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Magnesium in PDB 6icz: Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom

Enzymatic activity of Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom

All present enzymatic activity of Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 6icz:

The structure of Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom (pdb code 6icz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom, PDB code: 6icz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6icz

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Magnesium binding site 1 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:22.2
occ:1.00
 OG1 C:THR143 1.6 32.2 1.0
O1G C:GTP1500 1.8 18.5 1.0
O1B C:GTP1500 2.3 18.5 1.0
CB C:THR143 2.9 32.2 1.0
PG C:GTP1500 3.1 18.5 1.0
PB C:GTP1500 3.3 18.5 1.0
O3B C:GTP1500 3.6 18.5 1.0
N C:THR143 3.7 32.2 1.0
CA C:THR143 3.7 32.2 1.0
O3A C:GTP1500 3.7 18.5 1.0
CG2 C:THR143 3.9 32.2 1.0
O2G C:GTP1500 4.0 18.5 1.0
O3G C:GTP1500 4.1 18.5 1.0
O2A C:GTP1500 4.5 18.5 1.0
OD1 C:ASP204 4.5 43.9 1.0
OD2 C:ASP204 4.5 43.9 1.0
O2B C:GTP1500 4.6 18.5 1.0
PA C:GTP1500 4.6 18.5 1.0
CB C:LYS142 4.6 28.8 1.0
CA C:GLY180 4.7 29.4 1.0
C C:LYS142 4.7 28.8 1.0
CG C:ASP204 4.8 43.9 1.0
CE C:LYS142 4.9 28.8 1.0
O1A C:GTP1500 4.9 18.5 1.0
OD2 C:ASP169 5.0 61.0 1.0

Magnesium binding site 2 out of 9 in 6icz

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Magnesium binding site 2 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg200

b:19.6
occ:1.00
 O3' G:G-1 2.1 94.9 1.0
OP2 F:U74 2.1 32.7 1.0
OP1 F:G72 2.2 32.7 1.0
P F:U74 3.4 32.7 1.0
C3' G:G-1 3.5 94.9 1.0
OP1 F:G54 3.7 32.7 1.0
P F:G72 3.7 32.7 1.0
OP1 F:U74 4.1 32.7 1.0
C4' G:G-1 4.2 94.9 1.0
O5' F:U74 4.2 32.7 1.0
O2' G:G-1 4.2 94.9 1.0
O5' F:G72 4.3 32.7 1.0
C2' G:G-1 4.4 94.9 1.0
MG F:MG201 4.4 24.4 1.0
C5' F:U74 4.5 32.7 1.0
O3' F:G71 4.5 32.7 1.0
O3' F:A73 4.6 25.4 1.0
O5' F:G54 4.6 32.7 1.0
C5' F:G72 4.6 32.7 1.0
C5' G:G-1 4.6 94.9 1.0
OP2 F:G72 4.6 32.7 1.0
P F:G54 4.7 32.7 1.0
C3' F:A73 4.8 25.4 1.0
C4' F:A73 5.0 25.4 1.0
C5' F:A73 5.0 25.4 1.0

Magnesium binding site 3 out of 9 in 6icz

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Magnesium binding site 3 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:24.4
occ:1.00
 O3' G:G167 2.0 38.0 1.0
OP1 F:U74 2.0 32.7 1.0
OP1 F:A53 2.1 32.7 1.0
O2' G:G167 2.1 38.0 1.0
OP2 F:G54 2.5 32.7 1.0
OP1 F:G54 2.6 32.7 1.0
C3' G:G167 2.7 38.0 1.0
C2' G:G167 2.9 38.0 1.0
P F:G54 2.9 32.7 1.0
P F:U74 3.3 32.7 1.0
P F:A53 3.5 32.7 1.0
C1' G:G167 3.8 38.0 1.0
OP2 F:U74 3.8 32.7 1.0
O3' F:A53 4.0 32.7 1.0
O5' F:A53 4.0 32.7 1.0
C4' G:G167 4.1 38.0 1.0
O5' F:U74 4.2 32.7 1.0
O5' F:G54 4.2 32.7 1.0
C5' F:A53 4.3 32.7 1.0
OP2 F:A53 4.3 32.7 1.0
O3' F:A73 4.4 25.4 1.0
MG F:MG200 4.4 19.6 1.0
O3' F:U52 4.5 32.7 1.0
O4' G:G167 4.5 38.0 1.0
C3' F:A53 4.7 32.7 1.0
C5' F:G54 4.9 32.7 1.0
N9 G:G167 5.0 38.0 1.0
C4' F:A53 5.0 32.7 1.0

Magnesium binding site 4 out of 9 in 6icz

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Magnesium binding site 4 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:4.0
occ:1.00
 OP1 F:G75 2.4 25.1 1.0
P F:G75 3.8 25.1 1.0
O4 F:U57 3.9 32.7 1.0
O5' F:G75 4.3 25.1 1.0
OP2 F:A76 4.4 32.7 1.0
N7 F:A76 4.5 32.7 1.0
N7 F:G75 4.5 25.1 1.0
N7 F:A56 4.5 32.7 1.0
OP2 F:G75 4.6 25.1 1.0
C8 F:G75 4.7 25.1 1.0
N4 F:C77 4.7 32.7 1.0
C2' F:U74 4.8 32.7 1.0
O3' F:U74 4.8 32.7 1.0
C4 F:U57 4.8 32.7 1.0
N6 F:A76 4.9 32.7 1.0
C5 F:U57 4.9 32.7 1.0
C8 F:A56 5.0 32.7 1.0

Magnesium binding site 5 out of 9 in 6icz

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Magnesium binding site 5 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:32.7
occ:1.00
 OP2 F:G75 2.7 25.1 1.0
OP2 F:A56 3.8 32.7 1.0
P F:G75 3.8 25.1 1.0
OP2 F:G71 4.1 32.7 1.0
O3' F:U74 4.3 32.7 1.0
OP1 F:G75 4.3 25.1 1.0
OP1 F:A56 4.5 32.7 1.0
OP2 F:C55 4.7 32.7 1.0
P F:A56 4.7 32.7 1.0
N7 F:G71 4.8 32.7 1.0
OP2 F:G72 4.9 32.7 1.0
N7 F:G72 4.9 32.7 1.0
C8 F:G71 4.9 32.7 1.0

Magnesium binding site 6 out of 9 in 6icz

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Magnesium binding site 6 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:32.7
occ:1.00
 OP1 F:G71 2.1 32.7 1.0
OP1 F:C55 2.2 32.7 1.0
P F:C55 3.4 32.7 1.0
P F:G71 3.5 32.7 1.0
O3' F:G54 3.6 32.7 1.0
O5' F:G71 3.9 32.7 1.0
C5' F:G71 4.3 32.7 1.0
OP2 F:C55 4.3 32.7 1.0
OE1 A:GLN675 4.3 32.7 1.0
OP2 F:G71 4.3 32.7 1.0
O3' F:A70 4.5 32.7 1.0
O5' F:C55 4.5 32.7 1.0
C5' F:C55 4.6 32.7 1.0
O2' G:G-1 4.7 94.9 1.0
C3' F:G54 5.0 32.7 1.0

Magnesium binding site 7 out of 9 in 6icz

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Magnesium binding site 7 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:17.8
occ:1.00
 OP1 F:A48 2.1 32.7 1.0
P F:A48 3.4 32.7 1.0
OP2 F:A50 3.9 23.1 1.0
O5' F:A48 4.0 32.7 1.0
OP2 F:A48 4.2 32.7 1.0
O4 F:U52 4.2 32.7 1.0
O5' F:A47 4.4 32.7 1.0
C5' F:A48 4.5 32.7 1.0
O3' F:A47 4.6 32.7 1.0
OP2 F:A47 4.6 32.7 1.0
O4 F:U51 4.6 30.9 1.0
C3' F:A47 4.8 32.7 1.0
N7 F:A50 4.8 23.1 1.0
OP1 F:A47 4.8 32.7 1.0
P F:A47 4.8 32.7 1.0

Magnesium binding site 8 out of 9 in 6icz

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Magnesium binding site 8 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom 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
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:THR830 4.5 28.6 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 6icz

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Magnesium binding site 9 out of 9 in the Cryo-Em Structure of A Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom


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 Human Post-Catalytic Spliceosome (P Complex) at 3.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1503

b:66.3
occ:1.00
 N Q:ASP160 4.0 32.6 1.0
CA Q:VAL159 4.2 30.7 1.0
O Q:GLU158 4.3 35.4 1.0
C Q:VAL159 4.6 34.0 1.0
CB Q:ASP160 4.7 28.5 1.0
CB Q:VAL159 4.8 30.7 1.0
CA Q:ASP160 5.0 29.5 1.0

Reference:

X.Zhang, X.Zhan, C.Yan, W.Zhang, D.Liu, J.Lei, Y.Shi. Structures of the Human Spliceosomes Before and After Release of the Ligated Exon. Cell Res. V. 29 274 2019.
ISSN: ISSN 1748-7838
PubMed: 30728453
DOI: 10.1038/S41422-019-0143-X
Page generated: Tue Oct 1 03:18:36 2024

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