Magnesium in PDB 8xf0: Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77

Protein crystallography data

The structure of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77, PDB code: 8xf0 was solved by H.K.Nguyen, T.Teramoto, Y.Kakuta, K.S.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.86 / 2.50
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 169.99, 169.99, 125.968, 90, 90, 120
R / Rfree (%) 24.4 / 28.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 (pdb code 8xf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77, PDB code: 8xf0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8xf0

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:63.4
occ:1.00
 O A:SER162 3.0 59.7 1.0
OD2 A:ASP116 3.8 69.0 1.0
OD1 A:ASP116 4.0 71.0 1.0
C A:SER162 4.1 61.8 1.0
CG A:ASP116 4.1 65.3 1.0
O A:LEU161 4.6 53.8 1.0
OXT A:SER162 4.7 63.4 1.0
O A:ALA160 4.8 46.7 1.0
C A:LEU161 4.9 47.3 1.0

Magnesium binding site 2 out of 6 in 8xf0

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:57.3
occ:1.00
 O B:HOH311 2.1 51.4 1.0
O B:HOH312 2.2 52.9 1.0
O D:HOH304 2.2 52.7 1.0
O B:SER162 2.3 57.1 1.0
O D:SER162 2.4 59.9 1.0
MG D:MG202 3.0 51.2 1.0
OXT D:SER162 3.1 58.1 1.0
C D:SER162 3.1 58.6 1.0
C B:SER162 3.3 54.4 1.0
OXT B:SER162 3.5 55.0 1.0
O B:HOH304 3.7 62.5 1.0
O D:HOH307 3.8 56.2 1.0
O B:HOH302 4.0 51.1 1.0
OD2 B:ASP116 4.1 51.2 1.0
CA D:SER162 4.6 55.0 1.0
CA B:SER162 4.6 52.5 1.0
O B:ALA160 4.7 38.4 1.0
OD1 B:ASP116 4.8 53.7 1.0
CG B:ASP116 4.8 52.8 1.0
N B:SER162 4.9 53.5 1.0

Magnesium binding site 3 out of 6 in 8xf0

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:27.7
occ:1.00
 OE2 C:GLU117 2.0 47.1 1.0
OD2 C:ASP116 2.0 41.3 1.0
O C:HOH318 2.0 61.7 1.0
OXT F:SER162 2.1 57.2 1.0
O C:HOH302 2.3 39.3 1.0
O C:HOH320 2.3 43.3 1.0
CD C:GLU117 2.9 55.3 1.0
CG C:ASP116 3.2 44.5 1.0
C F:SER162 3.3 56.3 1.0
OE1 C:GLU117 3.3 51.0 1.0
NH1 C:ARG120 3.6 48.0 1.0
O F:SER162 3.8 56.6 1.0
NH2 C:ARG120 3.8 51.1 1.0
OD1 C:ASP116 3.9 50.9 1.0
CZ C:ARG120 4.2 55.0 1.0
CG C:GLU117 4.3 46.8 1.0
CB C:ASP116 4.4 37.6 1.0
CA F:SER162 4.4 48.8 1.0
CB F:SER162 4.7 52.6 1.0
N C:GLU117 4.8 40.4 1.0

Magnesium binding site 4 out of 6 in 8xf0

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:51.2
occ:1.00
 O B:HOH304 2.0 62.5 1.0
O D:HOH307 2.0 56.2 1.0
OXT D:SER162 2.1 58.1 1.0
O B:HOH302 2.2 51.1 1.0
O D:HOH301 2.4 57.3 1.0
MG B:MG202 3.0 57.3 1.0
OXT B:SER162 3.2 55.0 1.0
C D:SER162 3.2 58.6 1.0
O D:SER162 3.6 59.9 1.0
O B:SER162 3.9 57.1 1.0
OD2 D:ASP116 3.9 59.7 1.0
C B:SER162 4.0 54.4 1.0
O D:ALA160 4.1 45.5 1.0
O D:HOH304 4.4 52.7 1.0
OD1 D:ASP116 4.4 54.7 1.0
CA D:SER162 4.4 55.0 1.0
O B:HOH312 4.5 52.9 1.0
CG D:ASP116 4.5 51.8 1.0
N D:SER162 4.5 53.2 1.0

Magnesium binding site 5 out of 6 in 8xf0

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:56.3
occ:1.00
 O E:HOH307 2.2 53.5 1.0
O E:SER162 2.8 67.6 1.0
O E:HOH309 3.3 53.0 1.0
OD2 E:ASP116 3.5 66.7 1.0
OD1 E:ASP116 3.6 68.6 1.0
C E:SER162 3.9 69.0 1.0
CG E:ASP116 4.0 67.8 1.0
O E:ALA160 4.4 66.9 1.0
OXT E:SER162 4.4 75.8 1.0
N E:SER162 4.8 71.5 1.0
CA E:SER162 4.9 64.8 1.0
C E:LEU161 5.0 66.0 1.0

Magnesium binding site 6 out of 6 in 8xf0

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Dissociated C-Phycocyanin Alpha-Chain From Thermoleptolyngbya Sp. O-77 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:33.0
occ:1.00
 OE2 F:GLU117 1.9 52.2 1.0
O F:HOH301 2.1 47.8 1.0
O C:SER162 2.1 54.5 1.0
O C:HOH306 2.1 35.6 1.0
OD2 F:ASP116 2.5 55.7 1.0
CD F:GLU117 3.0 55.2 1.0
C C:SER162 3.2 50.5 1.0
OE1 F:GLU117 3.5 56.3 1.0
CG F:ASP116 3.6 49.9 1.0
OXT C:SER162 3.7 51.2 1.0
NH1 F:ARG120 3.8 51.5 1.0
NH2 F:ARG120 3.8 49.6 1.0
CB F:ASP116 4.1 43.3 1.0
CZ F:ARG120 4.3 53.1 1.0
CG F:GLU117 4.3 49.6 1.0
CA C:SER162 4.4 43.5 1.0
CB C:SER162 4.7 48.2 1.0
OD1 F:ASP116 4.7 54.9 1.0
N F:GLU117 4.8 44.7 1.0

Reference:

H.K.Nguyen, T.Minato, T.Teramoto, S.Ogo, Y.Kakuta, K.S.Yoon. Disassembly and Reassembly of the Non-Conventional Thermophilic C-Phycocyanin. J.Biosci.Bioeng. V. 137 179 2024.
ISSN: ISSN 1389-1723
PubMed: 38238241
DOI: 10.1016/J.JBIOSC.2023.12.015
Page generated: Sat Oct 5 01:04:12 2024

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