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Magnesium in PDB 5l8f: Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.

Protein crystallography data

The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A., PDB code: 5l8f was solved by D.He, S.Hughes, S.Vanden-Hehir, A.Georgiev, K.Altenbach, E.Tarrant, C.L.Mackay, K.J.Waldron, D.J.Clarke, J.Marles-Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.41 / 2.25
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.096, 92.096, 217.105, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. (pdb code 5l8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A., PDB code: 5l8f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5l8f

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Magnesium binding site 1 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


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 Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:57.1
occ:1.00
 O C:HOH302 1.9 45.4 1.0
OE1 B:GLU64 2.1 45.0 1.0
OE2 B:GLU61 2.3 55.6 1.0
OE1 C:GLU61 2.8 69.9 1.0
CD B:GLU64 3.0 50.7 1.0
CD B:GLU61 3.4 54.5 1.0
OE2 B:GLU64 3.5 61.5 1.0
HE1 C:HIS57 3.8 60.7 1.0
OE1 B:GLU61 3.9 63.4 1.0
HB3 B:GLU64 3.9 37.6 1.0
CD C:GLU61 4.0 61.3 1.0
HA B:GLU61 4.0 41.2 1.0
CG B:GLU64 4.2 43.1 1.0
HB3 B:GLU61 4.4 55.0 1.0
CB B:GLU64 4.4 31.3 1.0
HB2 B:GLU64 4.5 37.6 1.0
HG2 B:GLU64 4.5 51.7 1.0
OE2 C:GLU61 4.6 56.0 1.0
CG B:GLU61 4.6 46.7 1.0
CE1 C:HIS57 4.7 50.6 1.0
CB B:GLU61 4.8 45.8 1.0
HG3 C:GLU61 4.8 60.5 1.0
CA B:GLU61 4.8 34.4 1.0
HE1 A:HIS83 4.9 57.0 1.0
HG3 B:GLU64 5.0 51.7 1.0
HE2 C:HIS57 5.0 58.3 1.0
HG2 B:GLU61 5.0 56.1 1.0

Magnesium binding site 2 out of 10 in 5l8f

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Magnesium binding site 2 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


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 Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:54.8
occ:1.00
 OE2 C:GLU61 2.5 56.0 1.0
OE1 C:GLU64 2.5 48.7 1.0
OE1 B:GLU61 2.6 63.4 1.0
CD C:GLU64 3.4 50.2 1.0
CD C:GLU61 3.5 61.3 1.0
HE2 B:HIS57 3.7 65.1 1.0
CD B:GLU61 3.7 54.5 1.0
OE2 C:GLU64 3.8 52.5 1.0
OE1 C:GLU61 3.9 69.9 1.0
OE2 B:GLU61 4.4 55.6 1.0
HB3 C:GLU64 4.4 49.3 1.0
HA C:GLU61 4.4 41.7 1.0
HG3 B:GLU61 4.5 56.1 1.0
NE2 B:HIS57 4.6 54.3 1.0
CG C:GLU64 4.7 46.7 1.0
CG B:GLU61 4.8 46.7 1.0
HB3 C:GLU61 4.9 55.7 1.0
CG C:GLU61 4.9 50.4 1.0
CB C:GLU64 4.9 41.1 1.0
HB2 C:GLU64 4.9 49.3 1.0
HG2 C:GLU64 4.9 56.1 1.0

Magnesium binding site 3 out of 10 in 5l8f

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Magnesium binding site 3 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


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 Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:60.9
occ:1.00
 OE1 E:GLU61 2.3 70.5 1.0
OE1 D:GLU64 2.5 48.5 1.0
OE2 D:GLU61 2.8 58.4 1.0
HE2 E:HIS57 3.0 54.0 1.0
CD D:GLU64 3.2 49.8 1.0
O E:HOH317 3.3 46.1 1.0
CD E:GLU61 3.5 62.0 1.0
OE2 D:GLU64 3.6 51.3 1.0
CD D:GLU61 3.7 59.4 1.0
NE2 E:HIS57 3.9 45.0 1.0
OE1 D:GLU61 4.0 68.5 1.0
HB3 D:GLU64 4.0 52.9 1.0
HG3 E:GLU61 4.1 60.8 1.0
CG D:GLU64 4.3 49.2 1.0
OE2 E:GLU61 4.3 56.8 1.0
HG2 D:GLU64 4.4 59.0 1.0
CG E:GLU61 4.5 50.7 1.0
HA D:GLU61 4.5 49.1 1.0
HE1 E:HIS57 4.5 48.1 1.0
CE1 E:HIS57 4.6 40.1 1.0
CB D:GLU64 4.6 44.0 1.0
HB3 D:GLU61 4.6 46.6 1.0
HB2 D:GLU64 4.8 52.9 1.0
CD2 E:HIS57 4.9 45.8 1.0

Magnesium binding site 4 out of 10 in 5l8f

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Magnesium binding site 4 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


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 Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:53.3
occ:1.00
 OE1 E:GLU64 2.1 44.8 1.0
OE1 D:GLU61 2.7 68.5 1.0
CD E:GLU64 2.8 53.5 1.0
OE2 E:GLU64 3.1 46.4 1.0
OE2 E:GLU61 3.2 56.8 1.0
HE1 D:HIS57 3.3 61.1 1.0
CD D:GLU61 4.0 59.4 1.0
CE1 D:HIS57 4.1 50.9 1.0
CG E:GLU64 4.1 53.0 1.0
HB3 E:GLU64 4.2 53.8 1.0
CD E:GLU61 4.2 62.0 1.0
HE2 D:HIS57 4.3 60.3 1.0
HG2 E:GLU64 4.3 63.6 1.0
HG3 D:GLU61 4.4 71.8 1.0
OE1 E:GLU61 4.5 70.5 1.0
NE2 D:HIS57 4.6 50.3 1.0
CB E:GLU64 4.6 44.8 1.0
HH F:TYR87 4.7 57.8 1.0
HB2 E:GLU64 4.7 53.8 1.0
CG D:GLU61 4.8 59.9 1.0
HG3 E:GLU64 4.8 63.6 1.0
OE2 D:GLU61 4.8 58.4 1.0
HA E:GLU61 4.9 51.7 1.0

Magnesium binding site 5 out of 10 in 5l8f

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Magnesium binding site 5 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


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 Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:48.0
occ:1.00
 O H:HOH301 2.3 43.9 1.0
OE1 F:GLU64 2.4 35.2 1.0
OE2 F:GLU61 2.5 47.1 1.0
OE1 H:GLU61 2.8 55.5 1.0
CD F:GLU64 3.2 33.6 1.0
CD F:GLU61 3.3 47.9 1.0
OE2 F:GLU64 3.4 37.4 1.0
OE1 F:GLU61 3.5 57.3 1.0
HE2 H:HIS57 3.8 44.0 1.0
CD H:GLU61 3.9 49.9 1.0
HB3 F:GLU64 4.3 39.6 1.0
HA F:GLU61 4.4 43.8 1.0
CG F:GLU64 4.4 37.3 1.0
HG3 H:GLU61 4.5 54.1 1.0
HG2 F:GLU64 4.6 44.8 1.0
NE2 H:HIS57 4.6 36.6 1.0
OE2 H:GLU61 4.6 49.4 1.0
HB3 F:GLU61 4.7 44.7 1.0
CG F:GLU61 4.8 39.0 1.0
CB F:GLU64 4.8 33.0 1.0
CG H:GLU61 4.9 45.1 1.0
MG F:MG202 4.9 47.9 1.0
HB2 F:GLU64 4.9 39.6 1.0

Magnesium binding site 6 out of 10 in 5l8f

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Magnesium binding site 6 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


