Magnesium in PDB 8xi2: Cryo-Em Structure of the Chlamydomonas C* Complex

Enzymatic activity of Cryo-Em Structure of the Chlamydomonas C* Complex

All present enzymatic activity of Cryo-Em Structure of the Chlamydomonas C* Complex:
2.3.2.27; 5.2.1.8;

Other elements in 8xi2:

The structure of Cryo-Em Structure of the Chlamydomonas C* Complex also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Chlamydomonas C* Complex (pdb code 8xi2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of the Chlamydomonas C* Complex, PDB code: 8xi2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8xi2

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Magnesium binding site 1 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:20.5
occ:1.00
 OG C:SER193 1.2 26.0 1.0
OG1 C:THR151 1.6 26.2 1.0
O3G C:GTP1001 2.0 28.2 1.0
CB C:SER193 2.6 26.0 1.0
O2B C:GTP1001 2.9 28.2 1.0
CB C:THR151 2.9 26.2 1.0
PG C:GTP1001 3.1 28.2 1.0
N C:SER193 3.3 26.0 1.0
O1G C:GTP1001 3.3 28.2 1.0
OD1 C:ASP182 3.3 29.9 1.0
CA C:SER193 3.4 26.0 1.0
O3B C:GTP1001 3.7 28.2 1.0
CG2 C:THR151 3.8 26.2 1.0
OD2 C:ASP182 3.8 29.9 1.0
PB C:GTP1001 3.8 28.2 1.0
N C:THR151 3.9 26.2 1.0
CA C:THR151 3.9 26.2 1.0
CG C:ASP182 4.0 29.9 1.0
OD2 C:ASP217 4.0 26.7 1.0
O3A C:GTP1001 4.3 28.2 1.0
O C:CYS218 4.3 25.8 1.0
C C:MET192 4.3 29.1 1.0
O2G C:GTP1001 4.4 28.2 1.0
O2A C:GTP1001 4.4 28.2 1.0
NH1 C:ARG179 4.7 29.2 1.0
C C:SER193 4.7 26.0 1.0
CE C:LYS150 4.8 24.8 1.0
CG C:ASP217 4.8 26.7 1.0
OD1 C:ASP217 4.8 26.7 1.0
PA C:GTP1001 4.8 28.2 1.0

Magnesium binding site 2 out of 7 in 8xi2

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Magnesium binding site 2 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:21.6
occ:1.00
 OP2 F:U67 2.0 17.9 1.0
OP1 F:G65 2.0 21.4 1.0
O3' 5:G-1 2.8 18.1 1.0
P F:U67 3.2 17.9 1.0
P F:G65 3.4 21.4 1.0
OP1 F:G47 3.5 21.4 1.0
OP1 F:U67 3.7 17.9 1.0
O5' F:G47 3.9 21.4 1.0
O5' F:U67 3.9 17.9 1.0
C3' 5:G-1 4.0 18.1 1.0
OP2 F:G65 4.2 21.4 1.0
P F:G47 4.2 21.4 1.0
O2' 5:G-1 4.3 18.1 1.0
C5' F:U67 4.3 17.9 1.0
O3' F:G64 4.3 21.4 1.0
O5' F:G65 4.3 21.4 1.0
C4' 5:G-1 4.5 18.1 1.0
O3' F:A66 4.5 20.8 1.0
MG F:MG202 4.5 21.6 1.0
C3' F:A66 4.8 20.8 1.0
C2' 5:G-1 4.8 18.1 1.0
OP2 F:G47 4.9 21.4 1.0
C5' F:G47 4.9 21.4 1.0
C5' F:G65 4.9 21.4 1.0
C5' 5:G-1 5.0 18.1 1.0

Magnesium binding site 3 out of 7 in 8xi2

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Magnesium binding site 3 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:21.6
occ:1.00
 OP1 F:U67 2.1 17.9 1.0
OP1 F:A46 2.7 21.4 1.0
OP2 F:G47 3.2 21.4 1.0
OP1 F:G47 3.4 21.4 1.0
P F:U67 3.4 17.9 1.0
P F:G47 3.7 21.4 1.0
OP2 F:U67 4.0 17.9 1.0
P F:A46 4.1 21.4 1.0
O3' F:A66 4.2 20.8 1.0
MG F:MG201 4.5 21.6 1.0
O5' F:U67 4.6 17.9 1.0
C5' F:A46 4.7 21.4 1.0
O5' F:A46 4.7 21.4 1.0
O5' F:G47 4.8 21.4 1.0
O3' F:U45 4.9 18.5 1.0
O3' F:A46 4.9 21.4 1.0

