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Magnesium in PDB 2xim: Arginine Residues As Stabilizing Elements in Proteins

Enzymatic activity of Arginine Residues As Stabilizing Elements in Proteins

All present enzymatic activity of Arginine Residues As Stabilizing Elements in Proteins:
5.3.1.5;

Protein crystallography data

The structure of Arginine Residues As Stabilizing Elements in Proteins, PDB code: 2xim was solved by N.T.Mrabet, A.Van Denbroek, I.Van Den Brande, P.Stanssens, Y.Laroche, A.-M.Lambeir, G.Matthyssens, J.Jenkins, M.Chiadmi, H.Vantilbeurgh, F.Rey, J.Janin, W.J.Quax, I.Lasters, M.Demaeyer, S.J.Wodak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.450, 143.450, 231.500, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Arginine Residues As Stabilizing Elements in Proteins (pdb code 2xim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Arginine Residues As Stabilizing Elements in Proteins, PDB code: 2xim:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2xim

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Magnesium binding site 1 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg395

b:21.5
occ:1.00
 OD2 A:ASP292 2.0 13.9 1.0
OD2 A:ASP245 2.0 14.1 1.0
OE1 A:GLU217 2.1 14.9 1.0
OE2 A:GLU181 2.1 15.6 1.0
O2 A:XYL397 2.3 20.2 1.0
O4 A:XYL397 2.4 22.0 1.0
CD A:GLU181 3.0 14.8 1.0
CG A:ASP292 3.1 13.2 1.0
CG A:ASP245 3.2 15.2 1.0
CD A:GLU217 3.3 14.7 1.0
OE1 A:GLU181 3.3 15.6 1.0
C4 A:XYL397 3.4 22.3 1.0
O3 A:XYL397 3.5 23.1 1.0
C2 A:XYL397 3.5 21.1 1.0
C3 A:XYL397 3.6 22.1 1.0
CB A:ASP292 3.7 12.7 1.0
CB A:ASP245 3.8 12.6 1.0
O A:HOH453 4.0 17.6 1.0
OE2 A:GLU217 4.0 16.8 1.0
OD1 A:ASP292 4.1 13.5 1.0
OD1 A:ASP245 4.2 15.0 1.0
CG A:GLU217 4.3 13.5 1.0
O A:HOH528 4.3 32.0 1.0
CE1 A:HIS220 4.3 11.6 1.0
CG A:GLU181 4.3 12.8 1.0
CB A:GLU217 4.4 11.8 1.0
NE2 A:HIS220 4.6 12.2 1.0
C5 A:XYL397 4.7 21.1 1.0
C1 A:XYL397 4.7 20.6 1.0
ND2 A:ASN215 4.7 5.8 1.0
MG A:MG396 5.0 45.3 1.0

Magnesium binding site 2 out of 8 in 2xim

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Magnesium binding site 2 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg396

b:45.3
occ:1.00
 O A:HOH528 2.1 32.0 1.0
OE2 A:GLU217 2.5 16.8 1.0
OD2 A:ASP255 2.5 27.0 1.0
O1 A:XYL397 2.7 23.2 1.0
OD1 A:ASP255 2.8 23.7 1.0
NE2 A:HIS220 2.9 12.2 1.0
OD1 A:ASP257 3.0 20.3 1.0
CG A:ASP255 3.0 22.8 1.0
O2 A:XYL397 3.5 20.2 1.0
CD A:GLU217 3.5 14.7 1.0
C1 A:XYL397 3.6 20.6 1.0
CD2 A:HIS220 3.6 11.9 1.0
OD2 A:ASP257 3.7 21.5 1.0
CG A:ASP257 3.7 18.3 1.0
CE1 A:HIS220 4.0 11.6 1.0
OE1 A:GLU217 4.0 14.9 1.0
NZ A:LYS183 4.1 7.9 1.0
C2 A:XYL397 4.1 21.1 1.0
O A:HOH560 4.3 44.4 1.0
CE A:LYS183 4.4 6.1 1.0
ND2 A:ASN247 4.4 9.8 1.0
CB A:ASP255 4.5 18.9 1.0
O A:HOH557 4.8 50.9 1.0
CG A:GLU217 4.8 13.5 1.0
CG A:HIS220 4.8 10.8 1.0
O A:HOH426 4.9 17.7 1.0
MG A:MG395 5.0 21.5 1.0
OD2 A:ASP292 5.0 13.9 1.0
ND1 A:HIS220 5.0 12.6 1.0