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 Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:47.9
occ:1.00
 OE2 H:GLU61 2.3 49.4 1.0
O H:HOH309 2.4 43.2 1.0
OE1 H:GLU64 2.5 33.0 1.0
O F:HOH303 2.8 45.3 1.0
OE1 F:GLU61 2.9 57.3 1.0
CD H:GLU61 3.2 49.9 1.0
CD H:GLU64 3.4 33.3 1.0
OE1 H:GLU61 3.5 55.5 1.0
OE2 H:GLU64 3.6 36.1 1.0
HE2 F:HIS57 4.1 51.5 1.0
CD F:GLU61 4.1 47.9 1.0
HA H:GLU61 4.3 40.6 1.0
HB3 H:GLU64 4.5 35.5 1.0
CG H:GLU61 4.6 45.1 1.0
CG H:GLU64 4.7 32.6 1.0
HB3 H:GLU61 4.7 38.2 1.0
HG3 F:GLU61 4.7 46.9 1.0
OE2 F:GLU61 4.8 47.1 1.0
NE2 F:HIS57 4.8 42.9 1.0
HE1 F:HIS57 4.9 72.6 1.0
MG F:MG201 4.9 48.0 1.0
HB2 H:GLU64 4.9 35.5 1.0
O G:HOH317 5.0 32.6 1.0
CB H:GLU64 5.0 29.6 1.0
HG2 H:GLU61 5.0 54.1 1.0

Magnesium binding site 7 out of 10 in 5l8f

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Magnesium binding site 7 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:56.7
occ:1.00
 O G:HOH303 2.2 55.0 1.0
HE1 I:HIS57 2.2 54.3 1.0
OE1 I:GLU61 2.3 59.5 1.0
O I:HOH326 2.3 54.7 1.0
OE1 G:GLU64 2.8 42.7 1.0
O G:HOH328 2.9 41.9 1.0
CE1 I:HIS57 3.0 45.3 1.0
OE2 G:GLU61 3.2 54.9 1.0
CD G:GLU64 3.3 42.7 1.0
CD I:GLU61 3.5 47.8 1.0
NE2 I:HIS57 3.5 48.3 1.0
OE2 G:GLU64 3.7 39.3 1.0
HG3 I:GLU61 3.7 50.8 1.0
CD G:GLU61 4.0 53.3 1.0
OE1 G:GLU61 4.1 59.9 1.0
CG I:GLU61 4.2 42.3 1.0
HB3 G:GLU64 4.2 49.0 1.0
ND1 I:HIS57 4.2 39.1 1.0
HG2 G:GLU64 4.4 44.1 1.0
CG G:GLU64 4.4 36.8 1.0
OE2 I:GLU61 4.5 47.0 1.0
O G:HOH316 4.5 47.0 1.0
HD1 I:HIS57 4.5 47.0 1.0
HG2 I:GLU61 4.7 50.8 1.0
CB G:GLU64 4.8 40.8 1.0
HH H:TYR87 4.8 50.0 1.0
O G:HOH338 4.8 41.6 1.0
CD2 I:HIS57 4.9 39.5 1.0
HB3 G:GLU61 4.9 54.9 1.0

Magnesium binding site 8 out of 10 in 5l8f

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Magnesium binding site 8 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:37.8
occ:1.00
 HE1 G:TRP80 2.0 39.9 1.0
HD2 G:ARG22 2.5 32.5 1.0
NE1 G:TRP80 2.7 33.2 1.0
HD1 G:TRP80 2.7 35.1 1.0
OD2 G:ASP77 2.8 34.1 1.0
HE2 H:LYS63 2.9 29.2 1.0
HD11 G:ILE26 3.0 37.9 1.0
CD1 G:TRP80 3.0 29.2 1.0
O H:HOH305 3.0 29.0 1.0
HE G:ARG22 3.1 37.6 1.0
HD22 G:LEU73 3.2 35.4 1.0
CD G:ARG22 3.4 27.1 1.0
HB3 G:ARG22 3.4 35.7 1.0
HG11 H:VAL36 3.5 32.0 1.0
NE G:ARG22 3.6 31.3 1.0
HG12 H:VAL36 3.6 32.0 1.0
O H:HOH304 3.6 37.5 1.0
CE H:LYS63 3.8 24.3 1.0
CG G:ASP77 3.8 33.9 1.0
HZ1 H:LYS63 3.8 41.0 1.0
HB2 G:ASP77 3.9 37.6 1.0
CD1 G:ILE26 3.9 31.6 1.0
CG1 H:VAL36 3.9 26.6 1.0
CD2 G:LEU73 3.9 29.5 1.0
HD21 G:LEU73 4.0 35.4 1.0
CE2 G:TRP80 4.0 24.7 1.0
HZ3 H:LYS63 4.0 41.0 1.0
HD3 G:ARG22 4.0 32.5 1.0
HG13 H:VAL36 4.1 32.0 1.0
NZ H:LYS63 4.1 34.2 1.0
HD12 G:ILE26 4.1 37.9 1.0
HD23 G:LEU73 4.1 35.4 1.0
CB G:ARG22 4.2 29.8 1.0
HE3 H:LYS63 4.2 29.2 1.0
CG G:ARG22 4.3 28.2 1.0
CB G:ASP77 4.3 31.3 1.0
CG G:TRP80 4.4 25.6 1.0
HD13 G:ILE26 4.5 37.9 1.0
HB3 G:ASP77 4.5 37.6 1.0
OD2 H:ASP40 4.5 32.4 1.0
HG2 G:ARG22 4.5 33.8 1.0
HG13 G:ILE26 4.5 33.5 1.0
HB2 G:ARG22 4.5 35.7 1.0
HD3 H:LYS63 4.5 34.4 1.0
HZ2 G:TRP80 4.6 35.2 1.0
CG1 G:ILE26 4.7 27.9 1.0
CD H:LYS63 4.7 28.7 1.0
CZ2 G:TRP80 4.8 29.4 1.0
HG2 H:LYS63 4.8 41.0 1.0
OD1 G:ASP77 4.8 37.9 1.0
CZ G:ARG22 4.8 39.2 1.0
CD2 G:TRP80 4.8 30.5 1.0
HG12 G:ILE26 4.8 33.5 1.0
HZ2 H:LYS63 5.0 41.0 1.0
HD13 G:LEU73 5.0 29.2 1.0

