Atomistry » Magnesium » PDB 6ia7-6iji » 6icz
Atomistry »
  Magnesium »
    PDB 6ia7-6iji »
      6icz »

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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Go back to Magnesium Binding Sites List in 6icz
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy