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Magnesium in PDB 2jiy: Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W)

Protein crystallography data

The structure of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W), PDB code: 2jiy was solved by P.K.Fyfe, J.A.Potter, J.Cheng, C.M.Williams, A.J.Watson, M.R.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.97 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.785, 139.785, 185.454, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 20.7

Other elements in 2jiy:

The structure of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) (pdb code 2jiy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W), PDB code: 2jiy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2jiy

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Magnesium binding site 1 out of 5 in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1282

b:37.0
occ:1.00
MG L:BCL1282 0.0 37.0 1.0
ND L:BCL1282 2.0 36.4 1.0
NB L:BCL1282 2.1 38.1 1.0
NC L:BCL1282 2.1 37.1 1.0
NA L:BCL1282 2.2 37.8 1.0
NE2 M:HIS182 2.3 33.1 1.0
C4D L:BCL1282 2.9 36.2 1.0
C1B L:BCL1282 3.1 38.3 1.0
C1D L:BCL1282 3.1 35.8 1.0
C1C L:BCL1282 3.1 35.9 1.0
C4C L:BCL1282 3.1 35.8 1.0
C4B L:BCL1282 3.1 38.1 1.0
C4A L:BCL1282 3.1 37.9 1.0
CD2 M:HIS182 3.2 33.4 1.0
C1A L:BCL1282 3.2 37.2 1.0
CE1 M:HIS182 3.4 33.7 1.0
CHD L:BCL1282 3.4 36.2 1.0
CHB L:BCL1282 3.4 37.7 1.0
CHC L:BCL1282 3.4 37.1 1.0
CHA L:BCL1282 3.5 36.4 1.0
C3D L:BCL1282 4.2 34.6 1.0
C2D L:BCL1282 4.2 35.9 1.0
C2B L:BCL1282 4.3 39.2 1.0
C3B L:BCL1282 4.3 38.9 1.0
C3C L:BCL1282 4.4 33.8 1.0
CG M:HIS182 4.4 33.5 1.0
C2C L:BCL1282 4.4 35.6 1.0
ND1 M:HIS182 4.4 32.8 1.0
C3A L:BCL1282 4.5 38.7 1.0
C2A L:BCL1282 4.5 41.3 1.0
C5 M:BCL1303 4.7 46.2 0.5
C6 M:BCL1303 4.7 47.5 0.5
CE2 L:PHE181 4.8 36.5 1.0
CBD L:BCL1282 4.9 37.0 1.0

Magnesium binding site 2 out of 5 in 2jiy

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Magnesium binding site 2 out of 5 in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1283

b:32.3
occ:1.00
MG L:BCL1283 0.0 32.3 1.0
ND L:BCL1283 2.0 31.6 1.0
NC L:BCL1283 2.1 31.3 1.0
NB L:BCL1283 2.1 31.3 1.0
NA L:BCL1283 2.2 32.1 1.0
NE2 L:HIS173 2.3 29.8 1.0
C4D L:BCL1283 3.0 32.5 1.0
C1C L:BCL1283 3.0 31.1 1.0
C1B L:BCL1283 3.1 29.9 1.0
C4B L:BCL1283 3.1 30.0 1.0
C1D L:BCL1283 3.1 31.2 1.0
C4C L:BCL1283 3.1 30.5 1.0
C4A L:BCL1283 3.1 32.2 1.0
CE1 L:HIS173 3.2 31.1 1.0
C1A L:BCL1283 3.2 32.7 1.0
CD2 L:HIS173 3.3 31.1 1.0
CHC L:BCL1283 3.4 31.1 1.0
CHD L:BCL1283 3.4 31.6 1.0
CHB L:BCL1283 3.4 31.5 1.0
CHA L:BCL1283 3.5 31.3 1.0
CBB M:BCL1303 3.6 40.4 0.5
CBB M:BCL1303 3.6 18.7 0.5
CAB M:BCL1303 3.7 20.8 0.5
OBB M:BCL1303 3.9 20.6 0.5
CAB M:BCL1303 3.9 40.7 0.5
OBB M:BCL1303 4.0 41.4 0.5
C3D L:BCL1283 4.2 30.5 1.0
C2D L:BCL1283 4.3 32.4 1.0
C2B L:BCL1283 4.3 29.5 1.0
C3B L:BCL1283 4.3 30.3 1.0
ND1 L:HIS173 4.3 31.2 1.0
C2C L:BCL1283 4.4 31.3 1.0
C3C L:BCL1283 4.4 31.2 1.0
C3A L:BCL1283 4.4 33.6 1.0
CG L:HIS173 4.4 32.5 1.0
C3B M:BCL1303 4.5 18.4 0.5
C2A L:BCL1283 4.5 32.1 1.0
CD2 L:PHE167 4.6 33.4 1.0
C3B M:BCL1303 4.7 40.2 0.5
CBD L:BCL1283 5.0 31.2 1.0

