Magnesium in PDB 6zym: Human C Complex Spliceosome - High-Resolution Core

Enzymatic activity of Human C Complex Spliceosome - High-Resolution Core

All present enzymatic activity of Human C Complex Spliceosome - High-Resolution Core:
3.6.4.13; 5.2.1.8;

Other elements in 6zym:

The structure of Human C Complex Spliceosome - High-Resolution Core also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human C Complex Spliceosome - High-Resolution Core (pdb code 6zym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human C Complex Spliceosome - High-Resolution Core, PDB code: 6zym:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6zym

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Magnesium binding site 1 out of 5 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg101

b:36.1
occ:1.00
 OP1 6:G72 2.0 22.1 1.0
OP2 Y:G59 2.1 33.3 1.0
OP2 6:U74 2.2 46.7 1.0
P Y:G59 3.2 33.3 1.0
O5' Y:G59 3.3 33.3 1.0
P 6:G72 3.4 22.1 1.0
P 6:U74 3.6 46.7 1.0
OP1 Y:G59 3.9 33.3 1.0
C5' Y:G59 4.0 33.3 1.0
OP1 6:G54 4.0 15.7 1.0
O3' 6:G71 4.1 46.7 1.0
OP1 6:U74 4.2 46.7 1.0
OP2 6:G72 4.2 22.1 1.0
O5' 6:G72 4.3 22.1 1.0
C5' 6:G72 4.4 22.1 1.0
O2' Y:A155 4.5 33.8 1.0
O5' 6:U74 4.5 46.7 1.0
O3' 6:A73 4.7 46.7 1.0
P 6:G54 4.8 15.7 1.0
OP2 6:G54 4.8 15.7 1.0
C5' 6:U74 4.9 46.7 1.0
O5' 6:G54 4.9 15.7 1.0

Magnesium binding site 2 out of 5 in 6zym

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Magnesium binding site 2 out of 5 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg102

b:20.1
occ:1.00
 OP1 6:G71 2.1 46.7 1.0
OP1 6:C55 2.5 46.7 1.0
O5' 6:G71 3.2 46.7 1.0
P 6:G71 3.2 46.7 1.0
P 6:C55 3.8 46.7 1.0
O3' 6:G54 3.9 15.7 1.0
OE1 A:GLN675 4.2 35.2 1.0
O3' 6:A70 4.2 39.6 1.0
OP2 6:G71 4.4 46.7 1.0
C5' 6:G71 4.4 46.7 1.0
C5' 6:C55 4.5 46.7 1.0
O5' 6:C55 4.6 46.7 1.0
OP2 6:C55 4.9 46.7 1.0

Magnesium binding site 3 out of 5 in 6zym

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Magnesium binding site 3 out of 5 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg103

b:21.3
occ:1.00
 OP2 6:G75 2.0 46.7 1.0
P 6:G75 3.4 46.7 1.0
OP2 6:G71 3.7 46.7 1.0
O3' 6:U74 3.9 46.7 1.0
C5' 6:G71 4.1 46.7 1.0
OP1 6:G75 4.1 46.7 1.0
OP2 6:A56 4.3 46.7 1.0
OP2 6:G72 4.4 22.1 1.0
C8 6:G71 4.5 46.7 1.0
N7 6:G71 4.5 46.7 1.0
O5' 6:G75 4.5 46.7 1.0
OP2 6:C55 4.6 46.7 1.0
OP1 6:C55 4.8 46.7 1.0
OP1 6:A56 4.8 46.7 1.0
O5' 6:G71 4.8 46.7 1.0
P 6:G71 4.8 46.7 1.0
C5' 6:G75 4.9 46.7 1.0
N7 6:G72 4.9 22.1 1.0

Magnesium binding site 4 out of 5 in 6zym

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Magnesium binding site 4 out of 5 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg104

b:16.1
occ:1.00
 OP1 6:G75 2.2 46.7 1.0
P 6:G75 3.6 46.7 1.0
O5' 6:G75 3.9 46.7 1.0
N7 6:G75 4.4 46.7 1.0
C8 6:G75 4.4 46.7 1.0
O4 6:U57 4.5 42.6 1.0
OP2 6:G75 4.6 46.7 1.0
N7 6:A76 4.6 37.2 1.0
C2' 6:U74 4.6 46.7 1.0
OP2 6:A76 4.6 37.2 1.0
N7 6:A56 4.6 46.7 1.0
O3' 6:U74 4.6 46.7 1.0
C3' 6:U74 4.7 46.7 1.0

Magnesium binding site 5 out of 5 in 6zym

Go back to Magnesium Binding Sites List in 6zym
Magnesium binding site 5 out of 5 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg105

b:33.6
occ:1.00
 OP2 6:A47 2.4 50.8 1.0
OP1 6:G46 2.6 43.7 1.0
P 6:A47 3.7 50.8 1.0
P 6:G46 3.8 43.7 1.0
OP2 6:U51 4.0 39.7 1.0
OP1 6:A47 4.2 50.8 1.0
OP2 6:G46 4.3 43.7 1.0
O5' 6:G46 4.4 43.7 1.0
OP2 6:U52 4.5 46.7 1.0
O3' 6:G46 4.6 43.7 1.0
C5 6:U52 4.6 46.7 1.0
C3' 6:G46 4.7 43.7 1.0
O4 6:U52 4.8 46.7 1.0
O5' 6:A47 4.8 50.8 1.0
C8 6:A47 4.9 50.8 1.0

Reference:

K.Bertram, L.El Ayoubi, O.Dybkov, D.E.Agafonov, C.L.Will, K.Hartmuth, H.Urlaub, B.Kastner, H.Stark, R.Luhrmann. Structural Insights Into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. Mol.Cell V. 80 127 2020.
ISSN: ISSN 1097-2765
PubMed: 33007253
DOI: 10.1016/J.MOLCEL.2020.09.012
Page generated: Tue Dec 15 03:18:37 2020

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