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Magnesium in PDB 7w5a: The Cryo-Em Structure of Human Pre-C*-II Complex

Enzymatic activity of The Cryo-Em Structure of Human Pre-C*-II Complex

All present enzymatic activity of The Cryo-Em Structure of Human Pre-C*-II Complex:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 7w5a:

The structure of The Cryo-Em Structure of Human Pre-C*-II Complex also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Cryo-Em Structure of Human Pre-C*-II Complex (pdb code 7w5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the The Cryo-Em Structure of Human Pre-C*-II Complex, PDB code: 7w5a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7w5a

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Magnesium binding site 1 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:52.5
occ:1.00
 O2B C:GTP1500 2.0 53.7 1.0
O1G C:GTP1500 2.1 53.7 1.0
O2G C:GTP1500 2.3 53.7 1.0
PG C:GTP1500 2.6 53.7 1.0
OG1 C:THR143 2.9 53.0 1.0
PB C:GTP1500 3.1 53.7 1.0
O3B C:GTP1500 3.3 53.7 1.0
CA C:GLY180 3.8 74.0 1.0
O3G C:GTP1500 3.9 53.7 1.0
N C:GLY180 4.0 74.0 1.0
CB C:THR143 4.0 53.0 1.0
O1B C:GTP1500 4.1 53.7 1.0
O3A C:GTP1500 4.2 53.7 1.0
O2A C:GTP1500 4.4 53.7 1.0
OD1 C:ASP204 4.5 69.3 1.0
OD2 C:ASP204 4.5 69.3 1.0
PA C:GTP1500 4.7 53.7 1.0
N C:THR143 4.7 53.0 1.0
O C:THR205 4.8 62.8 1.0
CA C:PRO206 4.8 59.8 1.0
CG2 C:THR143 4.9 53.0 1.0
O1A C:GTP1500 4.9 53.7 1.0
CG C:ASP204 5.0 69.3 1.0
CA C:THR143 5.0 53.0 1.0

Magnesium binding site 2 out of 9 in 7w5a

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Magnesium binding site 2 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg200

b:12.8
occ:1.00
 O3' 4:G-1 1.8 54.1 1.0
OP2 F:U74 2.0 36.9 1.0
OP1 F:G72 2.2 31.1 1.0
C3' 4:G-1 3.2 54.1 1.0
P F:U74 3.3 39.4 1.0
P F:G72 3.7 30.3 1.0
C4' 4:G-1 3.8 54.1 1.0
O2' 4:G-1 3.8 54.1 1.0
OP1 F:U74 3.8 41.0 1.0
OP1 F:G54 3.9 53.6 1.0
O5' F:U74 4.0 35.6 1.0
C2' 4:G-1 4.1 54.1 1.0
O2' G:G120 4.2 38.0 1.0
C5' 4:G-1 4.3 54.1 1.0
C5' F:A73 4.4 55.2 1.0
O3' F:G71 4.5 30.1 1.0
O3' F:A73 4.5 43.2 1.0
O5' F:G72 4.5 32.4 1.0
OP1 G:C121 4.6 78.6 1.0
OP2 F:G72 4.6 30.9 1.0
OP2 G:U122 4.6 78.6 1.0
C5' F:U74 4.6 33.4 1.0
O5' F:G54 4.7 45.4 1.0
C5' F:G72 4.8 35.1 1.0
C4' F:A73 4.8 51.6 1.0
P F:G54 4.8 48.5 1.0
C3' F:A73 4.9 46.5 1.0
O5' F:A73 5.0 51.8 1.0

Magnesium binding site 3 out of 9 in 7w5a

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Magnesium binding site 3 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:94.8
occ:1.00
 OP1 F:A53 1.4 104.1 1.0
OP2 F:G54 2.0 50.6 1.0
OP1 F:U74 2.1 41.0 1.0
P F:A53 2.5 100.0 1.0
O5' F:A53 3.2 84.4 1.0
P F:G54 3.2 48.5 1.0
OP2 F:A53 3.2 88.1 1.0
P F:U74 3.6 39.4 1.0
OP1 F:G54 3.6 53.6 1.0
C5' F:A53 3.7 67.5 1.0
O3' F:U52 3.8 93.4 1.0
O5' F:U74 4.1 35.6 1.0
N3 G:G120 4.2 38.0 1.0
O3' F:A53 4.2 46.5 1.0
O5' F:G54 4.3 45.4 1.0
O3' F:A73 4.3 43.2 1.0
C3' F:A53 4.4 47.1 1.0
N2 G:G120 4.5 38.0 1.0
OP2 F:U74 4.6 36.9 1.0
C5' F:G54 4.6 42.3 1.0
C4' F:A53 4.6 54.9 1.0
OP2 G:U122 4.7 78.6 1.0
C2 G:G120 4.8 38.0 1.0
C1' G:G120 4.9 38.0 1.0

