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Magnesium in PDB 5mdx: Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana

Enzymatic activity of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana

All present enzymatic activity of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana:
1.10.3.9;

Other elements in 5mdx:

The structure of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 308 in 5mdx

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Magnesium binding site 1 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.1
occ:1.00
MG A:CLA402 0.0 0.1 1.0
NB A:CLA402 2.0 0.1 1.0
ND A:CLA402 2.0 0.1 1.0
NC A:CLA402 2.1 0.1 1.0
NA A:CLA402 2.1 0.1 1.0
NE2 A:HIS198 2.2 0.9 1.0
C4D A:CLA402 2.8 0.1 1.0
C4B A:CLA402 3.0 0.1 1.0
C1B A:CLA402 3.0 0.1 1.0
CE1 A:HIS198 3.1 0.9 1.0
C1C A:CLA402 3.1 0.1 1.0
C4A A:CLA402 3.1 0.1 1.0
C4C A:CLA402 3.1 0.1 1.0
C1A A:CLA402 3.1 0.1 1.0
C1D A:CLA402 3.1 0.1 1.0
CD2 A:HIS198 3.3 0.9 1.0
CHB A:CLA402 3.4 0.1 1.0
CHA A:CLA402 3.4 0.1 1.0
CHC A:CLA402 3.4 0.1 1.0
CHD A:CLA402 3.6 0.1 1.0
CAB D:CLA403 4.1 0.1 1.0
C3D A:CLA402 4.1 0.1 1.0
ND1 A:HIS198 4.2 0.9 1.0
C3B A:CLA402 4.3 0.1 1.0
C2B A:CLA402 4.3 0.1 1.0
C2D A:CLA402 4.4 0.1 1.0
CG A:HIS198 4.4 0.9 1.0
CE A:MET183 4.4 0.5 1.0
C2C A:CLA402 4.4 0.1 1.0
C3C A:CLA402 4.4 0.1 1.0
C3A A:CLA402 4.4 0.1 1.0
C2A A:CLA402 4.4 0.1 1.0
CBB D:CLA403 4.5 0.1 1.0
CBD A:CLA402 4.9 0.1 1.0
CHC D:CLA403 4.9 0.1 1.0
O1D A:CLA402 5.0 0.1 1.0

Magnesium binding site 2 out of 308 in 5mdx

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Magnesium binding site 2 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:0.1
occ:1.00
MG A:CLA403 0.0 0.1 1.0
NB A:CLA403 2.0 0.1 1.0
ND A:CLA403 2.0 0.1 1.0
NC A:CLA403 2.1 0.1 1.0
NA A:CLA403 2.1 0.1 1.0
C4D A:CLA403 2.8 0.1 1.0
C4B A:CLA403 3.0 0.1 1.0
C1B A:CLA403 3.0 0.1 1.0
C1C A:CLA403 3.1 0.1 1.0
C4A A:CLA403 3.1 0.1 1.0
C4C A:CLA403 3.1 0.1 1.0
C1A A:CLA403 3.1 0.1 1.0
C1D A:CLA403 3.1 0.1 1.0
O2A A:CLA403 3.3 0.1 1.0
CHB A:CLA403 3.4 0.1 1.0
CHC A:CLA403 3.4 0.1 1.0
CHA A:CLA403 3.4 0.1 1.0
CHD A:CLA403 3.6 0.1 1.0
CBB D:PHO402 3.8 0.1 1.0
C3D A:CLA403 4.1 0.1 1.0
C3B A:CLA403 4.3 0.1 1.0
C2B A:CLA403 4.3 0.1 1.0
CGA A:CLA403 4.3 0.1 1.0
C2D A:CLA403 4.3 0.1 1.0
C2C A:CLA403 4.4 0.1 1.0
C3C A:CLA403 4.4 0.1 1.0
C3A A:CLA403 4.4 0.1 1.0
C2A A:CLA403 4.4 0.1 1.0
CAB D:PHO402 4.7 0.1 1.0
O2A D:CLA403 4.8 0.1 1.0
CBD A:CLA403 4.9 0.1 1.0
O1A A:CLA403 5.0 0.1 1.0