Magnesium binding site 3 out of 8 in 2xim

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Magnesium binding site 3 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg395

b:28.0
occ:1.00
 OE1 B:GLU217 2.0 18.9 1.0
OE2 B:GLU181 2.1 18.0 1.0
OD2 B:ASP245 2.2 19.3 1.0
OD2 B:ASP292 2.2 15.2 1.0
O2 B:XYL397 2.3 28.4 1.0
O4 B:XYL397 2.5 27.4 1.0
CD B:GLU181 3.0 17.6 1.0
CD B:GLU217 3.2 17.1 1.0
CG B:ASP245 3.3 16.6 1.0
OE1 B:GLU181 3.3 17.4 1.0
CG B:ASP292 3.3 14.1 1.0
C2 B:XYL397 3.5 27.9 1.0
C4 B:XYL397 3.5 28.3 1.0
C3 B:XYL397 3.7 27.9 1.0
O3 B:XYL397 3.7 27.8 1.0
CB B:ASP245 3.8 12.7 1.0
CB B:ASP292 3.8 12.2 1.0
O B:HOH459 3.9 16.8 1.0
OE2 B:GLU217 3.9 19.7 1.0
CE1 B:HIS220 4.1 14.4 1.0
CB B:GLU217 4.1 13.5 1.0
CG B:GLU217 4.1 15.4 1.0
OD1 B:ASP245 4.2 17.8 1.0
CG B:GLU181 4.3 15.8 1.0
O B:HOH534 4.3 33.8 1.0
OD1 B:ASP292 4.4 14.8 1.0
NE2 B:HIS220 4.5 14.7 1.0
C1 B:XYL397 4.7 26.7 1.0
ND2 B:ASN215 4.7 13.1 1.0
C5 B:XYL397 4.8 27.6 1.0
MG B:MG396 4.8 41.2 1.0
O1 B:XYL397 4.9 24.0 1.0
ND1 B:HIS220 5.0 14.3 1.0

Magnesium binding site 4 out of 8 in 2xim

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Magnesium binding site 4 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg396

b:41.2
occ:1.00
 O B:HOH534 2.0 33.8 1.0
OE2 B:GLU217 2.6 19.7 1.0
O1 B:XYL397 2.7 24.0 1.0
OD2 B:ASP255 2.7 27.3 1.0
NE2 B:HIS220 2.8 14.7 1.0
OD1 B:ASP255 2.9 23.9 1.0
OD1 B:ASP257 3.0 19.5 1.0
CG B:ASP255 3.1 23.4 1.0
CD B:GLU217 3.6 17.1 1.0
CD2 B:HIS220 3.6 12.9 1.0
O2 B:XYL397 3.6 28.4 1.0
OD2 B:ASP257 3.6 20.1 1.0
C1 B:XYL397 3.7 26.7 1.0
CG B:ASP257 3.8 17.6 1.0
CE1 B:HIS220 3.8 14.4 1.0
OE1 B:GLU217 4.0 18.9 1.0
NZ B:LYS183 4.0 10.8 1.0
C2 B:XYL397 4.3 27.9 1.0
CE B:LYS183 4.3 10.3 1.0
ND2 B:ASN247 4.4 11.2 1.0
CB B:ASP255 4.5 18.0 1.0
O B:HOH563 4.6 52.7 1.0
CG B:HIS220 4.8 13.0 1.0
MG B:MG395 4.8 28.0 1.0
CG B:GLU217 4.9 15.4 1.0
O B:HOH431 4.9 20.5 1.0
ND1 B:HIS220 4.9 14.3 1.0
OD2 B:ASP292 4.9 15.2 1.0