Magnesium binding site 4 out of 9 in 7w5a

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Magnesium binding site 4 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:24.7
occ:1.00
 OP1 F:G75 2.2 31.2 1.0
P F:G75 3.4 26.9 1.0
O5' F:G75 3.8 28.9 1.0
OP2 F:G75 4.0 28.6 1.0
N7 F:G75 4.2 31.4 1.0
C8 F:G75 4.4 30.6 1.0
O4 F:U57 4.6 32.9 1.0
OP2 F:A76 4.6 33.0 1.0
O3' F:U74 4.7 26.8 1.0
N7 F:A76 4.8 31.3 1.0
C2' F:U74 4.9 31.1 1.0

Magnesium binding site 5 out of 9 in 7w5a

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Magnesium binding site 5 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:7.6
occ:1.00
 OP2 F:G75 2.3 28.6 1.0
P F:G75 3.7 26.9 1.0
OP2 F:G71 3.7 26.5 1.0
O3' F:U74 4.2 26.8 1.0
OP2 F:G72 4.2 30.9 1.0
OP2 F:A56 4.3 25.8 1.0
OP1 F:G75 4.5 31.2 1.0
N7 F:G71 4.6 26.9 1.0
C5' F:G71 4.7 30.9 1.0
N7 F:G72 4.7 26.9 1.0
O5' F:G75 4.7 28.9 1.0
C8 F:G71 4.7 27.2 1.0
P F:G71 4.9 28.3 1.0

Magnesium binding site 6 out of 9 in 7w5a

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Magnesium binding site 6 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:8.6
occ:1.00
 OP1 F:C55 1.9 28.7 1.0
OP1 F:G71 2.2 26.2 1.0
P F:C55 3.2 27.0 1.0
P F:G71 3.6 28.3 1.0
O3' F:G54 3.6 33.0 1.0
O5' F:C55 3.9 26.5 1.0
OE1 A:GLN675 3.9 40.7 1.0
O5' F:G71 4.2 29.4 1.0
OP2 F:C55 4.4 25.4 1.0
O3' F:A70 4.5 30.7 1.0
C5' F:G71 4.6 30.9 1.0
C5' F:C55 4.6 26.7 1.0
OP2 F:G71 4.6 26.5 1.0
CD A:GLN675 4.8 40.7 1.0

Magnesium binding site 7 out of 9 in 7w5a

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Magnesium binding site 7 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:33.4
occ:1.00
 OP1 F:A48 2.2 48.7 1.0
P F:A48 3.5 50.2 1.0
OP2 F:A50 3.7 94.2 1.0
O5' F:A48 3.9 54.1 1.0
O4 F:U51 4.1 47.3 1.0
O4 F:U52 4.4 41.8 1.0
OP2 F:A47 4.4 60.6 1.0
OP2 F:A48 4.5 44.9 1.0
OP1 F:A47 4.5 60.6 1.0
O3' F:A47 4.6 49.0 1.0
N7 F:A50 4.6 46.0 1.0
C5 F:U51 4.7 53.4 1.0
C4 F:U51 4.8 48.8 1.0
P F:A47 4.8 55.6 1.0
O5' F:A47 4.8 49.7 1.0
C3' F:A47 4.9 42.4 1.0
OP1 F:G49 4.9 60.2 1.0

Magnesium binding site 8 out of 9 in 7w5a

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Magnesium binding site 8 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1502

b:47.8
occ:1.00
 O3B Q:ATP1501 2.7 28.2 1.0
CB Q:THR830 3.1 28.6 1.0
O2B Q:ATP1501 3.7 28.1 1.0
PB Q:ATP1501 3.8 30.2 1.0
O1G Q:ATP1501 3.8 39.7 1.0
PG Q:ATP1501 3.9 32.4 1.0
CB Q:GLN861 4.0 24.9 1.0
CA Q:THR830 4.4 25.4 1.0
N Q:THR830 4.5 21.1 1.0
O1B Q:ATP1501 4.6 24.2 1.0
O2G Q:ATP1501 4.9 42.1 1.0
O3G Q:ATP1501 4.9 30.9 1.0

Magnesium binding site 9 out of 9 in 7w5a

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Magnesium binding site 9 out of 9 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:

Reference:

X.Zhan, Y.Lu, X.Zhang, C.Yan, Y.Shi. Mechanism of Exon Ligation By Human Spliceosome. Mol.Cell V. 82 2769 2022.
ISSN: ISSN 1097-2765
PubMed: 35705093
DOI: 10.1016/J.MOLCEL.2022.05.021
Page generated: Thu Oct 3 11:10:10 2024

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