Magnesium binding site 6 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg8086

b:36.1
occ:1.00
 O Y:HIS133 2.5 31.5 1.0
O Y:VAL139 2.6 33.4 1.0
O Y:HOH8879 2.7 41.0 1.0
O Y:HOH8859 2.7 35.2 1.0
O Y:LYS136 2.8 34.6 1.0
O 0:HOH7932 3.0 53.6 1.0
O Y:LYS137 3.4 33.3 1.0
CA Y:LYS137 3.4 33.0 1.0
C Y:LYS137 3.6 33.2 1.0
C Y:VAL139 3.6 33.8 1.0
C Y:LYS136 3.6 31.9 1.0
C Y:HIS133 3.7 32.6 1.0
N Y:LYS137 3.9 32.2 1.0
N Y:VAL139 4.3 31.8 1.0
CA Y:HIS133 4.4 32.7 1.0
N Y:SER140 4.5 35.7 1.0
O Y:HOH8836 4.5 36.2 1.0
CA Y:VAL139 4.5 32.6 1.0
CA Y:SER140 4.6 36.9 1.0
CB Y:HIS133 4.6 33.5 1.0
N Y:ARG138 4.6 33.9 1.0
CB Y:LYS137 4.6 33.2 1.0
N Y:HIS134 4.7 32.2 1.0
CA Y:LYS136 4.9 30.5 1.0
CB Y:VAL139 4.9 31.4 1.0
N Y:LYS136 5.0 30.7 1.0
CD2 Y:HIS133 5.0 34.5 1.0

Magnesium binding site 7 out of 93 in 3cd6

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Magnesium binding site 7 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8002

b:33.1
occ:1.00
 O6 0:G627 2.2 37.7 1.0
OP1 0:A2483 2.3 42.3 1.0
O 0:HOH7802 2.4 50.4 1.0
OP1 0:C2534 2.5 41.3 1.0
O 0:HOH4367 2.6 33.1 1.0
O 0:HOH7803 2.6 32.1 1.0
P 0:A2483 3.2 41.0 1.0
O 0:HOH7159 3.3 40.8 1.0
OP2 0:A2483 3.4 40.6 1.0
C6 0:G627 3.4 36.6 1.0
P 0:C2534 3.6 45.0 1.0
O4 0:U626 3.7 40.7 1.0
C5 0:U626 4.0 40.0 1.0
O5' 0:A2483 4.1 40.9 1.0
OP2 0:C2534 4.1 43.5 1.0
N1 0:G627 4.1 35.8 1.0
O2' 0:U625 4.2 31.0 1.0
C4 0:U626 4.2 39.6 1.0
O3' 0:C2533 4.2 41.3 1.0
O 0:HOH9274 4.3 37.8 1.0
O 0:HOH3554 4.4 48.6 1.0
O3' 0:G2482 4.5 42.2 1.0
C5 0:G627 4.5 35.6 1.0
O 0:HOH5919 4.6 70.5 1.0
O5' 0:C2534 4.9 42.0 1.0
OP2 0:U2535 4.9 45.4 1.0
O 0:HOH7529 4.9 50.8 1.0
OP2 0:C2533 4.9 42.2 1.0
N7 0:G627 5.0 35.3 1.0

Magnesium binding site 8 out of 93 in 3cd6

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Magnesium binding site 8 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8003

b:31.0
occ:1.00
 OP1 0:A2624 2.1 27.1 1.0
OP2 0:G877 2.2 33.1 1.0
O A:HOH8954 2.4 79.5 1.0
O A:HOH8933 2.5 42.4 1.0
OP2 0:A876 2.5 33.8 1.0
O 0:HOH3694 2.6 29.2 1.0
P 0:G877 3.2 33.4 1.0
OP1 0:G877 3.2 35.4 1.0
P 0:A2624 3.4 29.9 1.0
OD1 A:ASN195 3.7 32.7 1.0
P 0:A876 3.9 33.9 1.0
O3' 0:G2623 4.0 30.1 1.0
OP2 0:A2624 4.1 31.6 1.0
O 0:HOH9027 4.1 21.6 1.0
O3' 0:A876 4.2 32.1 1.0
O 0:HOH6322 4.2 45.4 1.0
O 0:HOH7217 4.3 64.3 1.0
O5' 0:G877 4.3 30.1 1.0
O5' 0:A876 4.4 32.2 1.0
O A:HOH8963 4.4 36.4 1.0
O3' 0:A875 4.5 30.1 1.0
O A:HOH9042 4.6 31.4 1.0
O5' 0:A2624 4.6 31.5 1.0
O A:ALA193 4.7 36.0 1.0
C5' 0:A876 4.7 32.3 1.0
CG A:ASN195 4.7 30.2 1.0
O A:HOH9035 4.8 45.7 1.0
C3' 0:A876 4.8 33.7 1.0
C5' 0:A2624 4.9 32.1 1.0