Magnesium binding site 3 out of 308 in 5mdx

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Magnesium binding site 3 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:0.1
occ:1.00
MG A:CLA405 0.0 0.1 1.0
NB A:CLA405 2.0 0.1 1.0
ND A:CLA405 2.0 0.1 1.0
NC A:CLA405 2.1 0.1 1.0
NA A:CLA405 2.1 0.1 1.0
NE2 A:HIS118 2.3 1.0 1.0
C4D A:CLA405 2.8 0.1 1.0
C4B A:CLA405 2.9 0.1 1.0
C1B A:CLA405 3.0 0.1 1.0
C1C A:CLA405 3.1 0.1 1.0
C4A A:CLA405 3.1 0.1 1.0
C1D A:CLA405 3.1 0.1 1.0
C4C A:CLA405 3.1 0.1 1.0
C1A A:CLA405 3.1 0.1 1.0
CE1 A:HIS118 3.2 1.0 1.0
CD2 A:HIS118 3.3 1.0 1.0
CHB A:CLA405 3.4 0.1 1.0
CHC A:CLA405 3.4 0.1 1.0
CHA A:CLA405 3.4 0.1 1.0
CHD A:CLA405 3.6 0.1 1.0
C3D A:CLA405 4.1 0.1 1.0
C3B A:CLA405 4.3 0.1 1.0
C2B A:CLA405 4.3 0.1 1.0
C2D A:CLA405 4.3 0.1 1.0
ND1 A:HIS118 4.3 1.0 1.0
C3C A:CLA405 4.4 0.1 1.0
C2C A:CLA405 4.4 0.1 1.0
C3A A:CLA405 4.4 0.1 1.0
CG A:HIS118 4.5 1.0 1.0
C2A A:CLA405 4.5 0.1 1.0
CG1 I:VAL12 4.5 0.3 1.0
CBD A:CLA405 4.9 0.1 1.0
O1D A:CLA405 4.9 0.1 1.0

Magnesium binding site 4 out of 308 in 5mdx

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Magnesium binding site 4 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.1
occ:1.00
MG B:CLA601 0.0 0.1 1.0
NB B:CLA601 2.0 0.1 1.0
ND B:CLA601 2.1 0.1 1.0
NC B:CLA601 2.1 0.1 1.0
NA B:CLA601 2.1 0.1 1.0
C4D B:CLA601 2.9 0.1 1.0
C4B B:CLA601 3.0 0.1 1.0
O B:TRP185 3.0 0.7 1.0
C1B B:CLA601 3.0 0.1 1.0
C1C B:CLA601 3.1 0.1 1.0
C4C B:CLA601 3.1 0.1 1.0
C4A B:CLA601 3.1 0.1 1.0
C1D B:CLA601 3.1 0.1 1.0
C1A B:CLA601 3.1 0.1 1.0
CHB B:CLA601 3.4 0.1 1.0
CHC B:CLA601 3.4 0.1 1.0
CHA B:CLA601 3.5 0.1 1.0
CHD B:CLA601 3.6 0.1 1.0
O2A B:CLA601 3.7 0.1 1.0
C3D B:CLA601 4.1 0.1 1.0
C B:TRP185 4.2 0.7 1.0
C3B B:CLA601 4.3 0.1 1.0
C2B B:CLA601 4.3 0.1 1.0
C2D B:CLA601 4.4 0.1 1.0
C3C B:CLA601 4.4 0.1 1.0
C2C B:CLA601 4.4 0.1 1.0
C3A B:CLA601 4.5 0.1 1.0
C2A B:CLA601 4.5 0.1 1.0
CGA B:CLA601 4.8 0.1 1.0
CBD B:CLA601 4.9 0.1 1.0
CA B:GLY186 5.0 0.0 1.0

