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Manganese in PDB 4wfb: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205

Protein crystallography data

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205, PDB code: 4wfb was solved by Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, E.Zimmerman, H.Rozenberg, A.Bashan, A.E.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.54 / 3.43
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 280.918, 280.918, 875.585, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 24.2

Other elements in 4wfb:

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 also contains other interesting chemical elements:

Magnesium (Mg) 111 atoms

Manganese 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 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 311;

Binding sites:

The binding sites of Manganese atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 (pdb code 4wfb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 311 binding sites of Manganese where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205, PDB code: 4wfb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 311 in 4wfb

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Manganese binding site 1 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3018

b:0.4
occ:1.00
OP2 X:G2075 4.6 31.9 1.0
OP2 X:C2074 4.7 31.1 1.0
N7 X:A2076 4.7 31.5 1.0
N7 X:G2075 4.8 32.4 1.0
N6 X:A2076 5.0 30.8 1.0

Manganese binding site 2 out of 311 in 4wfb

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Manganese binding site 2 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3019

b:0.6
occ:1.00
O6 X:G903 4.5 45.3 1.0
N7 X:G903 4.8 46.4 1.0

Manganese binding site 3 out of 311 in 4wfb

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Manganese binding site 3 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3020

b:1.0
occ:1.00
O6 X:G601 2.9 31.7 1.0
O6 X:G602 3.3 30.5 1.0
O6 X:G578 3.6 29.7 1.0
C6 X:G601 3.7 31.9 1.0
O4 X:U579 3.8 30.5 1.0
N4 X:C603 3.9 32.3 1.0
N7 X:G602 4.1 30.8 1.0
C5 X:G601 4.2 32.0 1.0
N7 X:G601 4.2 31.9 1.0
C6 X:G602 4.2 30.6 1.0
C5 X:G602 4.6 30.8 1.0
N1 X:G601 4.6 32.0 1.0
C6 X:G578 4.7 29.6 1.0
N4 X:C580 4.7 35.6 1.0
C4 X:U579 4.8 30.5 1.0
C4 X:C603 4.9 32.3 1.0

Manganese binding site 4 out of 311 in 4wfb

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Manganese binding site 4 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3021

b:0.1
occ:1.00
N7 X:A2604 3.1 31.0 1.0
N7 X:G2083 3.5 30.0 1.0
C8 X:G2083 3.7 29.6 1.0
OP2 X:A2081 3.8 29.7 1.0
C8 X:A2604 3.8 31.4 1.0
OP2 X:G2080 4.0 31.3 1.0
C5 X:A2604 4.3 30.6 1.0
MN X:MN3334 4.4 48.6 1.0
OP1 X:G2080 4.5 31.8 1.0
P X:G2080 4.5 31.4 1.0
N6 X:A2604 4.6 30.0 1.0
O5' X:G2080 4.6 30.9 1.0
C5 X:G2083 4.7 29.9 1.0
N9 X:G2083 4.9 29.2 1.0
C6 X:A2604 4.9 30.1 1.0

Manganese binding site 5 out of 311 in 4wfb

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Manganese binding site 5 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3022

b:0.1
occ:1.00
OP1 X:A2459 3.2 85.2 1.0
OP1 X:C252 3.2 62.8 1.0
OP2 X:A2459 3.2 84.6 1.0
P X:A2459 3.7 84.9 1.0
OP1 X:U2458 4.1 66.2 1.0
O2 X:C2421 4.2 57.8 1.0
P X:C252 4.3 64.1 1.0
C2' X:G251 4.4 61.3 1.0
OP2 X:U2458 4.5 68.8 1.0
O3' X:U2458 4.6 72.0 1.0
OP2 X:C252 4.6 65.5 1.0
O2' X:G251 4.6 62.5 1.0
P X:U2458 4.7 67.0 1.0
O5' X:U2458 5.0 68.0 1.0
O3' X:G251 5.0 62.9 1.0

Manganese binding site 6 out of 311 in 4wfb

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Manganese binding site 6 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3023

b:0.1
occ:1.00
O4 X:U812 2.6 79.4 1.0
C4 X:U812 3.2 78.2 1.0
N3 X:U812 3.9 78.6 1.0
O6 X:G740 4.0 74.7 1.0
C5 X:U812 4.0 76.4 1.0
O4 X:U739 4.7 69.5 1.0
N4 X:C811 4.8 79.3 1.0

Manganese binding site 7 out of 311 in 4wfb

Go back to Manganese Binding Sites List in 4wfb
Manganese binding site 7 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3024

b:0.1
occ:1.00
OP1 X:U1750 2.0 90.0 1.0
P X:U1750 3.2 88.9 1.0
OP2 X:U1750 3.6 87.6 1.0
O3' X:G1749 4.2 0.1 1.0
O5' X:U1750 4.3 88.3 1.0
C5' X:U1750 4.9 89.4 1.0

Manganese binding site 8 out of 311 in 4wfb

Go back to Manganese Binding Sites List in 4wfb
Manganese binding site 8 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3025

b:1.0
occ:1.00
O6 X:G189 3.8 70.0 1.0
N7 X:G189 4.3 72.3 1.0
O6 X:G190 4.3 66.6 1.0
C6 X:G189 4.6 71.2 1.0
C5 X:G189 4.8 72.3 1.0
N6 X:A191 4.9 75.3 1.0
N4 X:C188 4.9 69.5 1.0

Manganese binding site 9 out of 311 in 4wfb

Go back to Manganese Binding Sites List in 4wfb
Manganese binding site 9 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3032

b:0.1
occ:1.00
O4 X:U2116 2.4 0.1 1.0
C4 X:U2116 3.0 0.1 1.0
C5 X:U2116 3.1 0.0 1.0
C6 X:U2116 4.4 0.9 1.0
N3 X:U2116 4.4 0.2 1.0
N7 X:A2115 4.5 95.9 1.0
OP2 X:A2115 4.6 0.3 1.0
OP2 X:A2254 4.9 0.8 1.0

Manganese binding site 10 out of 311 in 4wfb

Go back to Manganese Binding Sites List in 4wfb
Manganese binding site 10 out of 311 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3033

b:0.7
occ:1.00
N2 X:G2278 3.2 40.1 1.0
N1 X:G2278 3.7 40.8 1.0
C2 X:G2278 3.9 40.1 1.0
C5' X:C2091 4.2 39.3 1.0
C4' X:C2091 4.3 38.7 1.0
N2 X:G2279 4.5 52.0 1.0
O3' X:C2091 4.6 39.2 1.0
N3 X:G2279 4.8 49.4 1.0
C2 X:G2279 4.8 51.0 1.0
C6 X:G2278 4.9 40.9 1.0

Reference:

Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, S.Paukner, E.Zimmerman, H.Rozenberg, A.Bashan, A.Yonath. Structural Insights Into Species-Specific Features of the Ribosome From the Pathogen Staphylococcus Aureus. Proc.Natl.Acad.Sci.Usa V. 112 E5805 2015.
ISSN: ESSN 1091-6490
PubMed: 26464510
DOI: 10.1073/PNAS.1517952112
Page generated: Tue Dec 15 04:31:48 2020

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