Magnesium in PDB 8a0x: Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna

Protein crystallography data

The structure of Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna, PDB code: 8a0x was solved by S.Hadzi, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.34 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.62, 113.62, 121.05, 90, 90, 90
R / Rfree (%) 23.8 / 26.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna (pdb code 8a0x). 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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna, PDB code: 8a0x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8a0x

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Magnesium binding site 1 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:30.0
occ:1.00
 NE2 A:GLN92 3.6 62.9 1.0
OG A:SER47 3.7 64.0 1.0
CG A:GLN92 4.3 61.2 1.0
CD A:GLN92 4.4 61.9 1.0
O A:SER47 4.6 66.7 1.0
MG A:MG203 4.6 30.0 1.0
CB A:SER47 4.7 65.3 1.0
C A:SER47 4.7 66.2 1.0
N A:ILE48 4.7 65.6 1.0
CA A:ILE48 4.8 64.7 1.0
CG1 A:ILE48 4.9 63.0 1.0
OE1 A:GLN51 4.9 78.6 1.0

Magnesium binding site 2 out of 10 in 8a0x

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Magnesium binding site 2 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:30.0
occ:1.00
 OD1 A:ASP43 2.8 72.7 1.0
CG A:ASP43 3.8 73.5 1.0
OD2 A:ASP43 4.1 75.7 1.0
OE1 A:GLU50 4.1 78.3 1.0
O A:ASP43 4.6 71.9 1.0
CG1 A:VAL46 4.6 68.5 1.0
CB A:SER47 4.8 65.3 1.0
CD A:GLU50 4.9 78.9 1.0
N A:SER47 4.9 66.5 1.0
CA A:SER47 4.9 65.9 1.0
CB A:VAL46 5.0 68.7 1.0

Magnesium binding site 3 out of 10 in 8a0x

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Magnesium binding site 3 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:30.0
occ:1.00
 MG A:MG201 4.6 30.0 1.0
O A:GLN92 4.7 60.1 1.0
CG A:GLN92 4.8 61.2 1.0

Magnesium binding site 4 out of 10 in 8a0x

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Magnesium binding site 4 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:30.0
occ:1.00
 OD1 B:ASP43 2.7 63.3 1.0
CG B:ASP43 3.7 64.6 1.0
OD2 B:ASP43 3.9 67.6 1.0
OE1 B:GLU50 4.2 78.8 1.0
CB B:SER47 4.4 61.8 1.0
O B:ASP43 4.6 58.0 1.0
CA B:SER47 4.9 60.6 1.0
N B:SER47 5.0 59.7 1.0

Magnesium binding site 5 out of 10 in 8a0x

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Magnesium binding site 5 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:30.0
occ:1.00
 O D:GLU12 3.5 74.1 1.0
NH1 D:ARG15 4.1 87.0 1.0
CG D:GLU12 4.1 75.7 1.0
CZ D:ARG15 4.4 86.3 1.0
C D:GLU12 4.4 70.7 1.0
OE1 D:GLU7 4.5 71.8 1.0
CA D:GLU12 4.5 67.5 1.0
CB D:GLU12 4.8 69.6 1.0
OE2 D:GLU7 4.8 70.7 1.0
NH2 D:ARG15 4.8 89.3 1.0
NE D:ARG15 4.8 81.7 1.0

Magnesium binding site 6 out of 10 in 8a0x

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Magnesium binding site 6 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:30.0
occ:1.00
 C2 F:DA17 2.9 74.9 1.0
N3 F:DA17 3.1 71.9 1.0
N3 E:DG17 3.2 84.2 1.0
O4' E:DG18 3.4 74.0 1.0
N2 E:DG17 3.5 84.7 1.0
C2 E:DG17 3.8 85.5 1.0
O4' F:DA18 3.8 63.1 1.0
N1 F:DA17 4.1 78.0 1.0
O2 E:DT16 4.1 89.9 1.0
C1' E:DG17 4.2 83.5 1.0
C4 E:DG17 4.2 85.4 1.0
C4' E:DG18 4.3 71.5 1.0
C4 F:DA17 4.3 72.4 1.0
C4' F:DA18 4.5 60.5 1.0
C1' E:DG18 4.5 74.7 1.0
N9 E:DG17 4.6 85.5 1.0
O4' E:DG17 4.7 84.0 1.0
N9 E:DG18 4.7 78.2 1.0
C5' E:DG18 4.7 72.1 1.0
C5' F:DA18 4.8 59.3 1.0
C2 E:DT16 5.0 90.0 1.0