Magnesium binding site 5 out of 308 in 5mdx

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Magnesium binding site 5 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:0.1
occ:1.00
MG B:CLA602 0.0 0.1 1.0
NB B:CLA602 2.0 0.1 1.0
ND B:CLA602 2.1 0.1 1.0
NC B:CLA602 2.1 0.1 1.0
NA B:CLA602 2.1 0.1 1.0
ND1 B:HIS201 2.2 0.1 1.0
C4D B:CLA602 2.9 0.1 1.0
CE1 B:HIS201 2.9 0.1 1.0
C4B B:CLA602 3.0 0.1 1.0
C1B B:CLA602 3.0 0.1 1.0
C1C B:CLA602 3.1 0.1 1.0
C4A B:CLA602 3.1 0.1 1.0
C4C B:CLA602 3.1 0.1 1.0
C1D B:CLA602 3.1 0.1 1.0
C1A B:CLA602 3.2 0.1 1.0
CG B:HIS201 3.4 0.1 1.0
CHB B:CLA602 3.4 0.1 1.0
CHC B:CLA602 3.5 0.1 1.0
CHA B:CLA602 3.5 0.1 1.0
CHD B:CLA602 3.6 0.1 1.0
CB B:HIS201 3.9 0.1 1.0
CD1 H:ILE57 4.1 0.3 1.0
C3D B:CLA602 4.2 0.1 1.0
NE2 B:HIS201 4.2 0.1 1.0
C3B B:CLA602 4.3 0.1 1.0
C2B B:CLA602 4.3 0.1 1.0
C2D B:CLA602 4.4 0.1 1.0
CD2 B:HIS201 4.4 0.1 1.0
C3C B:CLA602 4.4 0.1 1.0
C2C B:CLA602 4.4 0.1 1.0
C3A B:CLA602 4.4 0.1 1.0
CA B:HIS201 4.5 0.0 1.0
C2A B:CLA602 4.5 0.1 1.0
CBD B:CLA602 4.9 0.1 1.0

Magnesium binding site 6 out of 308 in 5mdx

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Magnesium binding site 6 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:0.1
occ:1.00
MG B:CLA603 0.0 0.1 1.0
NB B:CLA603 2.0 0.1 1.0
ND B:CLA603 2.0 0.1 1.0
NC B:CLA603 2.1 0.1 1.0
NA B:CLA603 2.1 0.1 1.0
NE2 B:HIS202 2.2 0.1 1.0
C4D B:CLA603 2.8 0.1 1.0
C4B B:CLA603 3.0 0.1 1.0
C1B B:CLA603 3.0 0.1 1.0
CD2 B:HIS202 3.1 0.1 1.0
C4A B:CLA603 3.1 0.1 1.0
C1C B:CLA603 3.1 0.1 1.0
C4C B:CLA603 3.1 0.1 1.0
C1D B:CLA603 3.1 0.1 1.0
C1A B:CLA603 3.1 0.1 1.0
CE1 B:HIS202 3.3 0.1 1.0
CHB B:CLA603 3.3 0.1 1.0
CHC B:CLA603 3.5 0.1 1.0
CHA B:CLA603 3.5 0.1 1.0
CHD B:CLA603 3.6 0.1 1.0
C3D B:CLA603 4.1 0.1 1.0
CG B:HIS202 4.3 0.1 1.0
C2B B:CLA603 4.3 0.1 1.0
C3B B:CLA603 4.3 0.1 1.0
ND1 B:HIS202 4.3 0.1 1.0
C2D B:CLA603 4.4 0.1 1.0
C3A B:CLA603 4.4 0.1 1.0
C3C B:CLA603 4.4 0.1 1.0
C2C B:CLA603 4.4 0.1 1.0
C2A B:CLA603 4.4 0.1 1.0
CBD B:CLA603 4.9 0.1 1.0
CMA B:CLA603 5.0 0.1 1.0

