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Magnesium in PDB 8j1z: The Global Structure of PRE50S Related to Dbpa in STATE3

Magnesium Binding Sites:

Magnesium binding site 1 out of 210 in 8j1z

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Magnesium binding site 1 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6001

b:45.2
occ:1.00
O6 a:G474 3.9 50.6 1.0
O6 a:G30 4.0 47.5 1.0
O4 a:U29 4.2 46.1 1.0
O6 a:G473 4.3 50.2 1.0
OP2 a:A447 4.3 48.3 1.0
N4 a:C31 4.3 49.6 1.0
C5 a:U29 4.3 46.1 1.0
OP2 a:A28 4.4 45.4 1.0
C4 a:U29 4.5 46.1 1.0
OP2 a:U29 4.6 46.1 1.0

Magnesium binding site 2 out of 210 in 8j1z

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Magnesium binding site 2 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6002

b:50.9
occ:1.00
OP2 a:U120 2.0 54.1 1.0
P a:U120 3.4 54.1 1.0
O6 a:G122 3.9 53.0 1.0
O3' a:A119 4.0 50.4 1.0
O6 a:G123 4.2 50.2 1.0
OP1 a:U120 4.2 54.1 1.0
N7 a:G122 4.2 53.0 1.0
OP1 a:G121 4.3 56.9 1.0
O5' a:U120 4.4 54.1 1.0
N7 a:G121 4.5 56.9 1.0
C5' a:U120 4.6 54.1 1.0
OP2 a:G122 4.6 53.0 1.0
C6 a:G122 4.7 53.0 1.0
C5 a:G122 4.8 53.0 1.0
C3' a:U120 4.8 54.1 1.0
C5 a:G121 4.9 56.9 1.0
N7 a:G123 5.0 50.2 1.0
C8 a:G121 5.0 56.9 1.0

Magnesium binding site 3 out of 210 in 8j1z

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Magnesium binding site 3 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6003

b:51.2
occ:1.00
OP1 a:U120 2.0 54.1 1.0
P a:U120 3.4 54.1 1.0
OP2 a:G123 3.9 50.2 1.0
O6 a:G124 4.0 49.2 1.0
O5' a:U120 4.1 54.1 1.0
OP2 a:U120 4.1 54.1 1.0
N7 a:G123 4.3 50.2 1.0
C5' a:U120 4.4 54.1 1.0
N7 a:G124 4.5 49.2 1.0
O3' a:A119 4.5 50.4 1.0
OP2 a:G122 4.7 53.0 1.0
C3' a:A119 4.7 50.4 1.0
C8 a:G123 4.8 50.2 1.0
C6 a:G124 4.9 49.2 1.0

Magnesium binding site 4 out of 210 in 8j1z

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Magnesium binding site 4 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6004

b:62.7
occ:1.00
OP2 a:A218 1.9 62.4 1.0
P a:A218 3.3 62.4 1.0
O5' a:A218 3.9 62.4 1.0
OP1 a:A218 4.1 62.4 1.0
N6 a:A219 4.1 65.0 1.0
O6 a:G220 4.2 67.2 1.0
N7 a:A218 4.2 62.4 1.0
N7 a:A219 4.3 65.0 1.0
C8 a:A218 4.3 62.4 1.0
OP1 a:A428 4.4 68.9 1.0
O5' a:A217 4.4 61.7 1.0
O3' a:A217 4.4 61.7 1.0
OP2 a:U427 4.6 70.0 1.0
C3' a:A217 4.6 61.7 1.0
OP1 a:A217 4.6 61.7 1.0
OP2 a:A217 4.7 61.7 1.0
OP1 a:U427 4.7 70.0 1.0
P a:A217 4.8 61.7 1.0
C5' a:A217 5.0 61.7 1.0

Magnesium binding site 5 out of 210 in 8j1z

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Magnesium binding site 5 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6005

b:64.0
occ:1.00
OP1 a:U419 2.1 68.9 1.0
P a:U419 3.5 68.9 1.0
O3' a:C418 3.9 70.6 1.0
C5' a:U419 4.1 68.9 1.0
N7 a:G230 4.1 74.0 1.0
O5' a:U419 4.2 68.9 1.0
OP2 a:U419 4.6 68.9 1.0
C8 a:G230 4.7 74.0 1.0

