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Magnesium in PDB 6cao: Structure of the Ribosomal Decoding Complex at Ambient Temperature

Protein crystallography data

The structure of Structure of the Ribosomal Decoding Complex at Ambient Temperature, PDB code: 6cao was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.22 / 3.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.300, 402.300, 176.400, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 27.2

Other elements in 6cao:

The structure of Structure of the Ribosomal Decoding Complex at Ambient Temperature also contains other interesting chemical elements:

Potassium (K) 37 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 303 in 6cao

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Magnesium binding site 1 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:

Magnesium binding site 2 out of 303 in 6cao

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Magnesium binding site 2 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1643

b:51.0
occ:1.00
O A:HOH2193 2.1 45.9 1.0
O A:HOH2084 2.1 55.6 1.0
O A:HOH2093 2.1 54.1 1.0
N7 A:G376 3.9 68.4 1.0
O6 A:G376 4.4 58.4 1.0
O6 A:G377 4.6 81.8 1.0
C5 A:G376 4.6 64.9 1.0
MG A:MG1831 4.7 44.1 1.0
C8 A:G376 4.7 67.2 1.0
C6 A:G376 4.8 67.4 1.0
C5 A:U375 4.8 88.8 1.0
N7 A:G377 4.9 75.0 1.0

Magnesium binding site 3 out of 303 in 6cao

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Magnesium binding site 3 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1644

b:59.5
occ:1.00
O A:HOH2173 2.1 54.2 1.0
O A:HOH2107 2.1 62.8 1.0
O A:HOH2138 2.1 61.1 1.0
O6 A:G650 3.3 61.3 1.0
N7 A:G650 3.9 64.0 1.0
O6 A:G649 4.0 55.4 1.0
N7 A:G649 4.0 74.4 1.0
C6 A:G650 4.2 62.9 1.0
C5 A:G650 4.4 61.0 1.0
OP2 A:A753 4.5 71.1 1.0
C5 A:G649 4.5 77.1 1.0
C6 A:G649 4.5 73.4 1.0
C8 A:G649 5.0 73.6 1.0

Magnesium binding site 4 out of 303 in 6cao

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Magnesium binding site 4 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1645

b:90.4
occ:1.00
O A:HOH2090 2.1 89.6 1.0
O A:HOH2060 2.1 91.7 1.0
OP2 A:C749 2.9 93.9 1.0
OP2 A:G750 3.0 95.7 1.0
OP1 A:C749 3.2 93.3 1.0
P A:C749 3.5 88.3 1.0
O2' A:C748 4.0 85.8 1.0
O3' A:C748 4.0 92.2 1.0
P A:G750 4.2 91.8 1.0
OP1 A:G750 4.6 96.6 1.0
O5' A:C749 5.0 72.1 1.0
C2' A:C748 5.0 83.4 1.0

Magnesium binding site 5 out of 303 in 6cao

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Magnesium binding site 5 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1646

b:27.5
occ:1.00
O2 A:U871 3.8 66.9 1.0
OP2 A:G855 4.3 58.0 1.0
N3 A:G818 4.7 61.4 1.0
C2 A:U871 4.7 60.6 1.0
C4 A:G818 4.9 64.4 1.0
C2 A:G818 4.9 62.8 1.0
O4' A:G818 5.0 60.6 1.0

Magnesium binding site 6 out of 303 in 6cao

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Magnesium binding site 6 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1647

b:68.4
occ:1.00
O A:HOH2007 2.1 85.7 1.0
O A:HOH2004 2.1 63.9 1.0
O A:HOH2046 2.1 65.6 1.0
O A:HOH2006 2.1 68.1 1.0
OP2 A:G117 2.8 55.5 1.0
OP2 A:G289 3.0 52.7 1.0
OP1 A:A116 3.4 55.9 1.0
P A:G117 3.7 54.3 1.0
O4 A:U118 3.8 75.8 1.0
C3' A:A288 3.8 46.2 1.0
OP1 A:G117 3.8 46.5 1.0
O5' A:A288 3.9 57.6 1.0
P A:G289 4.0 52.0 1.0
O3' A:A288 4.1 51.0 1.0
C8 A:A288 4.2 63.2 1.0
C5 A:U118 4.4 64.2 1.0
P A:A116 4.4 56.0 1.0
OP2 A:A116 4.4 62.3 1.0
C4 A:U118 4.4 68.1 1.0
OP2 A:A288 4.5 76.3 1.0
OP1 A:G289 4.5 51.7 1.0
N7 A:G117 4.5 70.3 1.0
C2' A:A288 4.6 45.5 1.0
O5' A:G117 4.6 57.9 1.0
N7 A:A288 4.7 64.2 1.0
P A:A288 4.7 68.0 1.0
C4' A:A288 4.8 48.2 1.0
N9 A:A288 4.8 59.1 1.0
C5' A:A288 4.9 51.3 1.0
C8 A:G117 4.9 67.4 1.0
O3' A:A116 4.9 57.3 1.0
C5' A:A116 5.0 51.2 1.0