Magnesium binding site 7 out of 308 in 5mdx

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Magnesium binding site 7 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:0.1
occ:1.00
MG B:CLA604 0.0 0.1 1.0
NB B:CLA604 2.0 0.1 1.0
ND B:CLA604 2.0 0.1 1.0
NC B:CLA604 2.1 0.1 1.0
NA B:CLA604 2.1 0.1 1.0
NE2 B:HIS455 2.2 0.8 1.0
C4D B:CLA604 2.8 0.1 1.0
C4B B:CLA604 3.0 0.1 1.0
C1B B:CLA604 3.0 0.1 1.0
C1C B:CLA604 3.0 0.1 1.0
C4A B:CLA604 3.1 0.1 1.0
C4C B:CLA604 3.1 0.1 1.0
C1D B:CLA604 3.1 0.1 1.0
C1A B:CLA604 3.1 0.1 1.0
CD2 B:HIS455 3.2 0.8 1.0
CE1 B:HIS455 3.2 0.8 1.0
CHB B:CLA604 3.4 0.1 1.0
CHA B:CLA604 3.4 0.1 1.0
CHC B:CLA604 3.4 0.1 1.0
CHD B:CLA604 3.6 0.1 1.0
C3D B:CLA604 4.1 0.1 1.0
C3B B:CLA604 4.3 0.1 1.0
ND1 B:HIS455 4.3 0.8 1.0
CG B:HIS455 4.3 0.8 1.0
C2D B:CLA604 4.3 0.1 1.0
C2B B:CLA604 4.3 0.1 1.0
C2C B:CLA604 4.4 0.1 1.0
C3C B:CLA604 4.4 0.1 1.0
C3A B:CLA604 4.4 0.1 1.0
C2A B:CLA604 4.5 0.1 1.0
CE1 B:PHE451 4.7 0.7 1.0
CBD B:CLA604 4.9 0.1 1.0
CBB B:CLA613 4.9 0.1 1.0
CAB B:CLA613 4.9 0.1 1.0

Magnesium binding site 8 out of 308 in 5mdx

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Magnesium binding site 8 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:0.1
occ:1.00
MG B:CLA605 0.0 0.1 1.0
NB B:CLA605 2.0 0.1 1.0
ND B:CLA605 2.0 0.1 1.0
NC B:CLA605 2.1 0.1 1.0
NA B:CLA605 2.1 0.1 1.0
NE2 B:HIS100 2.2 0.9 1.0
C4D B:CLA605 2.8 0.1 1.0
C4B B:CLA605 3.0 0.1 1.0
C1B B:CLA605 3.0 0.1 1.0
C1C B:CLA605 3.1 0.1 1.0
C4A B:CLA605 3.1 0.1 1.0
CD2 B:HIS100 3.1 0.9 1.0
C4C B:CLA605 3.1 0.1 1.0
C1A B:CLA605 3.1 0.1 1.0
C1D B:CLA605 3.1 0.1 1.0
CE1 B:HIS100 3.2 0.9 1.0
CHB B:CLA605 3.4 0.1 1.0
CHA B:CLA605 3.4 0.1 1.0
CHC B:CLA605 3.4 0.1 1.0
CHD B:CLA605 3.6 0.1 1.0
C3D B:CLA605 4.1 0.1 1.0
CG B:HIS100 4.3 0.9 1.0
C3B B:CLA605 4.3 0.1 1.0
ND1 B:HIS100 4.3 0.9 1.0
C2B B:CLA605 4.3 0.1 1.0
C2D B:CLA605 4.3 0.1 1.0
O2A B:CLA604 4.4 0.1 1.0
C2C B:CLA605 4.4 0.1 1.0
C3C B:CLA605 4.4 0.1 1.0
C3A B:CLA605 4.4 0.1 1.0
C2A B:CLA605 4.4 0.1 1.0
O1A B:CLA604 4.8 0.1 1.0
CBA B:CLA605 4.8 0.1 1.0
CBD B:CLA605 4.8 0.1 1.0
O2D B:CLA605 4.9 0.1 1.0
CGA B:CLA604 5.0 0.1 1.0