Magnesium binding site 6 out of 210 in 8j1z

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Magnesium binding site 6 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6006

b:50.4
occ:1.00
OP2 a:G450 2.6 46.1 1.0
OP2 a:G452 3.1 48.2 1.0
O e:GLY81 3.8 50.0 1.0
O e:SER80 3.8 49.5 1.0
P a:G450 3.9 46.1 1.0
C e:SER80 4.2 49.5 1.0
OP2 a:U451 4.3 48.8 1.0
CA e:SER80 4.4 49.5 1.0
P a:G452 4.4 48.2 1.0
OP1 a:G450 4.5 46.1 1.0
O5' a:G450 4.6 46.1 1.0
OP1 a:A449 4.7 45.5 1.0
CG2 e:VAL52 4.7 52.8 1.0
C e:GLY81 4.8 50.0 1.0
OP1 a:G452 4.8 48.2 1.0
OP2 a:A449 4.9 45.5 1.0
C5' a:U451 5.0 48.8 1.0
N e:GLY81 5.0 50.0 1.0

Magnesium binding site 7 out of 210 in 8j1z

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Magnesium binding site 7 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6007

b:43.3
occ:1.00
O6 a:G450 1.9 46.1 1.0
OP1 a:A453 2.0 47.9 1.0
C6 a:G450 3.1 46.1 1.0
P a:A453 3.4 47.9 1.0
O a:HOH6313 3.6 49.1 1.0
C5 a:G450 3.8 46.1 1.0
N7 a:G450 3.9 46.1 1.0
OP2 a:A453 4.1 47.9 1.0
N7 a:A449 4.1 45.5 1.0
O5' a:A453 4.1 47.9 1.0
N1 a:G450 4.2 46.1 1.0
OP1 a:A454 4.2 48.8 1.0
C5' a:A453 4.3 47.9 1.0
OP2 a:A449 4.4 45.5 1.0
O3' a:G452 4.5 48.2 1.0
N6 a:A449 4.6 45.5 1.0
C5' a:U448 4.8 46.9 1.0
C5 a:A449 4.9 45.5 1.0
C8 a:A449 4.9 45.5 1.0
OP2 a:A454 5.0 48.8 1.0

Magnesium binding site 8 out of 210 in 8j1z

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Magnesium binding site 8 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6008

b:47.6
occ:1.00
OP1 a:A526 1.9 49.4 1.0
OP1 a:C527 2.0 50.9 1.0
P a:A526 3.3 49.4 1.0
P a:C527 3.4 50.9 1.0
O5' a:A526 3.9 49.4 1.0
O5' a:C527 4.0 50.9 1.0
OP1 a:A528 4.0 50.6 1.0
OP2 a:A526 4.1 49.4 1.0
OP2 a:C527 4.2 50.9 1.0
C5' a:C527 4.4 50.9 1.0
O3' a:U525 4.4 49.2 1.0
O3' a:A526 4.5 49.4 1.0
C5' a:A526 4.5 49.4 1.0
C3' a:C527 4.7 50.9 1.0
C3' a:A526 4.8 49.4 1.0

Magnesium binding site 9 out of 210 in 8j1z

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Magnesium binding site 9 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6009

b:54.0
occ:1.00
OP2 a:C560 4.0 48.5 1.0
O a:HOH6314 4.0 56.9 1.0
OP1 a:A1008 4.0 54.2 1.0
OP1 a:C560 4.1 48.5 1.0
OP1 a:G2038 4.2 53.0 1.0
OP1 a:G559 4.4 49.2 1.0
P a:C560 4.5 48.5 1.0

Magnesium binding site 10 out of 210 in 8j1z

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Magnesium binding site 10 out of 210 in the The Global Structure of PRE50S Related to Dbpa in STATE3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Global Structure of PRE50S Related to Dbpa in STATE3 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg6010

b:52.9
occ:1.00
OP1 a:U567 2.0 54.1 1.0
P a:U567 3.3 54.1 1.0
O3' a:U566 3.5 51.5 1.0
O4 a:U810 3.9 48.4 1.0
O5' a:U567 4.0 54.1 1.0
OP2 a:G809 4.0 49.8 1.0
C5' a:U567 4.1 54.1 1.0
N7 a:G809 4.1 49.8 1.0
O k:HOH215 4.2 60.8 1.0
O a:HOH6379 4.2 59.6 1.0
OP2 a:G808 4.4 53.7 1.0
OP2 a:U567 4.5 54.1 1.0
C8 a:G809 4.6 49.8 1.0
NZ k:LYS29 4.7 51.9 1.0
C4 a:U810 4.8 48.4 1.0
ND1 k:HIS35 4.9 56.6 1.0
C3' a:U566 4.9 51.5 1.0

Reference:

T.Yu, J.Jiang, Q.Yu, X.Li, W.Dong, F.Zeng. Ptc Remodeling in PRE50S Intermediates: Insights Into the Role of Dead-Box Rna Helicase Dbpa To Be Published.
Page generated: Fri Oct 4 11:29:36 2024

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