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Sodium in PDB 3pip: Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit

Protein crystallography data

The structure of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit, PDB code: 3pip was solved by M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, H.Kinashi, H.Rozenberg, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.45
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 169.723, 408.562, 693.334, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 30.1

Other elements in 3pip:

The structure of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit also contains other interesting chemical elements:

Magnesium (Mg) 73 atoms
Potassium (K) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit (pdb code 3pip). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit, PDB code: 3pip:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3pip

Go back to Sodium Binding Sites List in 3pip
Sodium binding site 1 out of 5 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na2958

b:48.4
occ:1.00
N6 X:A2220 3.4 0.3 1.0
N7 X:A2220 3.5 0.6 1.0
O6 X:G2221 3.7 81.1 1.0
C5 X:A2220 4.0 0.8 1.0
C6 X:A2220 4.0 0.3 1.0
O4 X:U2222 4.2 94.7 1.0
C8 X:G2217 4.3 0.8 1.0
N7 X:G2217 4.3 0.5 1.0
O4 X:U2057 4.4 0.8 1.0
N7 X:G2221 4.5 99.9 1.0
C8 X:A2220 4.5 0.4 1.0
C6 X:G2221 4.6 92.6 1.0
N6 X:A2060 4.7 87.9 1.0
C5 X:G2221 4.9 95.8 1.0
C4 X:U2222 5.0 96.7 1.0

Sodium binding site 2 out of 5 in 3pip

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Sodium binding site 2 out of 5 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na2959

b:60.3
occ:1.00
O6 X:G1985 3.2 54.4 1.0
N7 X:G1985 3.4 58.6 1.0
O6 X:G1986 3.4 61.5 1.0
C6 X:G1985 3.9 62.2 1.0
C5 X:G1985 4.0 64.9 1.0
N2 X:G1670 4.1 55.2 1.0
C6 X:G1986 4.5 60.4 1.0
O6 X:G1987 4.6 77.9 1.0
N7 X:G1986 4.6 40.8 1.0
C8 X:G1985 4.6 44.8 1.0
N7 X:A1984 4.8 92.7 1.0
C5 X:G1986 4.9 52.8 1.0
N6 X:A1984 5.0 0.3 1.0

Sodium binding site 3 out of 5 in 3pip

Go back to Sodium Binding Sites List in 3pip
Sodium binding site 3 out of 5 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na2960

b:86.2
occ:1.00
C5' X:U1976 3.1 48.5 1.0
O5' X:U1976 3.1 52.5 1.0
C2 X:A1693 3.2 97.8 1.0
N3 X:A1693 3.4 94.2 1.0
C1' X:A1694 3.5 66.0 1.0
O4' X:A1694 3.6 69.0 1.0
N3 X:A1694 3.9 60.3 1.0
O4' X:U1976 3.9 69.9 1.0
O3' X:G1975 4.0 48.1 1.0
C4' X:U1976 4.1 56.4 1.0
N9 X:A1694 4.2 65.2 1.0
P X:U1976 4.2 0.8 1.0
C4 X:A1694 4.3 61.0 1.0
N1 X:A1693 4.3 97.3 1.0
O2' X:A1694 4.5 41.2 1.0
C3' X:G1975 4.6 45.0 1.0
C2' X:A1694 4.6 59.6 1.0
OP1 X:U1976 4.7 0.9 1.0
C4 X:A1693 4.7 88.0 1.0
C4' X:G1975 4.7 36.5 1.0
C2 X:A1694 4.8 72.2 1.0
C6 X:U1976 4.9 72.0 1.0
C4' X:A1694 4.9 64.0 1.0
C5' X:G1975 4.9 39.6 1.0

Sodium binding site 4 out of 5 in 3pip

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Sodium binding site 4 out of 5 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na2961

b:75.4
occ:1.00
OP1 X:A813 2.1 0.2 1.0
P X:A813 3.5 0.5 1.0
O2' X:G812 3.9 88.9 1.0
N3 X:C169 3.9 89.4 1.0
N1 X:A168 4.0 76.5 1.0
C2' X:G812 4.2 85.1 1.0
OP2 X:A813 4.2 0.4 1.0
O3' X:G812 4.3 83.7 1.0
O2 X:C169 4.4 94.4 1.0
O5' X:A813 4.5 94.3 1.0
N4 X:C169 4.6 0.5 1.0
C8 X:A813 4.6 1.0 1.0
N6 X:A168 4.6 86.5 1.0
C2 X:C169 4.7 89.6 1.0
C2 X:A168 4.7 75.3 1.0
C6 X:A168 4.7 82.8 1.0
N7 X:A813 4.7 0.8 1.0
C4 X:C169 4.8 97.8 1.0
C3' X:G812 4.8 80.7 1.0
O2' X:A815 4.8 77.6 1.0
O2' X:C180 4.9 91.7 1.0

Sodium binding site 5 out of 5 in 3pip

Go back to Sodium Binding Sites List in 3pip
Sodium binding site 5 out of 5 in the Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Synergistic Antibiotic Pair Lankamycin and Lankacidin in Complex with the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na2962

b:98.6
occ:1.00
N6 X:A189 3.9 0.6 1.0
O4 X:U187 4.1 0.9 1.0
O6 X:G188 4.2 0.6 1.0
C4 X:U187 4.5 0.4 1.0
C5 X:U187 4.5 0.2 1.0
N7 X:G188 4.6 0.1 1.0

Reference:

M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, H.Rozenberg, K.Arakawa, H.Kinashi, A.Yonath. Crystal Structure of the Synergistic Antibiotic Pair, Lankamycin and Lankacidin, in Complex with the Large Ribosomal Subunit. Proc.Natl.Acad.Sci.Usa V. 108 2717 2011.
ISSN: ISSN 0027-8424
PubMed: 21282615
DOI: 10.1073/PNAS.1019406108
Page generated: Tue Dec 15 06:21:28 2020

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