Magnesium binding site 9 out of 308 in 5mdx

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Magnesium binding site 9 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:0.1
occ:1.00
MG B:CLA606 0.0 0.1 1.0
NB B:CLA606 2.0 0.1 1.0
ND B:CLA606 2.1 0.1 1.0
NC B:CLA606 2.1 0.1 1.0
NA B:CLA606 2.1 0.1 1.0
ND1 B:HIS157 2.2 0.7 1.0
C4D B:CLA606 2.9 0.1 1.0
C4B B:CLA606 3.0 0.1 1.0
CE1 B:HIS157 3.0 0.7 1.0
C1B B:CLA606 3.1 0.1 1.0
C1C B:CLA606 3.1 0.1 1.0
C4A B:CLA606 3.1 0.1 1.0
C4C B:CLA606 3.1 0.1 1.0
C1D B:CLA606 3.1 0.1 1.0
C1A B:CLA606 3.2 0.1 1.0
CG B:HIS157 3.4 0.7 1.0
CHB B:CLA606 3.4 0.1 1.0
CHC B:CLA606 3.5 0.1 1.0
CHA B:CLA606 3.5 0.1 1.0
CHD B:CLA606 3.6 0.1 1.0
CB B:HIS157 3.9 0.7 1.0
C3D B:CLA606 4.1 0.1 1.0
NE2 B:HIS157 4.2 0.7 1.0
C3B B:CLA606 4.3 0.1 1.0
C2D B:CLA606 4.3 0.1 1.0
C2B B:CLA606 4.4 0.1 1.0
CD2 B:HIS157 4.4 0.7 1.0
C3C B:CLA606 4.4 0.1 1.0
C2C B:CLA606 4.4 0.1 1.0
C3A B:CLA606 4.4 0.1 1.0
CD B:PRO164 4.5 0.7 1.0
C2A B:CLA606 4.5 0.1 1.0
CA B:HIS157 4.8 0.7 1.0
CBD B:CLA606 4.9 0.1 1.0

Magnesium binding site 10 out of 308 in 5mdx

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Magnesium binding site 10 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg607

b:0.1
occ:1.00
MG B:CLA607 0.0 0.1 1.0
NB B:CLA607 2.0 0.1 1.0
ND B:CLA607 2.0 0.1 1.0
NC B:CLA607 2.1 0.1 1.0
NA B:CLA607 2.1 0.1 1.0
C4D B:CLA607 2.8 0.1 1.0
C4B B:CLA607 3.0 0.1 1.0
C1B B:CLA607 3.0 0.1 1.0
C1C B:CLA607 3.1 0.1 1.0
C4A B:CLA607 3.1 0.1 1.0
C4C B:CLA607 3.1 0.1 1.0
C1D B:CLA607 3.1 0.1 1.0
C1A B:CLA607 3.1 0.1 1.0
CHB B:CLA607 3.4 0.1 1.0
CHA B:CLA607 3.4 0.1 1.0
CHC B:CLA607 3.4 0.1 1.0
CHD B:CLA607 3.6 0.1 1.0
C3D B:CLA607 4.1 0.1 1.0
C3B B:CLA607 4.3 0.1 1.0
C2B B:CLA607 4.3 0.1 1.0
C2D B:CLA607 4.3 0.1 1.0
C2C B:CLA607 4.4 0.1 1.0
C3C B:CLA607 4.4 0.1 1.0
C3A B:CLA607 4.4 0.1 1.0
C2A B:CLA607 4.5 0.1 1.0
CE B:MET37 4.7 0.7 1.0
CBD B:CLA607 4.9 0.1 1.0

Reference:

L.S.Van Bezouwen, S.Caffarri, R.S.Kale, R.Kouril, A.W.H.Thunnissen, G.T.Oostergetel, E.J.Boekema. Subunit and Chlorophyll Organization of the Plant Photosystem II Supercomplex. Nat Plants V. 3 17080 2017.
ISSN: ESSN 2055-0278
PubMed: 28604725
DOI: 10.1038/NPLANTS.2017.80
Page generated: Sun Sep 29 21:20:09 2024

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