Magnesium binding site 5 out of 8 in 2xim

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Magnesium binding site 5 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg395

b:17.5
occ:1.00
 OE1 C:GLU217 2.0 18.4 1.0
OD2 C:ASP245 2.0 17.0 1.0
OD2 C:ASP292 2.1 13.3 1.0
OE2 C:GLU181 2.1 17.5 1.0
O2 C:XYL397 2.3 23.3 1.0
O4 C:XYL397 2.4 20.5 1.0
CD C:GLU181 3.0 15.8 1.0
CG C:ASP245 3.2 13.8 1.0
CG C:ASP292 3.2 14.2 1.0
CD C:GLU217 3.2 16.6 1.0
OE1 C:GLU181 3.3 16.1 1.0
C4 C:XYL397 3.5 20.9 1.0
C2 C:XYL397 3.5 22.2 1.0
CB C:ASP292 3.7 12.3 1.0
CB C:ASP245 3.7 11.1 1.0
C3 C:XYL397 3.9 21.4 1.0
OE2 C:GLU217 4.0 18.7 1.0
O3 C:XYL397 4.0 21.7 1.0
O C:HOH469 4.0 21.1 1.0
OD1 C:ASP245 4.1 13.6 1.0
CG C:GLU217 4.1 13.3 1.0
O C:HOH536 4.2 29.7 1.0
CB C:GLU217 4.2 9.6 1.0
OD1 C:ASP292 4.2 13.8 1.0
CE1 C:HIS220 4.2 13.6 1.0
CG C:GLU181 4.3 13.8 1.0
NE2 C:HIS220 4.5 12.7 1.0
ND2 C:ASN215 4.6 5.7 1.0
C1 C:XYL397 4.7 22.5 1.0
C5 C:XYL397 4.8 18.5 1.0
MG C:MG396 5.0 39.1 1.0

Magnesium binding site 6 out of 8 in 2xim

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Magnesium binding site 6 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg396

b:39.1
occ:1.00
 O C:HOH536 2.0 29.7 1.0
OD2 C:ASP255 2.3 25.3 1.0
OE2 C:GLU217 2.4 18.7 1.0
OD1 C:ASP257 2.7 16.7 1.0
OD1 C:ASP255 2.8 23.9 1.0
CG C:ASP255 2.9 22.2 1.0
NE2 C:HIS220 3.0 12.7 1.0
O1 C:XYL397 3.0 21.8 1.0
CD C:GLU217 3.5 16.6 1.0
CD2 C:HIS220 3.5 11.2 1.0
OD2 C:ASP257 3.5 19.5 1.0
CG C:ASP257 3.6 16.3 1.0
C1 C:XYL397 3.8 22.5 1.0
O2 C:XYL397 3.8 23.3 1.0
OE1 C:GLU217 4.0 18.4 1.0
O C:HOH575 4.0 75.9 1.0
CE1 C:HIS220 4.1 13.6 1.0
ND2 C:ASN247 4.2 9.0 1.0
NZ C:LYS183 4.3 7.8 1.0
CB C:ASP255 4.4 16.3 1.0
C2 C:XYL397 4.4 22.2 1.0
O C:HOH441 4.6 19.1 1.0
CG C:GLU217 4.8 13.3 1.0
CG C:HIS220 4.8 11.0 1.0
CE C:LYS183 4.8 6.8 1.0
MG C:MG395 5.0 17.5 1.0