Magnesium binding site 9 out of 93 in 3cd6

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Magnesium binding site 9 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8004

b:24.5
occ:1.00
 OP1 0:A459 2.2 25.7 1.0
O6 0:G456 2.3 39.6 1.0
O 0:HOH7809 2.3 34.9 1.0
O 0:HOH3815 2.3 25.2 1.0
O 0:HOH9799 2.4 26.6 1.0
O 0:HOH9054 2.4 32.2 1.0
C6 0:G456 3.4 41.5 1.0
P 0:A459 3.6 28.4 1.0
O 0:HOH6005 4.1 68.4 1.0
CE C:LYS85 4.1 27.4 1.0
C5 0:G456 4.2 40.4 1.0
N7 0:G456 4.2 38.4 1.0
NZ C:LYS85 4.2 28.9 1.0
C5' 0:A459 4.3 27.8 1.0
O 0:HOH3731 4.3 36.2 1.0
OP2 0:A455 4.3 28.9 1.0
O5' 0:A459 4.3 26.6 1.0
OP2 0:A459 4.3 33.1 1.0
O 0:HOH3540 4.4 40.0 1.0
N1 0:G456 4.5 42.4 1.0
N7 0:A455 4.5 36.2 1.0
CD C:LYS85 4.5 27.9 1.0
O 0:HOH9348 4.5 31.7 1.0
OP1 0:A460 4.6 27.3 1.0
O3' 0:G458 4.6 27.0 1.0
OP1 0:A477 4.7 33.8 1.0
C5' 0:U454 4.8 31.1 1.0
OP2 0:A477 4.9 30.8 1.0
N6 0:A455 5.0 37.9 1.0

Magnesium binding site 10 out of 93 in 3cd6

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Magnesium binding site 10 out of 93 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8005

b:28.9
occ:1.00
 OP2 0:A1839 2.2 35.4 1.0
OP1 0:A1836 2.2 30.5 1.0
OP1 0:U1838 2.2 31.1 1.0
O 0:HOH3638 2.5 45.0 1.0
O 0:HOH7825 2.5 31.7 1.0
O 0:HOH7826 2.6 32.7 1.0
P 0:U1838 3.4 30.8 1.0
P 0:A1839 3.5 36.0 1.0
P 0:A1836 3.6 30.8 1.0
OP2 0:U1838 3.9 31.9 1.0
O 0:HOH5551 4.0 52.0 1.0
O5' 0:A1839 4.0 33.8 1.0
N7 0:A1839 4.1 31.4 1.0
C2' 0:U1835 4.1 33.6 1.0
O 0:HOH9530 4.1 47.4 1.0
O5' 0:U1838 4.2 30.2 1.0
C8 0:A1839 4.3 32.6 1.0
OP2 0:A1836 4.3 34.4 1.0
O3' 0:U1838 4.4 32.9 1.0
O3' 0:U1835 4.4 29.4 1.0
O2' 0:U1835 4.4 35.9 1.0
C3' 0:U1838 4.4 31.0 1.0
C3' 0:U1835 4.4 33.1 1.0
O5' 0:A1836 4.5 32.1 1.0
O3' 0:G1837 4.6 30.6 1.0
O 0:HOH5606 4.6 53.0 1.0
OP1 0:A1839 4.6 37.2 1.0
C3' 0:G1837 4.7 33.2 1.0
O 0:HOH9657 4.7 30.5 1.0
C5' 0:U1838 4.7 30.0 1.0
O 0:HOH7900 4.9 33.4 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: Sun Aug 10 19:12:05 2025

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