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Magnesium in PDB 8hmg: The Open State of RGLG2-Vwa

Enzymatic activity of The Open State of RGLG2-Vwa

All present enzymatic activity of The Open State of RGLG2-Vwa:
2.3.2.27;

Protein crystallography data

The structure of The Open State of RGLG2-Vwa, PDB code: 8hmg was solved by Q.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 2.81
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 244.41, 244.41, 63.65, 90, 90, 120
R / Rfree (%) 18.3 / 20.8

Other elements in 8hmg:

The structure of The Open State of RGLG2-Vwa also contains other interesting chemical elements:

Calcium (Ca) 27 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Open State of RGLG2-Vwa (pdb code 8hmg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the The Open State of RGLG2-Vwa, PDB code: 8hmg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 8hmg

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Magnesium binding site 1 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:57.9
occ:1.00
OG A:SER132 2.1 58.5 1.0
OG1 A:THR224 2.1 52.3 1.0
OG1 A:THR130 2.1 51.2 1.0
O A:HOH503 2.1 66.9 1.0
O A:HOH512 2.1 51.3 1.0
OE1 D:GLU119 2.1 46.1 1.0
O A:GLN254 2.9 46.5 1.0
CB A:THR130 3.1 43.6 1.0
CD D:GLU119 3.2 48.7 1.0
CB A:THR224 3.2 48.6 1.0
CB A:SER132 3.2 48.1 1.0
CG2 A:THR224 3.5 49.1 1.0
OE2 D:GLU119 3.5 49.8 1.0
CG2 A:THR130 3.7 44.1 1.0
C A:GLN254 4.0 44.5 1.0
OD1 A:ASP252 4.1 54.2 1.0
N A:SER132 4.1 46.1 1.0
CA A:SER132 4.2 45.0 1.0
CB A:GLN254 4.3 45.6 1.0
OD2 A:ASP128 4.3 57.7 1.0
CA A:THR130 4.4 41.8 1.0
CA A:THR224 4.5 45.4 1.0
OD1 A:ASP128 4.5 47.9 1.0
CG D:GLU119 4.5 49.8 1.0
OD2 A:ASP252 4.5 43.1 1.0
CA A:GLN254 4.6 43.8 1.0
C A:THR130 4.7 42.5 1.0
CG A:ASP252 4.7 47.3 1.0
CG A:ASP128 4.8 47.2 1.0
N A:LYS131 4.8 44.0 1.0
N A:THR224 4.9 49.8 1.0

Magnesium binding site 2 out of 9 in 8hmg

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Magnesium binding site 2 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:64.6
occ:1.00
OG B:SER132 2.1 61.3 1.0
OG1 B:THR130 2.1 55.9 1.0
O B:HOH501 2.1 80.7 1.0
O B:HOH502 2.1 56.1 1.0
OG1 B:THR224 2.1 56.1 1.0
OE1 I:GLU119 2.1 68.8 1.0
O B:GLN254 2.9 64.7 1.0
CB B:THR130 3.1 55.3 1.0
CB B:THR224 3.2 52.3 1.0
CD I:GLU119 3.2 71.9 1.0
CB B:SER132 3.3 54.5 1.0
CG2 B:THR224 3.4 58.6 1.0
OE2 I:GLU119 3.7 83.3 1.0
CG2 B:THR130 3.7 55.5 1.0
C B:GLN254 4.0 54.6 1.0
OD1 B:ASP252 4.0 67.8 1.0
N B:SER132 4.2 49.4 1.0
OD2 B:ASP128 4.2 49.6 1.0
CB B:GLN254 4.3 59.5 1.0
CA B:SER132 4.3 52.3 1.0
OD2 B:ASP252 4.4 58.8 1.0
OD1 B:ASP128 4.4 53.4 1.0
CA B:THR130 4.4 52.2 1.0
CA B:THR224 4.5 52.1 1.0
CG I:GLU119 4.5 67.2 1.0
CA B:GLN254 4.6 59.2 1.0
CG B:ASP252 4.6 64.1 1.0
C B:THR130 4.7 52.0 1.0
CG B:ASP128 4.7 52.2 1.0
N B:LYS131 4.9 56.2 1.0
N B:THR224 4.9 52.1 1.0
N B:GLN254 5.0 56.6 1.0