Magnesium binding site 4 out of 7 in 8xi2

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Magnesium binding site 4 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:15.7
occ:1.00
 OP1 F:G68 2.8 21.4 1.0
N7 F:G68 3.8 21.4 1.0
N7 F:A69 4.0 21.4 1.0
P F:G68 4.1 21.4 1.0
O4 F:U50 4.1 21.4 1.0
C8 F:G68 4.2 21.4 1.0
N6 F:A69 4.4 21.4 1.0
OP2 F:G68 4.5 21.4 1.0
N4 F:C70 4.5 16.9 1.0
MG F:MG205 4.7 11.5 1.0
C5 F:G68 4.7 21.4 1.0
OP2 F:A69 4.7 21.4 1.0
O5' F:G68 4.8 21.4 1.0
C5 F:A69 4.9 21.4 1.0
O6 F:G51 4.9 21.4 1.0
C8 F:A69 5.0 21.4 1.0
C4 F:U50 5.0 21.4 1.0
O6 F:G68 5.0 21.4 1.0

Magnesium binding site 5 out of 7 in 8xi2

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Magnesium binding site 5 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg204

b:13.8
occ:1.00
 OP2 F:G68 2.5 21.4 1.0
N7 F:G65 3.7 21.4 1.0
N7 F:G64 3.9 21.4 1.0
P F:G68 3.9 21.4 1.0
C8 F:G64 4.1 21.4 1.0
C8 F:G65 4.3 21.4 1.0
OP2 F:G65 4.4 21.4 1.0
OP2 F:G64 4.5 21.4 1.0
O3' F:U67 4.6 17.9 1.0
C5 F:G64 4.6 21.4 1.0
OP1 F:G68 4.7 21.4 1.0
C8 F:G68 4.8 21.4 1.0
C5 F:G65 4.8 21.4 1.0
O5' F:G64 4.9 21.4 1.0
N9 F:G64 4.9 21.4 1.0
N7 F:G68 5.0 21.4 1.0
O6 F:G65 5.0 21.4 1.0

Magnesium binding site 6 out of 7 in 8xi2

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Magnesium binding site 6 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg205

b:11.5
occ:1.00
 OP2 F:A49 2.4 21.4 1.0
O2' F:U67 3.3 17.9 1.0
C8 F:A49 3.4 21.4 1.0
C6 F:C48 3.6 21.4 1.0
C5 F:C48 3.6 21.4 1.0
P F:A49 3.8 21.4 1.0
C2' F:U67 3.9 17.9 1.0
C3' F:C48 3.9 21.4 1.0
N7 F:A49 3.9 21.4 1.0
O4' F:A49 4.0 21.4 1.0
C5' F:A49 4.0 21.4 1.0
OP2 F:C48 4.0 21.4 1.0
N1 F:C48 4.1 21.4 1.0
OP1 F:G68 4.1 21.4 1.0
O5' F:A49 4.2 21.4 1.0
C4 F:C48 4.3 21.4 1.0
O3' F:U67 4.3 17.9 1.0
C2' F:C48 4.3 21.4 1.0
O3' F:C48 4.4 21.4 1.0
O5' F:C48 4.4 21.4 1.0
N9 F:A49 4.5 21.4 1.0
C2 F:C48 4.6 21.4 1.0
C4' F:A49 4.6 21.4 1.0
MG F:MG203 4.7 15.7 1.0
C3' F:U67 4.7 17.9 1.0
N3 F:C48 4.7 21.4 1.0
P F:G68 4.7 21.4 1.0
C1' F:C48 4.7 21.4 1.0
C1' F:A49 4.9 21.4 1.0
OP1 F:A49 4.9 21.4 1.0
N4 F:C48 4.9 21.4 1.0
P F:C48 4.9 21.4 1.0
OP2 F:G68 5.0 21.4 1.0
C4' F:C48 5.0 21.4 1.0

Magnesium binding site 7 out of 7 in 8xi2

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Magnesium binding site 7 out of 7 in the Cryo-Em Structure of the Chlamydomonas C* Complex


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 the Chlamydomonas C* Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg206

b:8.3
occ:1.00
 OP1 F:G64 2.1 21.4 1.0
OP1 F:C48 2.3 21.4 1.0
P F:C48 3.5 21.4 1.0
P F:G64 3.5 21.4 1.0
O3' F:G47 3.7 21.4 1.0
NE2 A:GLN739 4.0 3.4 1.0
O3' F:A63 4.3 21.4 1.0
C5' F:C48 4.3 21.4 1.0
O5' F:G64 4.3 21.4 1.0
O5' F:C48 4.4 21.4 1.0
C5' F:G64 4.4 21.4 1.0
OP2 F:G64 4.5 21.4 1.0
O2' 5:G-1 4.5 18.1 1.0
OP2 F:C48 4.6 21.4 1.0
CD A:GLN739 4.8 3.4 1.0
OE1 A:GLN739 4.9 3.4 1.0

Reference:

Y.Lu, X.Zhan. Structure of A Step II Catalytically Activated Spliceosome Form Chlamydomonas Reinhardtii To Be Published.
Page generated: Thu Oct 31 22:20:44 2024

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