Magnesium binding site 9 out of 10 in 5l8f

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Magnesium binding site 9 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg204

b:46.5
occ:1.00
 OE1 I:GLU64 2.2 32.2 1.0
OE2 I:GLU61 2.4 47.0 1.0
OE1 G:GLU61 2.7 59.9 1.0
CD I:GLU64 3.2 37.7 1.0
CD I:GLU61 3.4 47.8 1.0
HE1 G:HIS57 3.5 58.1 1.0
OE1 I:GLU61 3.6 59.5 1.0
OE2 I:GLU64 3.8 37.0 1.0
CD G:GLU61 3.9 53.3 1.0
HG3 G:GLU61 4.1 59.5 1.0
HB3 I:GLU64 4.1 51.8 1.0
HA I:GLU61 4.2 40.6 1.0
CE1 G:HIS57 4.3 48.4 1.0
CG I:GLU64 4.4 38.5 1.0
O G:HOH303 4.5 55.0 1.0
HB3 I:GLU61 4.5 44.4 1.0
CG G:GLU61 4.6 49.6 1.0
CB I:GLU64 4.6 43.1 1.0
HB2 I:GLU64 4.6 51.8 1.0
HG2 I:GLU64 4.7 46.2 1.0
CG I:GLU61 4.7 42.3 1.0
OE2 G:GLU61 4.8 54.9 1.0
O J:HOH319 4.9 31.4 1.0
NE2 G:HIS57 4.9 56.2 1.0
CB I:GLU61 5.0 37.0 1.0

Magnesium binding site 10 out of 10 in 5l8f

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Magnesium binding site 10 out of 10 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:47.3
occ:1.00
 O J:ALA96 2.4 55.9 1.0
O J:HOH339 2.5 40.5 1.0
O J:HOH327 3.0 45.5 1.0
HG23 J:THR86 3.2 35.9 1.0
C J:ALA96 3.6 57.3 1.0
HG22 J:THR86 3.8 35.9 1.0
CG2 J:THR86 3.8 29.9 1.0
HG21 J:THR86 3.9 35.9 1.0
HE1 J:TYR87 4.5 41.1 1.0
HA J:ALA96 4.7 68.2 1.0
CE1 J:TYR87 4.7 34.2 1.0
O J:THR86 4.8 41.7 1.0
CA J:ALA96 4.8 56.8 1.0

Reference:

D.He, S.Hughes, S.Vanden-Hehir, A.Georgiev, K.Altenbach, E.Tarrant, C.L.Mackay, K.J.Waldron, D.J.Clarke, J.Marles-Wright. Crystal Structure of Rhodospirillum Rubrum RRU_A0973 Mutant E32A, E62A, H65A. To Be Published.
Page generated: Sun Sep 29 19:45:18 2024

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