Atomistry » Magnesium » PDB 4ijm-4ix3 » 4ioc
Atomistry »
  Magnesium »
    PDB 4ijm-4ix3 »
      4ioc »

Magnesium in PDB 4ioc: Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans

Protein crystallography data

The structure of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans, PDB code: 4ioc was solved by S.Han, E.S.Marr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 169.640, 408.490, 692.910, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans (pdb code 4ioc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans, PDB code: 4ioc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 1 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2901

b:50.2
occ:1.00
O4 X:U2057 3.4 76.3 1.0
O4 X:U2222 3.5 72.8 1.0
N7 X:G2217 3.8 88.2 1.0
C8 X:G2217 4.1 88.4 1.0
C4 X:U2057 4.2 76.1 1.0
C4 X:U2222 4.3 70.9 1.0
C5 X:U2057 4.4 76.1 1.0
O6 X:G2221 4.4 80.0 1.0
O4 X:U2058 4.5 79.7 1.0
N7 X:A2220 4.5 79.8 1.0
N7 X:G2221 4.6 79.5 1.0
N6 X:A2220 4.6 78.3 1.0
C5 X:U2222 4.6 69.8 1.0
N6 X:A2060 4.8 77.0 1.0
C5 X:G2217 4.8 87.3 1.0
C5 X:A2220 4.9 79.0 1.0

Magnesium binding site 2 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 2 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2902

b:94.1
occ:1.00
OP2 X:G2415 3.3 75.4 1.0
OP1 X:G2415 3.5 75.6 1.0
OP2 X:G2225 3.8 82.5 1.0
P X:G2415 3.9 75.3 1.0
O2' X:U2224 4.4 78.0 1.0
O3' X:A2414 5.0 75.0 1.0

Magnesium binding site 3 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 3 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2903

b:89.7
occ:1.00
O4 X:U1370 2.4 97.3 1.0
OP2 X:C1385 3.6 0.5 1.0
C4 X:U1370 3.6 97.4 1.0
N1 X:G1371 4.1 0.9 1.0
N2 X:G1371 4.2 0.7 1.0
N3 X:U1370 4.4 97.6 1.0
C2 X:G1371 4.5 0.8 1.0
C5 X:U1370 4.7 97.6 1.0
O6 X:G1369 4.7 0.2 1.0
P X:C1385 4.7 0.3 1.0
OP1 X:C1385 4.8 0.1 1.0
C6 X:G1371 4.9 0.9 1.0
N7 X:G1369 5.0 0.6 1.0

Magnesium binding site 4 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 4 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2904

b:0.3
occ:1.00
OP1 X:A747 3.5 71.4 1.0
OP2 X:A747 3.5 70.7 1.0
OP1 X:G746 3.6 70.3 1.0
O5' X:G746 3.7 69.3 1.0
P X:A747 3.7 71.3 1.0
O3' X:G746 3.8 71.4 1.0
C5' X:G746 3.9 69.0 1.0
P X:G746 4.2 69.5 1.0
C3' X:G746 4.4 70.4 1.0
OP2 X:G772 4.7 71.8 1.0
C4' X:G746 4.7 69.3 1.0
OP2 X:G746 4.8 69.3 1.0

Magnesium binding site 5 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 5 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2905

b:65.5
occ:1.00
OP1 X:G772 2.9 74.5 1.0
OP1 X:C745 3.5 68.7 1.0
OP2 X:G773 4.1 66.2 1.0
P X:G772 4.1 72.6 1.0
OP2 X:G746 4.4 69.3 1.0
OP2 X:G772 4.5 71.8 1.0
OP1 X:G773 4.6 68.1 1.0
P X:C745 4.7 69.0 1.0
OP1 X:G746 4.8 70.3 1.0
P X:G773 4.8 66.5 1.0
O5' X:G772 4.9 70.0 1.0

Magnesium binding site 6 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 6 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2906

b:58.9
occ:1.00
OP2 X:G1767 1.9 67.0 1.0
P X:G1767 3.4 67.1 1.0
OP2 X:A1964 3.9 74.3 1.0
OP1 X:U1766 4.1 66.2 1.0
O5' X:G1767 4.2 66.8 1.0
OP2 X:U1766 4.2 66.4 1.0
N7 X:G1767 4.3 52.5 1.0
OP1 X:G1767 4.3 68.1 1.0
O3' X:U1766 4.3 65.7 1.0
C8 X:G1767 4.5 53.5 1.0
P X:U1766 4.6 66.0 1.0
O5' X:U1766 4.8 63.9 1.0
C4' X:G1963 5.0 72.7 1.0