Magnesium binding site 3 out of 5 in 2jiy

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Magnesium binding site 3 out of 5 in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1284

b:33.0
occ:1.00
MG L:BCL1284 0.0 33.0 1.0
ND L:BCL1284 2.0 29.9 1.0
NC L:BCL1284 2.1 31.5 1.0
NA L:BCL1284 2.1 30.5 1.0
NB L:BCL1284 2.1 30.9 1.0
NE2 L:HIS153 2.3 32.3 1.0
C4D L:BCL1284 2.9 29.9 1.0
C1C L:BCL1284 3.1 32.8 1.0
C4A L:BCL1284 3.1 30.4 1.0
C1D L:BCL1284 3.1 30.7 1.0
C4C L:BCL1284 3.1 30.9 1.0
C4B L:BCL1284 3.1 32.2 1.0
C1B L:BCL1284 3.1 31.3 1.0
C1A L:BCL1284 3.1 31.2 1.0
CD2 L:HIS153 3.2 34.6 1.0
CE1 L:HIS153 3.3 35.4 1.0
CHA L:BCL1284 3.4 30.9 1.0
CHC L:BCL1284 3.4 32.2 1.0
CHB L:BCL1284 3.4 30.6 1.0
CHD L:BCL1284 3.5 31.2 1.0
C3D L:BCL1284 4.2 29.8 1.0
C2D L:BCL1284 4.3 30.8 1.0
CBB L:BPH1285 4.3 32.5 1.0
C3B L:BCL1284 4.3 33.9 1.0
C2B L:BCL1284 4.3 32.4 1.0
CG L:HIS153 4.4 34.0 1.0
C3C L:BCL1284 4.4 31.4 1.0
C2C L:BCL1284 4.4 31.6 1.0
C3A L:BCL1284 4.4 32.0 1.0
ND1 L:HIS153 4.4 33.5 1.0
C2A L:BCL1284 4.4 31.7 1.0
CE2 M:TYR210 4.6 35.0 1.0
CBC L:BCL1284 4.8 28.4 1.0
CD1 L:LEU154 4.8 36.0 1.0
CBA L:BCL1284 4.9 35.4 1.0
CBD L:BCL1284 4.9 31.6 1.0
C19 L:BPH1285 4.9 35.3 1.0

Magnesium binding site 4 out of 5 in 2jiy

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Magnesium binding site 4 out of 5 in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1303

b:20.8
occ:0.50
MG M:BCL1303 0.0 20.8 0.5
MG M:BCL1303 0.4 40.4 0.5
NB M:BCL1303 1.8 40.2 0.5
NC M:BCL1303 1.9 40.6 0.5
ND M:BCL1303 2.0 19.1 0.5
NC M:BCL1303 2.1 21.4 0.5
NB M:BCL1303 2.1 20.0 0.5
NA M:BCL1303 2.2 20.0 0.5
NE2 M:HIS202 2.3 31.2 1.0
ND M:BCL1303 2.3 39.6 0.5
NA M:BCL1303 2.4 39.8 0.5
C4B M:BCL1303 2.7 40.1 0.5
C1C M:BCL1303 2.7 40.4 0.5
C1B M:BCL1303 2.9 39.9 0.5
C4D M:BCL1303 3.0 20.3 0.5
CHC M:BCL1303 3.0 40.4 0.5
C1C M:BCL1303 3.0 20.6 0.5
C4C M:BCL1303 3.1 40.2 0.5
C4C M:BCL1303 3.1 20.8 0.5
C4B M:BCL1303 3.1 19.7 0.5
C1B M:BCL1303 3.1 19.7 0.5
C1D M:BCL1303 3.1 20.0 0.5
C4A M:BCL1303 3.1 21.2 0.5
CE1 M:HIS202 3.2 33.5 1.0
C1A M:BCL1303 3.2 20.5 0.5
C4A M:BCL1303 3.3 39.9 0.5
CD2 M:HIS202 3.3 32.2 1.0
C4D M:BCL1303 3.3 40.1 0.5
C1D M:BCL1303 3.3 39.7 0.5
CHC M:BCL1303 3.4 20.3 0.5
CHB M:BCL1303 3.4 40.4 0.5
CHB M:BCL1303 3.5 20.3 0.5
CHA M:BCL1303 3.5 19.4 0.5
CHD M:BCL1303 3.5 20.4 0.5
C1A M:BCL1303 3.5 39.4 0.5
CHD M:BCL1303 3.6 40.1 0.5
CBB L:BCL1283 3.7 31.7 1.0
CHA M:BCL1303 3.8 39.7 0.5
CAB L:BCL1283 3.8 31.1 1.0
OBB L:BCL1283 3.9 32.9 1.0
C3B M:BCL1303 4.0 40.2 0.5
C2B M:BCL1303 4.0 40.1 0.5
C2C M:BCL1303 4.1 40.8 0.5
C3D M:BCL1303 4.2 20.5 0.5
C3C M:BCL1303 4.3 40.9 0.5
C2D M:BCL1303 4.3 20.3 0.5
C2B M:BCL1303 4.3 19.7 0.5
C3B M:BCL1303 4.3 18.4 0.5
C2C M:BCL1303 4.3 21.8 0.5
ND1 M:HIS202 4.3 33.9 1.0
C3C M:BCL1303 4.4 22.1 0.5
CG M:HIS202 4.4 30.9 1.0
C3D M:BCL1303 4.5 39.9 0.5
C3A M:BCL1303 4.5 20.7 0.5
C3B L:BCL1283 4.5 30.3 1.0
C2D M:BCL1303 4.5 39.8 0.5
C2A M:BCL1303 4.5 22.0 0.5
C3A M:BCL1303 4.6 39.1 0.5
C2A M:BCL1303 4.8 38.8 0.5
CBD M:BCL1303 4.9 19.4 0.5
CMC M:BCL1303 5.0 39.8 0.5
CMC M:BCL1303 5.0 19.3 0.5