Magnesium binding site 7 out of 303 in 6cao

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Magnesium binding site 7 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1648

b:58.8
occ:1.00
OP2 A:C48 2.7 73.1 1.0
OP1 A:A51 3.3 57.0 1.0
OP2 A:U49 3.7 73.7 1.0
OP1 A:G115 3.9 51.6 1.0
P A:C48 4.1 64.7 1.0
O23 A:PAR1603 4.1 0.8 1.0
P A:A51 4.6 51.7 1.0
OP1 A:C48 4.6 99.7 1.0
C23 A:PAR1603 4.7 92.7 1.0
O3' A:C47 4.8 58.0 1.0
C5' A:A51 4.8 61.9 1.0
O2' A:C47 4.9 51.4 1.0
C5' A:G115 5.0 53.7 1.0

Magnesium binding site 8 out of 303 in 6cao

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Magnesium binding site 8 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1649

b:0.7
occ:1.00
O A:HOH2068 2.1 0.5 1.0
O A:HOH2187 2.1 0.0 1.0
O A:HOH2087 2.1 0.5 1.0
O A:HOH2137 2.1 0.9 1.0
N7 A:G752 3.9 62.7 1.0
OP2 A:U751 4.2 70.5 1.0
OP2 A:U652 4.2 79.3 1.0
OP1 A:C651 4.2 88.1 1.0
OP1 A:U751 4.6 67.1 1.0
C8 A:G752 4.6 63.4 1.0
P A:U751 4.8 66.0 1.0
OP2 A:G752 4.9 74.2 1.0

Magnesium binding site 9 out of 303 in 6cao

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Magnesium binding site 9 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1650

b:49.6
occ:1.00
O A:HOH2156 2.1 43.7 1.0
O A:HOH2196 2.1 45.8 1.0
O A:HOH2089 2.1 46.1 1.0
O6 A:G800 3.4 54.5 1.0
O A:HOH2066 3.8 64.5 1.0
N7 A:G799 3.9 56.5 1.0
C6 A:G800 4.1 54.7 1.0
O6 A:G799 4.2 66.1 1.0
OP2 A:A781 4.4 53.2 1.0
N1 A:G800 4.5 54.3 1.0
C5 A:G799 4.8 56.5 1.0
N7 A:G798 4.8 57.9 1.0
OP2 A:A780 4.8 64.7 1.0
C6 A:G799 4.8 59.0 1.0
C8 A:G799 4.9 57.1 1.0
O6 A:G798 5.0 56.6 1.0
OP1 A:A781 5.0 64.3 1.0

Magnesium binding site 10 out of 303 in 6cao

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Magnesium binding site 10 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1651

b:30.8
occ:1.00
N7 A:G1508 3.7 49.5 1.0
N7 A:A1507 3.8 54.6 1.0
C8 A:A1507 4.1 55.8 1.0
O6 A:G1508 4.3 48.9 1.0
O A:HOH2183 4.5 0.9 1.0
OP2 A:G1508 4.5 72.7 1.0
O A:HOH2111 4.5 0.2 1.0
C5 A:A1507 4.6 54.0 1.0
C8 A:G1508 4.6 49.7 1.0
C5 A:G1508 4.6 49.2 1.0
C6 A:G1508 4.8 49.0 1.0
N9 A:A1507 4.9 50.1 1.0

Reference:

E.H.Dao, F.Poitevin, R.G.Sierra, C.Gati, Y.Rao, H.I.Ciftci, F.Aksit, A.Mcgurk, T.Obrinski, P.Mgbam, B.Hayes, C.De Lichtenberg, F.Pardo-Avila, N.Corsepius, L.Zhang, M.H.Seaberg, M.S.Hunter, M.Liang, J.E.Koglin, S.Wakatsuki, H.Demirci. Structure of the 30S Ribosomal Decoding Complex at Ambient Temperature. Rna V. 24 1667 2018.
ISSN: ESSN 1469-9001
PubMed: 30139800
DOI: 10.1261/RNA.067660.118
Page generated: Tue Oct 1 09:19:10 2024

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