Magnesium binding site 7 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 7 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2907

b:51.8
occ:1.00
OP1 X:C1765 2.0 72.8 1.0
P X:C1765 3.5 71.8 1.0
OP1 X:A1777 3.7 64.9 1.0
O2' X:G1763 4.0 69.9 1.0
O6 X:G1767 4.1 53.0 1.0
O5' X:C1765 4.2 69.9 1.0
OP2 X:C1765 4.2 72.6 1.0
N2 X:G1763 4.2 73.2 1.0
OP2 X:A1777 4.2 64.8 1.0
OP2 X:U1766 4.2 66.4 1.0
N3 X:G1763 4.4 71.8 1.0
P X:A1777 4.5 65.2 1.0
O3' X:A1764 4.5 70.0 1.0
C5' X:C1765 4.7 68.1 1.0
C2 X:G1763 4.8 71.8 1.0
N4 X:C1779 4.9 65.1 1.0
C2' X:G1763 5.0 70.2 1.0
N6 X:A1780 5.0 56.3 1.0

Magnesium binding site 8 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 8 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2908

b:37.5
occ:1.00
N7 X:A2034 3.8 60.0 1.0
OP1 X:G2557 4.0 52.4 1.0
OP2 X:A2593 4.3 56.0 1.0
OP2 X:A2034 4.3 50.9 1.0
N7 X:A2593 4.3 54.0 1.0
OP2 X:C2033 4.4 57.9 1.0
C8 X:A2034 4.4 60.2 1.0
OP1 X:C2033 4.6 57.0 1.0
C8 X:A2593 4.6 53.7 1.0
P X:C2033 4.8 56.3 1.0
O5' X:C2033 4.9 53.1 1.0
OP2 X:G2557 4.9 51.5 1.0
C5 X:A2034 4.9 59.0 1.0
P X:G2557 5.0 52.3 1.0
N6 X:A2034 5.0 59.3 1.0

Magnesium binding site 9 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 9 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2909

b:97.9
occ:1.00
OP2 X:G2743 3.3 96.5 1.0
OP2 X:G2742 3.8 0.1 1.0
OP2 X:A2718 3.9 99.5 1.0
OP2 X:G2717 4.2 97.2 1.0
P X:G2742 4.6 0.2 1.0
O5' X:G2742 4.7 0.1 1.0
P X:G2743 4.8 97.5 1.0
OP1 X:G2742 4.8 0.7 1.0
O5' X:G2717 4.9 95.8 1.0
P X:G2717 4.9 97.1 1.0

Magnesium binding site 10 out of 35 in 4ioc

Go back to Magnesium Binding Sites List in 4ioc
Magnesium binding site 10 out of 35 in the Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Compound 4F Bound to Large Ribosomal Subunit (50S) From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg2910

b:41.4
occ:1.00
OP1 X:A2556 2.0 52.9 1.0
OP1 X:G2555 2.3 62.0 1.0
P X:A2556 3.4 52.2 1.0
P X:G2555 3.6 61.2 1.0
O3' X:C2554 3.8 60.4 1.0
OP1 X:G2036 3.9 57.6 1.0
OP2 X:G2036 4.0 56.4 1.0
O3' X:G2555 4.2 53.6 1.0
OP2 X:G2035 4.2 56.9 1.0
OP2 X:A2556 4.3 52.2 1.0
O5' X:A2556 4.4 49.8 1.0
P X:G2036 4.5 56.6 1.0
OP2 X:G2555 4.5 61.3 1.0
C3' X:G2555 4.7 54.2 1.0
C5' X:G2035 4.7 53.3 1.0
O5' X:G2555 4.7 57.8 1.0
O5' X:G2035 4.8 54.3 1.0
C5' X:G2555 4.9 55.2 1.0

Reference:

T.V.Magee, S.Han, S.P.Mccurdy, T.T.Nguyen, K.Granskog, E.S.Marr, B.A.Maguire, M.D.Huband, J.M.Chen, T.A.Subashi, V.Shanmugasundaram. Novel 3-O-Carbamoyl Erythromycin A Derivatives (Carbamolides) with Activity Against Resistant Staphylococcal and Streptococcal Isolates. Bioorg.Med.Chem.Lett. V. 23 1727 2013.
ISSN: ISSN 0960-894X
PubMed: 23414806
DOI: 10.1016/J.BMCL.2013.01.067
Page generated: Fri Aug 16 16:48:49 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy