Magnesium in PDB 6zxh: Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2

Enzymatic activity of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2

All present enzymatic activity of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2:
2.7.11.1; 4.2.99.18;

Other elements in 6zxh:

The structure of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium 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 - 131;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 (pdb code 6zxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 131 binding sites of Magnesium where determined in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2, PDB code: 6zxh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 131 in 6zxh

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Magnesium binding site 1 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1902

b:5.5
occ:1.00
O6 2:G1387 2.1 5.8 1.0
OP2 2:G1385 2.4 5.8 1.0
C6 2:G1387 3.2 5.8 1.0
P 2:G1385 3.6 5.8 1.0
N1 2:G1387 3.9 5.8 1.0
O5' 2:G1385 4.0 5.8 1.0
N7 2:A1386 4.2 5.8 1.0
C5 2:G1387 4.2 5.8 1.0
OP1 2:G1385 4.3 5.8 1.0
N6 2:A1386 4.4 5.8 1.0
N7 2:G1387 4.6 5.8 1.0
OG D:SER160 4.7 5.8 1.0
N1 2:A1388 4.7 5.8 1.0
O5' 2:C1384 4.8 5.8 1.0
O3' 2:C1384 4.9 5.8 1.0
OP2 2:A1386 4.9 5.8 1.0
C6 2:A1388 5.0 5.8 1.0
C5 2:A1386 5.0 5.8 1.0

Magnesium binding site 2 out of 131 in 6zxh

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Magnesium binding site 2 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1903

b:5.2
occ:1.00
OP2 2:G1387 2.2 5.8 1.0
P 2:G1387 3.5 5.8 1.0
O6 2:G1481 3.9 5.8 1.0
N3 2:C1482 3.9 5.8 1.0
O5' 2:G1387 4.0 5.8 1.0
N4 2:C1389 4.2 5.8 1.0
OP1 2:A1386 4.2 5.8 1.0
OP1 2:G1387 4.2 5.8 1.0
O2 2:C1482 4.3 5.8 1.0
N7 2:A1388 4.4 5.8 1.0
C2 2:C1482 4.6 5.8 1.0
C4 2:C1389 4.6 5.8 1.0
N4 2:C1482 4.7 5.8 1.0
O3' 2:A1386 4.7 5.8 1.0
C8 2:G1387 4.7 5.8 1.0
C6 2:G1481 4.7 5.8 1.0
OP2 2:A1386 4.8 5.8 1.0
N7 2:G1387 4.8 5.8 1.0
C4 2:C1482 4.8 5.8 1.0
OP2 2:A1388 4.8 5.8 1.0
P 2:A1386 4.8 5.8 1.0
N3 2:C1389 4.9 5.8 1.0
N1 2:G1481 5.0 5.8 1.0
O5' 2:A1386 5.0 5.8 1.0

Magnesium binding site 3 out of 131 in 6zxh

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Magnesium binding site 3 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1904

b:5.8
occ:1.00
OP1 2:OMG1490 2.2 5.8 1.0
OP2 2:G1491 2.3 5.8 1.0
OP1 2:C1331 2.4 5.8 1.0
P 2:G1491 3.4 5.8 1.0
P 2:OMG1490 3.7 5.8 1.0
P 2:C1331 3.7 5.8 1.0
OP1 2:G1491 3.8 5.8 1.0
O3' 2:OMG1490 4.0 5.8 1.0
O2' 2:A1489 4.0 5.8 1.0
C5' 2:OMG1490 4.2 5.8 1.0
OP2 2:C1331 4.2 5.8 1.0
C3' 2:OMG1490 4.4 5.8 1.0
O5' 2:OMG1490 4.5 5.8 1.0
O5' 2:C1331 4.6 5.8 1.0
OP2 2:OMG1490 4.6 5.8 1.0
O5' 2:G1491 4.6 5.8 1.0
O3' 2:A1489 4.6 5.8 1.0
OD2 z:ASP151 4.7 10.2 1.0
C3' 2:A1489 4.8 5.8 1.0
O3' 2:G1330 4.8 5.8 1.0
C2' 2:A1489 4.9 5.8 1.0
OD1 z:ASP151 4.9 10.2 1.0
C4' 2:OMG1490 4.9 5.8 1.0

Magnesium binding site 4 out of 131 in 6zxh

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Magnesium binding site 4 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1905

b:4.4
occ:1.00
OP2 2:C1331 2.2 5.8 1.0
OP2 2:OMG1490 2.3 5.8 1.0
P 2:C1331 3.5 5.8 1.0
P 2:OMG1490 3.5 5.8 1.0
OP1 2:OMG1490 3.8 5.8 1.0
O3' 2:G1330 3.9 5.8 1.0
O3' 2:A1489 4.0 5.8 1.0
N7 2:G1491 4.1 5.8 1.0
OP1 2:C1331 4.2 5.8 1.0
O2' 2:G1330 4.2 5.8 1.0
O4 2:U1492 4.3 5.8 1.0
C8 2:G1491 4.6 5.8 1.0
O5' 2:C1331 4.6 5.8 1.0
N7 2:OMG1490 4.7 5.8 1.0
OP2 2:G1491 4.7 5.8 1.0
O5' 2:OMG1490 4.8 5.8 1.0
C8 2:OMG1490 4.8 5.8 1.0
O2' 2:A1489 4.8 5.8 1.0

Magnesium binding site 5 out of 131 in 6zxh

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Magnesium binding site 5 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1906

b:5.8
occ:1.00
O4 2:U1492 2.7 5.8 1.0
O6 2:G1491 2.9 5.8 1.0
O6 2:G1335 3.0 5.8 1.0
C4 2:U1492 3.7 5.8 1.0
N4 2:C1336 3.8 5.8 1.0
C6 2:G1491 3.8 5.8 1.0
N2 2:G1330 3.8 5.8 1.0
N3 2:U1492 4.0 5.8 1.0
C6 2:G1335 4.1 5.8 1.0
C2 2:G1330 4.3 5.8 1.0
N7 2:G1335 4.4 5.8 1.0
OP2 2:G1334 4.4 5.8 1.0
C5 2:G1491 4.5 5.8 1.0
N3 2:G1330 4.6 5.8 1.0
N1 2:G1491 4.6 5.8 1.0
C5 2:G1335 4.6 5.8 1.0
N7 2:G1491 4.7 5.8 1.0
C4 2:C1336 4.7 5.8 1.0

Magnesium binding site 6 out of 131 in 6zxh

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Magnesium binding site 6 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1907

b:5.8
occ:1.00
O6 2:G1330 2.5 5.8 1.0
O6 2:G1334 2.9 5.8 1.0
O4 2:U1496 3.4 5.8 1.0
C6 2:G1330 3.6 5.8 1.0
N2 2:G1335 3.7 5.8 1.0
C6 2:G1334 3.8 5.8 1.0
N1 2:G1334 3.9 5.8 1.0
O2 2:U1492 4.0 5.8 1.0
N6 2:A1498 4.0 5.8 1.0
C2 2:G1335 4.1 5.8 1.0
N1 2:G1330 4.1 5.8 1.0
N1 2:G1335 4.1 5.8 1.0
O2' 2:U1492 4.2 5.8 1.0
C4 2:U1496 4.3 5.8 1.0
C5' 2:C1493 4.4 5.8 1.0
C5 2:U1496 4.4 5.8 1.0
N7 2:G1495 4.4 5.8 1.0
C2' 2:U1492 4.5 5.8 1.0
C6 2:A1498 4.6 5.8 1.0
N7 2:A1498 4.7 5.8 1.0
O4' 2:C1493 4.7 5.8 1.0
OP1 2:G1495 4.7 5.8 1.0
C2 2:U1492 4.7 5.8 1.0
C4' 2:C1493 4.7 5.8 1.0
C5 2:A1498 4.9 5.8 1.0
C5 2:G1330 4.9 5.8 1.0
N3 2:G1335 4.9 5.8 1.0
O6 2:G1495 5.0 5.8 1.0

Magnesium binding site 7 out of 131 in 6zxh

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Magnesium binding site 7 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1908

b:5.1
occ:1.00
OP1 2:G1226 2.2 5.8 1.0
OP2 2:G1227 2.8 5.8 1.0
P 2:G1226 3.5 5.8 1.0
OP2 2:G1226 3.9 5.8 1.0
P 2:G1227 4.2 5.8 1.0
MG 2:MG1987 4.2 8.7 1.0
N7 2:A1228 4.3 5.8 1.0
O5' 2:G1226 4.3 5.8 1.0
O6 2:G1528 4.4 5.8 1.0
O6 2:G1229 4.6 5.8 1.0
C5' 2:G1226 4.6 5.8 1.0
O3' 2:U1225 4.6 5.8 1.0
O5' 2:G1227 4.8 5.8 1.0
OP1 2:G1227 4.8 5.8 1.0
N6 2:A1228 4.9 5.8 1.0
OP2 2:A1228 5.0 5.8 1.0

