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Cadmium in PDB 3i55: Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit, PDB code: 3i55 was solved by G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.98 / 3.11
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.324, 299.649, 574.241, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26

Other elements in 3i55:

The structure of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium (Sr) 108 atoms
Magnesium (Mg) 93 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit (pdb code 3i55). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit, PDB code: 3i55:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3i55

Go back to Cadmium Binding Sites List in 3i55
Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:0.2
occ:1.00
 O O:HOH5650 2.5 53.1 1.0
ND1 O:HIS40 2.8 48.8 1.0
O O:HOH5322 3.1 79.5 1.0
CG O:HIS40 3.7 49.1 1.0
CE1 O:HIS40 3.7 48.4 1.0
CB O:HIS40 3.8 50.4 1.0
CG O:ARG37 4.6 59.4 1.0
CZ O:ARG37 4.6 58.2 1.0
O O:HOH3002 4.7 65.8 1.0
CB O:ARG37 4.8 58.8 1.0
NH2 O:ARG37 4.8 57.9 1.0
NE O:ARG37 4.8 58.3 1.0
NH1 O:ARG37 4.8 56.4 1.0
NE2 O:HIS40 4.9 49.0 1.0
CD2 O:HIS40 4.9 49.3 1.0
O O:HOH7077 4.9 46.0 1.0
CA O:ARG37 4.9 58.1 1.0

Cadmium binding site 2 out of 5 in 3i55

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Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:0.0
occ:1.00
 CB U:CYS36 3.0 0.3 1.0
SG U:CYS6 3.1 0.9 1.0
CB U:TYR8 3.3 0.8 1.0
N U:CYS32 3.4 0.1 1.0
CA U:PHE31 3.6 0.9 1.0
CD2 U:PHE31 3.7 0.7 1.0
CB U:PHE31 3.8 0.4 1.0
CD2 U:TYR8 3.9 0.9 1.0
SG U:CYS36 3.9 0.9 1.0
N U:CYS9 3.9 0.7 1.0
C U:PHE31 4.0 0.7 1.0
CG U:TYR8 4.0 0.0 1.0
CG U:PHE31 4.1 0.9 1.0
SG U:CYS32 4.2 0.9 1.0
SG U:CYS9 4.2 1.0 1.0
CA U:TYR8 4.3 0.2 1.0
CA U:CYS36 4.3 0.8 1.0
N U:SER33 4.4 0.5 1.0
CB U:CYS9 4.4 0.8 1.0
C U:CYS36 4.5 0.3 1.0
N U:TYR8 4.5 0.2 1.0
CA U:CYS32 4.5 0.3 1.0
O U:HIS30 4.5 0.3 1.0
O U:SER33 4.6 0.4 1.0
CB U:CYS32 4.6 0.9 1.0
C U:TYR8 4.6 0.8 1.0
CE2 U:PHE31 4.7 0.4 1.0
O U:CYS36 4.8 0.7 1.0
N U:PHE31 4.8 0.3 1.0
CA U:CYS9 4.8 0.8 1.0
OG U:SER33 4.8 0.1 1.0
N U:GLU37 4.9 0.1 1.0
CB U:CYS6 4.9 0.2 1.0
C U:CYS32 5.0 1.0 1.0

Cadmium binding site 3 out of 5 in 3i55

Go back to Cadmium Binding Sites List in 3i55
Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:0.0
occ:1.00
 CB Z:CYS84 2.9 0.4 1.0
CB Z:ASN65 3.4 0.8 1.0
SG Z:CYS66 3.4 0.1 1.0
SG Z:CYS81 3.4 0.7 1.0
N Z:CYS84 3.7 0.5 1.0
N Z:CYS66 3.8 0.6 1.0
CB Z:CYS66 3.8 0.9 1.0
CA Z:CYS84 3.8 0.3 1.0
CB Z:CYS81 4.1 0.9 1.0
CD2 Z:TYR83 4.1 0.7 1.0
C Z:ASN65 4.1 0.9 1.0
CA Z:ASN65 4.2 0.2 1.0
CB Z:TYR86 4.2 0.1 1.0
SG Z:CYS84 4.2 0.5 1.0
CB Z:CYS63 4.4 0.9 1.0
C Z:CYS84 4.4 0.8 1.0
CA Z:CYS66 4.4 0.9 1.0
N Z:ASN65 4.5 0.6 1.0
SG Z:CYS63 4.5 0.1 1.0
CG Z:ASN65 4.6 0.6 1.0
CB Z:TYR83 4.7 0.6 1.0
N Z:TYR86 4.7 0.4 1.0
ND2 Z:ASN65 4.8 0.4 1.0
N Z:ASP85 4.8 0.4 1.0
O Z:ASN65 4.9 0.7 1.0
CG Z:TYR83 4.9 0.2 1.0
C Z:TYR83 4.9 0.1 1.0
O Z:CYS63 4.9 0.2 1.0
O Z:CYS84 5.0 0.4 1.0
CE2 Z:TYR83 5.0 0.2 1.0