Magnesium binding site 3 out of 9 in 8hmg

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Magnesium binding site 3 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:50.1
occ:1.00
OG1 C:THR130 2.1 46.6 1.0
O C:HOH502 2.1 64.2 1.0
OG C:SER132 2.1 53.8 1.0
O C:HOH505 2.1 49.6 1.0
OG1 C:THR224 2.1 48.1 1.0
OE1 B:GLU119 2.7 43.8 1.0
O C:GLN254 2.8 48.3 1.0
CB C:THR224 3.1 44.5 1.0
CB C:THR130 3.1 41.6 1.0
CG2 C:THR224 3.3 48.8 1.0
CB C:SER132 3.4 45.1 1.0
CD B:GLU119 3.5 53.1 1.0
CG2 C:THR130 3.7 42.8 1.0
OE2 B:GLU119 3.7 57.9 1.0
OD1 C:ASP252 3.9 53.1 1.0
C C:GLN254 3.9 41.5 1.0
OD2 C:ASP128 4.0 71.0 1.0
CB C:GLN254 4.2 50.0 1.0
OD1 C:ASP128 4.3 62.0 1.0
N C:SER132 4.3 45.0 1.0
OD2 C:ASP252 4.4 47.0 1.0
CA C:SER132 4.4 44.7 1.0
CA C:THR224 4.4 44.6 1.0
CA C:THR130 4.5 42.0 1.0
CA C:GLN254 4.5 46.3 1.0
CG C:ASP252 4.5 53.3 1.0
CG C:ASP128 4.6 57.7 1.0
C C:THR130 4.8 44.5 1.0
N C:GLN254 4.8 47.4 1.0
N C:VAL255 4.9 40.6 1.0
CG B:GLU119 4.9 59.7 1.0
N C:THR224 4.9 48.3 1.0

Magnesium binding site 4 out of 9 in 8hmg

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Magnesium binding site 4 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:73.7
occ:1.00
OG1 D:THR224 2.1 57.9 1.0
OG1 D:THR130 2.1 57.2 1.0
OG D:SER132 2.1 70.5 1.0
O D:HOH502 2.1 107.4 1.0
O D:HOH506 2.1 63.3 1.0
OE1 H:GLU119 2.1 76.2 1.0
O D:GLN254 2.9 70.2 1.0
CB D:THR130 3.1 56.6 1.0
CB D:THR224 3.2 59.1 1.0
CD H:GLU119 3.2 79.4 1.0
CB D:SER132 3.3 57.8 1.0
CG2 D:THR224 3.4 63.6 1.0
OE2 H:GLU119 3.6 68.8 1.0
CG2 D:THR130 3.7 54.9 1.0
C D:GLN254 4.0 63.7 1.0
OD1 D:ASP252 4.1 56.1 1.0
N D:SER132 4.1 53.9 1.0
OD2 D:ASP128 4.2 71.7 1.0
CA D:SER132 4.3 58.4 1.0
CB D:GLN254 4.3 66.1 1.0
CA D:THR130 4.4 52.0 1.0
OD1 D:ASP128 4.4 60.0 1.0
CA D:THR224 4.4 56.6 1.0
OD2 D:ASP252 4.4 68.5 1.0
CG H:GLU119 4.5 79.3 1.0
CA D:GLN254 4.6 65.5 1.0
CG D:ASP252 4.7 67.6 1.0
C D:THR130 4.7 53.4 1.0
CG D:ASP128 4.8 63.0 1.0
N D:THR224 4.9 61.3 1.0
N D:LYS131 4.9 62.7 1.0