Magnesium binding site 7 out of 8 in 2xim

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Magnesium binding site 7 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg395

b:16.7
occ:1.00
 OD2 D:ASP292 2.0 12.9 1.0
OE2 D:GLU181 2.0 18.9 1.0
OE1 D:GLU217 2.1 14.9 1.0
OD2 D:ASP245 2.1 18.8 1.0
O2 D:XYL397 2.3 21.8 1.0
O4 D:XYL397 2.4 22.3 1.0
CD D:GLU181 3.0 17.1 1.0
CG D:ASP292 3.1 11.3 1.0
CG D:ASP245 3.2 16.6 1.0
CD D:GLU217 3.3 15.0 1.0
OE1 D:GLU181 3.3 17.1 1.0
C4 D:XYL397 3.5 22.4 1.0
C2 D:XYL397 3.6 21.6 1.0
O3 D:XYL397 3.6 22.2 1.0
CB D:ASP245 3.7 15.1 1.0
CB D:ASP292 3.7 10.4 1.0
C3 D:XYL397 3.8 22.4 1.0
O D:HOH475 3.8 18.1 1.0
CG D:GLU217 4.1 13.0 1.0
OD1 D:ASP292 4.1 10.9 1.0
CB D:GLU217 4.1 11.7 1.0
OE2 D:GLU217 4.1 16.2 1.0
OD1 D:ASP245 4.2 15.8 1.0
CE1 D:HIS220 4.2 8.1 1.0
CG D:GLU181 4.3 14.1 1.0
O D:HOH540 4.4 31.6 1.0
C1 D:XYL397 4.6 21.5 1.0
ND2 D:ASN215 4.6 10.8 1.0
NE2 D:HIS220 4.6 8.1 1.0
MG D:MG396 4.7 11.2 1.0
C5 D:XYL397 4.7 22.2 1.0

Magnesium binding site 8 out of 8 in 2xim

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Magnesium binding site 8 out of 8 in the Arginine Residues As Stabilizing Elements in Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Arginine Residues As Stabilizing Elements in Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg396

b:11.2
occ:1.00
 O D:HOH540 2.3 31.6 1.0
OE2 D:GLU217 2.3 16.2 1.0
O1 D:XYL397 2.5 19.6 1.0
OD2 D:ASP255 2.5 24.0 1.0
NE2 D:HIS220 2.7 8.1 1.0
OD1 D:ASP255 2.9 20.9 1.0
OD1 D:ASP257 3.0 21.2 1.0
CG D:ASP255 3.2 20.6 1.0
C1 D:XYL397 3.2 21.5 1.0
CD D:GLU217 3.2 15.0 1.0
O2 D:XYL397 3.4 21.8 1.0
CD2 D:HIS220 3.6 8.3 1.0
OE1 D:GLU217 3.6 14.9 1.0
CE1 D:HIS220 3.7 8.1 1.0
CG D:ASP257 3.8 19.6 1.0
OD2 D:ASP257 3.8 22.2 1.0
O D:HOH577 3.9 62.5 1.0
C2 D:XYL397 4.0 21.6 1.0
NZ D:LYS183 4.4 10.2 1.0
ND2 D:ASN247 4.4 6.9 1.0
OD2 D:ASP292 4.6 12.9 1.0
CG D:GLU217 4.6 13.0 1.0
CE D:LYS183 4.6 8.3 1.0
CB D:ASP255 4.6 16.0 1.0
MG D:MG395 4.7 16.7 1.0
CG D:HIS220 4.7 7.2 1.0
ND1 D:HIS220 4.8 7.3 1.0
O D:HOH449 4.9 16.4 1.0
O3 D:XYL397 4.9 22.2 1.0

Reference:

N.T.Mrabet, A.Van Den Broeck, I.Van Den Brande, P.Stanssens, Y.Laroche, A.M.Lambeir, G.Matthijssens, J.Jenkins, M.Chiadmi, H.Van Tilbeurgh, F.Rey, J.Janin, W.J.Quax, I.Lasters, M.Demaeyer, S.J.Wodak. Arginine Residues As Stabilizing Elements in Proteins. Biochemistry V. 31 2239 1992.
ISSN: ISSN 0006-2960
PubMed: 1540579
DOI: 10.1021/BI00123A005
Page generated: Mon Dec 14 07:46:43 2020

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