Cadmium binding site 4 out of 5 in 3i55

Go back to Cadmium Binding Sites List in 3i55
Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:78.5
occ:1.00
 SG 1:CYS37 2.4 52.5 1.0
SG 1:CYS34 2.5 45.4 1.0
SG 1:CYS22 2.5 47.2 1.0
SG 1:CYS19 2.5 49.9 1.0
CB 1:CYS22 3.1 48.0 1.0
CB 1:CYS19 3.2 49.0 1.0
CB 1:CYS34 3.2 41.0 1.0
CB 1:CYS37 3.3 47.6 1.0
N 1:CYS22 3.5 49.9 1.0
N 1:CYS37 3.8 46.8 1.0
CA 1:CYS22 3.9 48.0 1.0
CB 1:PHE39 4.0 57.6 1.0
CA 1:CYS37 4.1 47.6 1.0
N 1:PHE39 4.6 53.7 1.0
C 1:CYS22 4.6 46.9 1.0
CB 1:ARG21 4.6 47.8 1.0
N 1:GLY23 4.6 45.5 1.0
C 1:CYS37 4.6 47.4 1.0
C 1:ARG21 4.7 50.7 1.0
CA 1:CYS34 4.7 42.3 1.0
CA 1:CYS19 4.7 49.0 1.0
CB 1:SER36 4.8 43.1 1.0
N 1:GLY38 4.8 48.3 1.0
N 1:ARG21 4.9 50.5 1.0
CD 1:ARG21 4.9 44.0 1.0
CA 1:ARG21 4.9 49.7 1.0
CA 1:PHE39 5.0 56.5 1.0
C 1:SER36 5.0 45.5 1.0

Cadmium binding site 5 out of 5 in 3i55

Go back to Cadmium Binding Sites List in 3i55
Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Co-Crystal Structure of Mycalamide A Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:0.0
occ:1.00
 CB 3:CYS11 3.5 0.6 1.0
CB 3:CYS14 3.9 0.7 1.0
N 3:CYS14 4.0 0.3 1.0
SG 3:CYS14 4.2 0.1 1.0
SG 3:CYS11 4.2 0.6 1.0
CE1 3:HIS20 4.2 0.4 1.0
CB 3:HIS13 4.4 0.2 1.0
O 3:CYS11 4.4 0.9 1.0
SG 3:CYS71 4.5 0.9 1.0
CA 3:CYS14 4.5 0.6 1.0
CA 3:CYS11 4.5 0.7 1.0
NE2 3:HIS20 4.5 0.3 1.0
CG 3:GLU16 4.7 0.5 1.0
N 3:CYS11 4.7 0.7 1.0
C 3:CYS11 4.8 0.0 1.0
NE2 3:GLN18 4.8 0.7 1.0
O 3:GLU16 4.9 0.6 1.0
C 3:HIS13 5.0 1.0 1.0
OE1 3:GLU16 5.0 0.5 1.0

Reference:

G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore. Structures of Triacetyloleandomycin and Mycalamide A Bind to the Large Ribosomal Subunit of Haloarcula Marismortui. Antimicrob.Agents Chemother. V. 53 5010 2009.
ISSN: ISSN 0066-4804
PubMed: 19738021
DOI: 10.1128/AAC.00817-09
Page generated: Thu Jul 10 12:41:45 2025

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