Magnesium binding site 5 out of 9 in 8hmg

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Magnesium binding site 5 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:67.4
occ:1.00
OG E:SER132 2.1 57.1 1.0
OG1 E:THR224 2.1 57.8 1.0
O E:HOH501 2.1 78.4 1.0
OG1 E:THR130 2.1 61.9 1.0
O E:HOH504 2.1 68.4 1.0
OE1 G:GLU119 2.1 65.8 1.0
O E:GLN254 2.8 73.7 1.0
CB E:THR130 3.1 53.8 1.0
CD G:GLU119 3.2 66.2 1.0
CB E:THR224 3.2 57.4 1.0
CB E:SER132 3.3 47.6 1.0
CG2 E:THR224 3.5 61.9 1.0
OE2 G:GLU119 3.7 58.9 1.0
CG2 E:THR130 3.7 52.1 1.0
C E:GLN254 4.0 64.3 1.0
OD1 E:ASP252 4.1 56.6 1.0
N E:SER132 4.1 46.1 1.0
CB E:GLN254 4.2 61.6 1.0
CA E:SER132 4.3 48.0 1.0
OD2 E:ASP128 4.3 73.7 1.0
CA E:THR130 4.4 53.2 1.0
OD2 E:ASP252 4.5 61.7 1.0
CG G:GLU119 4.5 68.9 1.0
OD1 E:ASP128 4.5 69.0 1.0
CA E:THR224 4.5 55.8 1.0
CA E:GLN254 4.6 66.6 1.0
CG E:ASP252 4.7 59.7 1.0
C E:THR130 4.7 55.3 1.0
CG E:ASP128 4.8 60.9 1.0
N E:LYS131 4.9 59.6 1.0
N E:THR224 4.9 60.2 1.0

Magnesium binding site 6 out of 9 in 8hmg

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Magnesium binding site 6 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg404

b:60.9
occ:1.00
OG F:SER132 2.0 56.4 1.0
OG1 F:THR224 2.1 55.5 1.0
OG1 F:THR130 2.1 70.8 1.0
O F:HOH508 2.1 63.2 1.0
O E:HOH502 2.1 84.8 1.0
OE1 E:GLU119 2.1 59.8 1.0
O F:GLN254 2.9 70.2 1.0
CB F:THR130 3.1 61.8 1.0
CD E:GLU119 3.1 65.7 1.0
CB F:THR224 3.2 54.5 1.0
CB F:SER132 3.2 51.5 1.0
OE2 E:GLU119 3.5 65.4 1.0
CG2 F:THR224 3.5 60.6 1.0
CG2 F:THR130 3.7 53.0 1.0
N F:SER132 4.1 52.4 1.0
C F:GLN254 4.1 54.6 1.0
OD1 F:ASP252 4.1 50.4 1.0
CA F:SER132 4.2 54.4 1.0
CB F:GLN254 4.3 63.9 1.0
OD2 F:ASP128 4.4 80.7 1.0
CA F:THR130 4.4 65.1 1.0
CG E:GLU119 4.4 69.3 1.0
CA F:THR224 4.5 54.0 1.0
OD2 F:ASP252 4.5 56.6 1.0
OD1 F:ASP128 4.5 76.0 1.0
C F:THR130 4.6 62.0 1.0
CA F:GLN254 4.7 64.3 1.0
CG F:ASP252 4.7 57.9 1.0
N F:LYS131 4.8 56.5 1.0
N F:THR224 4.8 56.2 1.0
CG F:ASP128 4.9 65.6 1.0

Magnesium binding site 7 out of 9 in 8hmg

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Magnesium binding site 7 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg404

