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Manganese in PDB 4wf9: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin

Protein crystallography data

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin, PDB code: 4wf9 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) 50.19 / 3.43
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 282.660, 282.660, 877.075, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.2

Other elements in 4wf9:

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

Magnesium (Mg) 149 atoms

Manganese Binding Sites:

Manganese binding site 1 out of 231 in 4wf9

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Manganese binding site 1 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3032

b:0.1
occ:1.00
OP2 X:G190 3.7 72.8 1.0
OP2 X:A191 3.8 86.5 1.0
N7 X:A191 4.0 68.5 1.0
O6 X:G192 4.0 75.8 1.0
N7 X:G192 4.2 76.5 1.0
O5' X:G190 4.5 77.7 1.0
P X:G190 4.5 78.8 1.0
C8 X:A191 4.6 69.1 1.0
OP1 X:G190 4.7 83.3 1.0
C6 X:G192 4.7 71.6 1.0
C5 X:G192 4.8 71.7 1.0

Manganese binding site 2 out of 231 in 4wf9

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Manganese binding site 2 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3033

b:0.0
occ:1.00
O6 X:G214 3.6 68.9 1.0
N7 X:G214 3.9 69.8 1.0
O6 X:G215 3.9 71.8 1.0
N4 X:C213 4.3 73.7 1.0
C6 X:G214 4.3 70.1 1.0
C5 X:G214 4.5 70.6 1.0
N7 X:G215 4.5 78.4 1.0
C4 X:C213 4.7 75.7 1.0
C5 X:C213 4.7 72.6 1.0
C6 X:G215 4.8 74.8 1.0
C8 X:G214 5.0 70.9 1.0

Manganese binding site 3 out of 231 in 4wf9

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Manganese binding site 3 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3034

b:82.0
occ:1.00
OP2 X:G2609 2.3 49.1 1.0
OP2 X:G2610 2.5 59.5 1.0
O4 X:U2611 3.4 60.1 1.0
P X:G2609 3.6 47.3 1.0
O3' X:G2608 3.8 60.8 1.0
P X:G2610 3.9 65.9 1.0
C4 X:U2611 4.1 62.7 1.0
C5 X:U2611 4.1 68.9 1.0
MN X:MN3035 4.2 0.1 1.0
O2' X:G2608 4.2 51.7 1.0
N7 X:G2610 4.4 48.5 1.0
O5' X:G2609 4.6 51.6 1.0
O5' X:G2610 4.6 66.5 1.0
OP1 X:G2609 4.6 46.3 1.0
C8 X:G2610 4.7 54.3 1.0
OP1 X:G2610 4.8 70.7 1.0
C3' X:G2609 4.9 60.8 1.0
O3' X:G2609 4.9 65.0 1.0

Manganese binding site 4 out of 231 in 4wf9

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Manganese binding site 4 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3035

b:0.1
occ:1.00
OP1 X:G2610 2.1 70.7 1.0
P X:G2610 3.0 65.9 1.0
OP2 X:G2610 3.1 59.5 1.0
O3' X:G2609 4.1 65.0 1.0
O5' X:G2610 4.2 66.5 1.0
MN X:MN3034 4.2 82.0 1.0
OP2 X:G2609 4.4 49.1 1.0
N7 X:G2635 4.5 63.4 1.0
OP2 X:U2611 4.5 89.2 1.0
O6 X:G2635 4.7 65.3 1.0

Manganese binding site 5 out of 231 in 4wf9

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Manganese binding site 5 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3036

b:96.6
occ:1.00
N7 X:A2480 4.0 38.4 1.0
O6 X:G2482 4.1 39.8 1.0
O6 X:G2481 4.1 38.2 1.0
N7 X:G2481 4.3 38.1 1.0
N4 X:C2523 4.4 40.8 1.0
N1 X:A2524 4.5 44.4 1.0
C2 X:A2524 4.6 40.1 1.0
C8 X:A2480 4.8 38.5 1.0
N6 X:A2480 4.8 37.8 1.0
OP2 X:C2479 4.8 61.4 1.0
OP2 X:A2480 4.9 45.5 1.0
C6 X:G2481 4.9 37.8 1.0
C5 X:A2480 4.9 37.8 1.0

Manganese binding site 6 out of 231 in 4wf9

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Manganese binding site 6 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3037

b:0.5
occ:1.00
OP2 X:A126 3.5 70.1 1.0
N7 X:A126 4.1 66.9 1.0
C8 X:A126 4.5 68.3 1.0
P X:A126 4.9 77.1 1.0

Manganese binding site 7 out of 231 in 4wf9

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Manganese binding site 7 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3038

b:0.6
occ:1.00
OP2 X:G1340 2.9 59.2 1.0
OP1 X:A1652 3.1 67.0 1.0
OP1 X:C1651 3.4 83.0 1.0
OP1 X:G1340 3.6 56.8 1.0
P X:G1340 3.7 58.7 1.0
C5' X:A1652 4.3 62.9 1.0
OP1 X:G1650 4.4 56.4 1.0
P X:A1652 4.6 63.3 1.0
O5' X:C1651 4.6 79.2 1.0
P X:C1651 4.6 83.1 1.0
C3' X:C1651 4.7 72.8 1.0
O5' X:G1340 4.7 63.6 1.0
OP2 X:A1341 4.8 58.2 1.0
C5' X:G1650 4.9 59.8 1.0
C5' X:C1651 4.9 74.5 1.0
O3' X:U1339 5.0 76.4 1.0
O5' X:A1652 5.0 61.0 1.0

Manganese binding site 8 out of 231 in 4wf9

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Manganese binding site 8 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3039

b:0.9
occ:1.00
OP1 X:U2022 2.3 46.4 1.0
P X:U2022 3.7 47.1 1.0
OP1 X:U2538 4.0 44.2 1.0
O3' X:C2021 4.1 47.5 1.0
OP2 X:A2024 4.4 44.5 1.0
O B:ARG138 4.5 45.6 1.0
OP2 X:U2022 4.6 46.9 1.0
O5' X:U2022 4.7 48.0 1.0
CB B:SER137 4.8 53.6 1.0
C5' X:U2022 4.9 48.6 1.0
OG B:SER137 4.9 53.7 1.0

Manganese binding site 9 out of 231 in 4wf9

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Manganese binding site 9 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3040

b:0.4
occ:1.00
O2 X:C988 3.5 40.1 1.0
N7 X:A868 3.6 44.8 1.0
N7 X:G869 3.8 48.7 1.0
OP2 X:A868 3.9 42.6 1.0
O6 X:G869 4.0 44.4 1.0
C8 X:A868 4.3 46.2 1.0
C5 X:A868 4.4 47.5 1.0
N4 X:C870 4.4 44.5 1.0
N6 X:A868 4.5 45.1 1.0
C5 X:G869 4.6 49.8 1.0
C2 X:C988 4.7 39.6 1.0
C6 X:G869 4.7 47.8 1.0
C6 X:A868 4.8 47.8 1.0
C8 X:G869 4.9 51.8 1.0
O5' X:A868 5.0 45.5 1.0

Manganese binding site 10 out of 231 in 4wf9

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Manganese binding site 10 out of 231 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Telithromycin


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 Telithromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn3041

b:0.9
occ:1.00
N4 X:C695 3.9 63.4 1.0
OP2 X:G694 4.5 67.3 1.0
N7 X:G696 4.6 75.6 1.0
C5 X:C695 4.7 61.8 1.0
C4 X:C695 4.8 62.8 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 04:30:39 2020

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