Magnesium binding site 8 out of 131 in 6zxh

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Magnesium binding site 8 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1909

b:3.6
occ:1.00
O6 2:G1227 2.9 5.8 1.0
N7 2:G1227 2.9 5.8 1.0
N7 2:G1226 3.0 5.8 1.0
OP2 2:G1226 3.0 5.8 1.0
OP2 2:U1225 3.2 5.8 1.0
N7 2:G1638 3.4 5.8 1.0
C6 2:G1227 3.5 5.8 1.0
C5 2:G1227 3.5 5.8 1.0
C8 2:G1226 3.7 5.8 1.0
O5' 2:U1225 3.8 5.8 1.0
C8 2:G1638 3.8 5.8 1.0
P 2:U1225 3.9 5.8 1.0
C5 2:G1226 4.1 5.8 1.0
C8 2:G1227 4.1 5.8 1.0
C5 2:G1638 4.2 5.8 1.0
O6 2:G1226 4.3 5.8 1.0
P 2:G1226 4.4 5.8 1.0
C5 2:U1225 4.5 5.8 1.0
C6 2:U1225 4.5 5.8 1.0
OP1 2:U1225 4.5 5.8 1.0
C6 2:G1226 4.6 5.8 1.0
C3' 2:U1225 4.6 5.8 1.0
O5' 2:G1226 4.7 5.8 1.0
N9 2:G1638 4.7 5.8 1.0
C6 2:G1638 4.8 5.8 1.0
O6 2:G1638 4.8 5.8 1.0
C4 2:G1227 4.8 5.8 1.0
N1 2:G1227 4.8 5.8 1.0
C5' 2:U1225 4.9 5.8 1.0
O3' 2:U1225 4.9 5.8 1.0
C4 2:G1638 4.9 5.8 1.0
N9 2:G1226 5.0 5.8 1.0

Magnesium binding site 9 out of 131 in 6zxh

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Magnesium binding site 9 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1910

b:5.8
occ:1.00
O T:GLY86 2.4 6.0 1.0
O3' 2:U1530 2.6 5.8 1.0
OP1 2:A1531 3.1 5.8 1.0
OP2 2:G1606 3.2 5.8 1.0
P 2:A1531 3.5 5.8 1.0
C T:GLY86 3.5 6.0 1.0
C3' 2:U1530 3.7 5.8 1.0
C4' 2:U1530 3.9 5.8 1.0
O2' 2:U1530 3.9 5.8 1.0
N T:GLY86 3.9 6.0 1.0
CA T:GLY86 4.0 6.0 1.0
OP1 2:G1606 4.0 5.8 1.0
P 2:G1606 4.1 5.8 1.0
NH2 T:ARG84 4.1 5.8 1.0
O5' 2:A1531 4.2 5.8 1.0
CZ T:ARG84 4.3 5.8 1.0
O T:MET88 4.3 6.1 1.0
C5' 2:U1530 4.4 5.8 1.0
C2' 2:U1530 4.4 5.8 1.0
N T:ASN85 4.5 6.5 1.0
CB T:ARG84 4.5 5.8 1.0
NE T:ARG84 4.6 5.8 1.0
N T:VAL87 4.7 5.8 1.0
OP2 2:A1531 4.7 5.8 1.0
NH1 T:ARG84 4.7 5.8 1.0
C T:ASN85 4.8 6.5 1.0
CG T:ARG84 4.9 5.8 1.0
O5' 2:G1606 4.9 5.8 1.0
C T:ARG84 4.9 5.8 1.0
CA T:ARG84 5.0 5.8 1.0
C5' 2:G1606 5.0 5.8 1.0

Magnesium binding site 10 out of 131 in 6zxh

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Magnesium binding site 10 out of 131 in the Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of A Late Human Pre-40S Ribosomal Subunit - State H2 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1911

b:6.4
occ:1.00
OP2 2:G1605 2.2 5.8 1.0
OP1 2:G1604 2.4 5.8 1.0
P 2:G1604 3.5 5.8 1.0
P 2:G1605 3.6 5.8 1.0
O5' 2:G1605 3.8 5.8 1.0
OP2 2:G1604 3.9 5.8 1.0
N7 2:G1606 4.1 5.8 1.0
O5' 2:G1604 4.2 5.8 1.0
OE2 T:GLU44 4.5 7.3 1.0
O3' 2:G1604 4.5 5.8 1.0
OP1 2:G1605 4.6 5.8 1.0
NH1 S:ARG38 4.7 8.2 1.0
O2' 2:A1537 4.7 5.8 1.0
O3' 2:G1605 4.7 5.8 1.0
C8 2:G1606 4.8 5.8 1.0
C3' 2:G1604 4.8 5.8 1.0
C5' 2:G1604 4.8 5.8 1.0
C3' 2:G1605 4.8 5.8 1.0
O3' 2:G1603 4.9 9.1 1.0
C8 2:G1605 4.9 5.8 1.0

Reference:

M.Ameismeier, I.Zemp, J.Van Den Heuvel, M.Thoms, O.Berninghausen, U.Kutay, R.Beckmann. Structural Basis For the Final Steps of Human 40S Ribosome Maturation. Nature V. 587 683 2020.
ISSN: ESSN 1476-4687
PubMed: 33208940
DOI: 10.1038/S41586-020-2929-X
Page generated: Thu Dec 17 12:36:42 2020

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