Magnesium binding site 7 out of 10 in 8a0x

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Magnesium binding site 7 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:30.0
occ:1.00
 O4' F:DC20 3.8 71.8 1.0
O3' F:DC20 3.9 75.2 1.0
N3 F:DG19 4.2 74.2 1.0
C1' F:DC20 4.2 72.8 1.0
C4' F:DC20 4.2 74.3 1.0
C1' F:DG19 4.3 68.9 1.0
O3' F:DG19 4.3 70.3 1.0
O4' F:DG19 4.4 67.6 1.0
C4' F:DG19 4.5 66.5 1.0
C3' F:DC20 4.6 76.5 1.0
OP1 F:DG21 4.8 80.7 1.0
N2 F:DG19 4.8 76.5 1.0
C3' F:DG19 5.0 68.5 1.0

Magnesium binding site 8 out of 10 in 8a0x

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Magnesium binding site 8 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg102

b:30.0
occ:1.00
 OP2 F:DG21 2.2 83.9 1.0
C5' F:DG21 3.0 81.2 1.0
P F:DG21 3.4 82.2 1.0
C3' F:DC20 3.5 76.5 1.0
O5' F:DG21 3.7 79.7 1.0
O3' F:DC20 3.9 75.2 1.0
C2' F:DC20 4.1 76.8 1.0
C4' F:DG21 4.3 81.8 1.0
C8 F:DG21 4.5 81.6 1.0
C3' F:DG21 4.5 84.7 1.0
C2' F:DG21 4.6 85.1 1.0
C4' F:DC20 4.6 74.3 1.0
OP1 F:DG21 4.7 80.7 1.0
C5' F:DC20 4.7 76.2 1.0
C7 F:DT22 5.0 81.9 1.0

Magnesium binding site 9 out of 10 in 8a0x

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Magnesium binding site 9 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg103

b:30.0
occ:1.00
 C6 F:DT28 2.8 136.6 1.0
C2' F:DA27 3.0 120.6 1.0
C7 F:DT28 3.0 139.8 1.0
C5' F:DT28 3.2 128.1 1.0
C5 F:DT28 3.3 139.1 1.0
O4' F:DT28 3.7 131.3 1.0
N1 F:DT28 3.9 135.7 1.0
C4' F:DT28 4.0 128.6 1.0
C1' F:DA27 4.0 122.0 1.0
C2' F:DT28 4.1 131.6 1.0
C1' F:DT28 4.1 133.0 1.0
OP2 F:DT28 4.2 130.3 1.0
C3' F:DA27 4.2 118.0 1.0
N9 F:DA27 4.4 124.4 1.0
O5' F:DT28 4.4 125.9 1.0
C8 F:DA27 4.5 125.6 1.0
C3' F:DT28 4.5 128.3 1.0
O3' F:DA27 4.6 115.7 1.0
P F:DT28 4.7 129.7 1.0
C4 F:DT28 4.7 141.0 1.0

Magnesium binding site 10 out of 10 in 8a0x

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Magnesium binding site 10 out of 10 in the Crystal Structure of the HIGB2-HIGA2 Tetramer in Complex with Operator Dna


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 the HIGB2-HIGA2 Tetramer in Complex with Operator Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg104

b:30.0
occ:1.00
 O3' F:DG8 3.9 95.1 1.0
OP1 F:DT9 4.0 87.5 1.0
C5' F:DG8 4.3 100.2 1.0
NH2 A:ARG49 4.4 76.4 1.0
C4' F:DG8 4.5 99.7 1.0
CG1 A:VAL46 4.5 68.5 1.0
P F:DT9 4.6 88.7 1.0
NH2 A:ARG56 4.7 75.0 1.0
C3' F:DG8 4.8 97.3 1.0
OE2 A:GLU50 5.0 79.6 1.0

Reference:

S.Hadzi, R.Loris. Fuzzy Dna Recognition By A Prokaryotic Transcription Factor To Be Published.
Page generated: Thu Oct 3 17:10:26 2024

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