b:80.8
occ:1.00
O G:HOH504 2.1 90.0 1.0
OG1 G:THR224 2.2 71.6 1.0
OG G:SER132 2.2 80.1 1.0
OG1 G:THR130 2.3 71.0 1.0
O G:GLN254 2.4 66.7 1.0
CB G:THR224 3.1 60.9 1.0
CG2 G:THR224 3.2 62.6 1.0
CB G:SER132 3.4 73.4 1.0
CB G:THR130 3.4 67.3 1.0
C G:GLN254 3.5 64.2 1.0
OD1 G:ASP252 3.8 89.6 1.0
CB G:GLN254 3.9 77.8 1.0
CG2 G:THR130 3.9 66.2 1.0
OD2 G:ASP128 4.1 87.3 1.0
CA G:GLN254 4.1 73.0 1.0
OD2 G:ASP252 4.4 79.5 1.0
CA G:THR224 4.5 61.1 1.0
CG G:ASP252 4.5 86.2 1.0
OD1 G:ASP128 4.5 84.7 1.0
N G:SER132 4.5 71.8 1.0
N G:GLN254 4.5 74.3 1.0
CA G:SER132 4.5 69.1 1.0
N G:VAL255 4.5 61.2 1.0
CG G:ASP128 4.7 77.7 1.0
CA G:THR130 4.8 67.7 1.0
CA G:VAL255 5.0 61.7 1.0
N G:THR224 5.0 62.3 1.0

Magnesium binding site 8 out of 9 in 8hmg

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Magnesium binding site 8 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg404

b:67.9
occ:1.00
O H:HOH502 2.1 78.7 1.0
OG1 H:THR224 2.1 59.9 1.0
OG H:SER132 2.2 69.2 1.0
OG1 H:THR130 2.3 50.8 1.0
O H:GLN254 2.4 62.0 1.0
CB H:THR224 3.1 58.2 1.0
CG2 H:THR224 3.3 69.2 1.0
CB H:SER132 3.4 59.0 1.0
CB H:THR130 3.4 50.4 1.0
C H:GLN254 3.5 56.7 1.0
OD1 H:ASP252 3.8 74.9 1.0
CB H:GLN254 3.9 62.4 1.0
CG2 H:THR130 3.9 51.2 1.0
OD2 H:ASP128 4.1 61.3 1.0
CA H:GLN254 4.2 61.6 1.0
OD2 H:ASP252 4.4 73.3 1.0
CG H:ASP252 4.5 67.8 1.0
CA H:THR224 4.5 54.3 1.0
OD1 H:ASP128 4.5 60.4 1.0
N H:SER132 4.5 51.4 1.0
CA H:SER132 4.5 55.6 1.0
N H:VAL255 4.6 52.9 1.0
N H:GLN254 4.6 59.4 1.0
CG H:ASP128 4.7 54.5 1.0
CA H:THR130 4.8 52.0 1.0
N H:THR224 5.0 51.4 1.0

Magnesium binding site 9 out of 9 in 8hmg

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Magnesium binding site 9 out of 9 in the The Open State of RGLG2-Vwa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Open State of RGLG2-Vwa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg404

b:64.6
occ:1.00
OG I:SER132 2.1 64.8 1.0
OG1 I:THR130 2.1 51.5 1.0
OG1 I:THR224 2.1 57.4 1.0
O I:HOH501 2.1 55.1 1.0
O I:GLN254 2.8 58.3 1.0
CB I:THR224 3.2 53.8 1.0
CB I:THR130 3.2 49.7 1.0
CG2 I:THR224 3.3 59.8 1.0
CB I:SER132 3.3 56.4 1.0
CG2 I:THR130 3.7 51.0 1.0
OD1 I:ASP252 3.8 65.7 1.0
C I:GLN254 3.9 60.0 1.0
OD2 I:ASP128 4.0 64.8 1.0
CB I:GLN254 4.2 65.3 1.0
N I:SER132 4.3 52.8 1.0
OD1 I:ASP128 4.3 69.9 1.0
OD2 I:ASP252 4.3 65.1 1.0
CA I:SER132 4.4 54.6 1.0
CA I:THR224 4.5 54.0 1.0
CG I:ASP252 4.5 66.7 1.0
CA I:THR130 4.5 52.3 1.0
CA I:GLN254 4.5 63.6 1.0
CG I:ASP128 4.6 58.5 1.0
C I:THR130 4.8 56.5 1.0
N I:GLN254 4.8 61.6 1.0
N I:VAL255 4.9 54.5 1.0
N I:THR224 5.0 54.0 1.0

Reference:

Q.Wang, Q.Wang. N/A N/A.
Page generated: Thu Dec 28 09:12:24 2023

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