Magnesium in PDB 6ff4: Human Bact Spliceosome Core Structure

Enzymatic activity of Human Bact Spliceosome Core Structure

All present enzymatic activity of Human Bact Spliceosome Core Structure:
5.2.1.8;

Other elements in 6ff4:

The structure of Human Bact Spliceosome Core Structure also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Bact Spliceosome Core Structure (pdb code 6ff4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Bact Spliceosome Core Structure, PDB code: 6ff4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ff4

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Magnesium binding site 1 out of 4 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg201

b:14.1
occ:1.00
OP1 6:A53 2.3 37.0 1.0
OP2 6:G54 2.5 37.0 1.0
OP2 6:U74 3.1 37.0 1.0
P 6:A53 3.8 37.0 1.0
P 6:G54 4.0 37.0 1.0
P 6:U74 4.0 37.0 1.0
OP1 6:U74 4.0 37.0 1.0
O 7:GLY9 4.2 22.8 1.0
C5' 6:A53 4.2 37.0 1.0
O5' 6:A53 4.4 37.0 1.0
O3' 6:U52 4.4 37.0 1.0
OP2 Z:G243 4.5 22.0 1.0
O3' 6:A73 4.6 37.0 1.0
O5' 6:G54 4.7 37.0 1.0
CG 7:LYS10 4.8 29.8 1.0
OP2 6:A53 4.8 37.0 1.0
OP1 6:G54 4.8 37.0 1.0
O3' 6:A53 4.9 37.0 1.0
N 7:GLY9 4.9 22.8 1.0
C 7:GLY9 4.9 22.8 1.0

Magnesium binding site 2 out of 4 in 6ff4

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Magnesium binding site 2 out of 4 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg202

b:37.0
occ:1.00
OP2 6:G75 2.0 37.0 1.0
P 6:G75 3.5 37.0 1.0
OP2 6:G71 4.0 37.0 1.0
O3' 6:U74 4.1 37.0 1.0
OP1 6:G75 4.3 37.0 1.0
OP2 6:A56 4.3 37.0 1.0
OP2 6:G72 4.3 37.0 1.0
O5' 6:G75 4.4 37.0 1.0
C5' 6:G75 4.6 37.0 1.0
O5' 6:G71 4.7 37.0 1.0
N7 6:G72 4.7 37.0 1.0
OP2 6:C55 4.8 37.0 1.0
N7 6:G71 4.8 37.0 1.0
P 6:G71 4.9 37.0 1.0
OP1 6:C55 5.0 37.0 1.0
C8 6:G71 5.0 37.0 1.0

Magnesium binding site 3 out of 4 in 6ff4

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Magnesium binding site 3 out of 4 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg203

b:37.0
occ:1.00
OP1 6:G75 2.2 37.0 1.0
P 6:G75 3.6 37.0 1.0
O5' 6:G75 4.0 37.0 1.0
OP2 6:A76 4.2 37.0 1.0
N7 6:A76 4.3 37.0 1.0
C2' 6:U74 4.4 37.0 1.0
C3' 6:U74 4.4 37.0 1.0
O3' 6:U74 4.5 37.0 1.0
O4 6:U57 4.6 29.7 1.0
OP2 6:G75 4.7 37.0 1.0
C2 6:U74 4.7 37.0 1.0
O2 6:U74 4.8 37.0 1.0
N4 6:C77 4.8 40.6 1.0
C8 6:A76 4.9 37.0 1.0
N1 6:U74 4.9 37.0 1.0
N3 6:U74 4.9 37.0 1.0
N7 6:A56 5.0 37.0 1.0

Magnesium binding site 4 out of 4 in 6ff4

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Magnesium binding site 4 out of 4 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg204

b:37.0
occ:1.00
OP1 6:G71 2.6 37.0 1.0
OP1 6:C55 2.9 37.0 1.0
O3' 6:G54 4.0 37.0 1.0
P 6:G71 4.0 37.0 1.0
P 6:C55 4.1 37.0 1.0
C5' 6:G71 4.3 37.0 1.0
O5' 6:G71 4.5 37.0 1.0
O3' 6:A70 4.6 37.0 1.0
OE1 A:GLN675 4.6 23.1 1.0
C5' 6:C55 4.7 37.0 1.0
O5' 6:C55 4.9 37.0 1.0

Reference:

D.Haselbach, I.Komarov, D.E.Agafonov, K.Hartmuth, B.Graf, O.Dybkov, H.Urlaub, B.Kastner, R.Luhrmann, H.Stark. Structure and Conformational Dynamics of the Human Spliceosomal Bactcomplex. Cell V. 172 454 2018.
ISSN: ISSN 1097-4172
PubMed: 29361316
DOI: 10.1016/J.CELL.2018.01.010
Page generated: Mon Dec 14 22:41:39 2020

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