Magnesium binding site 5 out of 5 in 2jiy

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Magnesium binding site 5 out of 5 in the Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Photosynthetic Reaction Center Mutant with Ala M149 Replaced with Trp (Chain M, AM149W) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1303

b:40.4
occ:0.50
MG M:BCL1303 0.0 40.4 0.5
MG M:BCL1303 0.4 20.8 0.5
ND M:BCL1303 1.7 19.1 0.5
NA M:BCL1303 2.0 20.0 0.5
ND M:BCL1303 2.0 39.6 0.5
NC M:BCL1303 2.1 40.6 0.5
NB M:BCL1303 2.1 40.2 0.5
NA M:BCL1303 2.2 39.8 0.5
NC M:BCL1303 2.2 21.4 0.5
NE2 M:HIS202 2.4 31.2 1.0
NB M:BCL1303 2.4 20.0 0.5
C4D M:BCL1303 2.6 20.3 0.5
C1D M:BCL1303 2.9 20.0 0.5
C4D M:BCL1303 2.9 40.1 0.5
C1A M:BCL1303 2.9 20.5 0.5
C1C M:BCL1303 3.0 40.4 0.5
C4B M:BCL1303 3.1 40.1 0.5
C1D M:BCL1303 3.1 39.7 0.5
C1B M:BCL1303 3.1 39.9 0.5
C4A M:BCL1303 3.1 21.2 0.5
CHA M:BCL1303 3.1 19.4 0.5
C4C M:BCL1303 3.1 40.2 0.5
C4C M:BCL1303 3.1 20.8 0.5
C4A M:BCL1303 3.2 39.9 0.5
C1A M:BCL1303 3.2 39.4 0.5
CD2 M:HIS202 3.2 32.2 1.0
C1C M:BCL1303 3.3 20.6 0.5
C1B M:BCL1303 3.3 19.7 0.5
CHC M:BCL1303 3.4 40.4 0.5
CHD M:BCL1303 3.4 20.4 0.5
CE1 M:HIS202 3.4 33.5 1.0
CHA M:BCL1303 3.4 39.7 0.5
C4B M:BCL1303 3.5 19.7 0.5
CHD M:BCL1303 3.5 40.1 0.5
CHB M:BCL1303 3.5 40.4 0.5
CHB M:BCL1303 3.6 20.3 0.5
CBB L:BCL1283 3.6 31.7 1.0
CHC M:BCL1303 3.7 20.3 0.5
CAB L:BCL1283 3.9 31.1 1.0
C3D M:BCL1303 3.9 20.5 0.5
OBB L:BCL1283 4.0 32.9 1.0
C2D M:BCL1303 4.0 20.3 0.5
C3D M:BCL1303 4.2 39.9 0.5
C2D M:BCL1303 4.2 39.8 0.5
C3B M:BCL1303 4.3 40.2 0.5
C2B M:BCL1303 4.3 40.1 0.5
C2A M:BCL1303 4.3 22.0 0.5
C2C M:BCL1303 4.4 40.8 0.5
C3A M:BCL1303 4.4 20.7 0.5
C3C M:BCL1303 4.4 40.9 0.5
CG M:HIS202 4.4 30.9 1.0
C3A M:BCL1303 4.5 39.1 0.5
ND1 M:HIS202 4.5 33.9 1.0
C3C M:BCL1303 4.5 22.1 0.5
C2A M:BCL1303 4.5 38.8 0.5
CBD M:BCL1303 4.5 19.4 0.5
C2C M:BCL1303 4.6 21.8 0.5
C2B M:BCL1303 4.6 19.7 0.5
C3B M:BCL1303 4.7 18.4 0.5
C3B L:BCL1283 4.7 30.3 1.0
O2D M:BCL1303 4.8 19.9 0.5
CBD M:BCL1303 4.9 40.0 0.5
CAD M:BCL1303 4.9 20.5 0.5
O2D M:BCL1303 5.0 41.7 0.5

Reference:

P.K.Fyfe, J.A.Potter, J.Cheng, C.M.Williams, A.J.Watson, M.R.Jones. Structural Responses to Cavity-Creating Mutations in An Integral Membrane Protein. Biochemistry V. 46 10461 2007.
ISSN: ISSN 0006-2960
PubMed: 17711306
DOI: 10.1021/BI701085W
Page generated: Mon Dec 14 07:29:40 2020

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