Magnesium in PDB 2p88: Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579

Protein crystallography data

The structure of Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579, PDB code: 2p88 was solved by A.A.Fedorov, L.Song, E.V.Fedorov, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.42 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.953, 94.610, 135.956, 90.00, 90.16, 90.00
R / Rfree (%) 22.1 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 (pdb code 2p88). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579, PDB code: 2p88:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2p88

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Magnesium binding site 1 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:41.9
occ:1.00
 OD2 A:ASP191 2.3 31.8 1.0
OD2 A:ASP243 2.3 28.7 1.0
OE2 A:GLU218 2.4 31.0 1.0
O A:HOH531 2.4 43.1 1.0
O A:HOH530 2.6 33.0 1.0
CG A:ASP191 3.3 32.4 1.0
CD A:GLU218 3.4 32.6 1.0
CG A:ASP243 3.5 27.4 1.0
OD1 A:ASN193 3.5 33.4 1.0
OD1 A:ASP191 3.7 33.4 1.0
NZ A:LYS163 3.7 49.8 1.0
NZ A:LYS161 3.8 41.6 1.0
NZ A:LYS267 4.0 25.6 1.0
CB A:ASP243 4.0 22.9 1.0
OE1 A:GLU218 4.1 31.4 1.0
OE1 A:GLU244 4.2 30.3 1.0
ND2 A:ASN265 4.3 26.9 1.0
CG A:GLU218 4.3 28.9 1.0
CG A:ASN193 4.5 33.7 1.0
OD1 A:ASP243 4.5 27.2 1.0
CE A:LYS161 4.6 41.6 1.0
CB A:ASP191 4.6 31.1 1.0
CE A:LYS267 4.8 23.4 1.0
CD A:GLU244 4.8 31.5 1.0
ND2 A:ASN193 4.9 35.3 1.0
OE2 A:GLU244 5.0 35.2 1.0

Magnesium binding site 2 out of 8 in 2p88

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Magnesium binding site 2 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:37.6
occ:1.00
 OE2 B:GLU218 2.3 28.4 1.0
OD2 B:ASP191 2.4 31.2 1.0
OD2 B:ASP243 2.5 26.9 1.0
O B:HOH534 2.8 36.9 1.0
NZ B:LYS161 3.3 43.4 1.0
CD B:GLU218 3.4 30.5 1.0
CG B:ASP191 3.6 32.3 1.0
NZ B:LYS163 3.6 49.7 1.0
CG B:ASP243 3.7 26.6 1.0
NZ B:LYS267 3.7 28.1 1.0
ND2 B:ASN265 3.9 31.2 1.0
OE1 B:GLU218 3.9 29.8 1.0
OD1 B:ASN193 4.0 34.4 1.0
OD1 B:ASP191 4.2 33.2 1.0
CE B:LYS161 4.2 43.9 1.0
CB B:ASP243 4.4 23.6 1.0
CE B:LYS267 4.4 24.3 1.0
CG B:GLU218 4.5 29.1 1.0
CB B:ASP191 4.7 30.8 1.0
OD1 B:ASP243 4.7 25.8 1.0
OE1 B:GLU244 4.8 28.4 1.0
CE B:LYS163 4.9 50.2 1.0
O B:HOH529 5.0 41.4 1.0
CG B:ASN193 5.0 34.7 1.0

Magnesium binding site 3 out of 8 in 2p88

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Magnesium binding site 3 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:54.6
occ:1.00
 OD2 C:ASP243 2.6 26.4 1.0
OE2 C:GLU218 2.6 34.3 1.0
OD2 C:ASP191 2.6 25.5 1.0
O C:HOH541 2.7 27.9 1.0
NZ C:LYS161 3.3 35.0 1.0
NZ C:LYS163 3.5 37.8 1.0
NZ C:LYS267 3.6 16.4 1.0
CD C:GLU218 3.6 32.4 1.0
CG C:ASP243 3.8 24.4 1.0
CG C:ASP191 3.8 26.4 1.0
ND2 C:ASN265 3.9 23.6 1.0
O C:HOH521 3.9 33.6 1.0
O C:HOH542 4.0 27.6 1.0
OD1 C:ASN193 4.1 29.8 1.0
OE1 C:GLU218 4.2 30.1 1.0
CE C:LYS161 4.2 37.5 1.0
CE C:LYS267 4.3 18.2 1.0
OD1 C:ASP191 4.3 28.7 1.0
CB C:ASP243 4.5 19.3 1.0
OD1 C:ASP243 4.7 23.8 1.0
CG C:GLU218 4.8 29.0 1.0
CB C:ASP191 4.9 26.3 1.0
OE1 C:GLU244 4.9 25.9 1.0
CE C:LYS163 4.9 37.4 1.0

Magnesium binding site 4 out of 8 in 2p88

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Magnesium binding site 4 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:42.1
occ:1.00
 OD2 D:ASP243 2.3 31.2 1.0
OE2 D:GLU218 2.5 34.5 1.0
OD2 D:ASP191 2.5 25.2 1.0
O D:HOH537 2.6 21.3 1.0
CG D:ASP243 3.5 29.1 1.0
CD D:GLU218 3.5 32.6 1.0
NZ D:LYS161 3.6 40.2 1.0
CG D:ASP191 3.6 26.4 1.0
NZ D:LYS163 3.7 41.5 1.0
NZ D:LYS267 3.7 19.1 1.0
OD1 D:ASN193 3.8 30.2 1.0
ND2 D:ASN265 4.0 23.5 1.0
OD1 D:ASP191 4.1 26.8 1.0
CB D:ASP243 4.2 25.8 1.0
OE1 D:GLU218 4.2 31.1 1.0
CE D:LYS267 4.4 18.2 1.0
OE1 D:GLU244 4.5 33.6 1.0
CE D:LYS161 4.5 41.9 1.0
OD1 D:ASP243 4.5 29.6 1.0
CG D:GLU218 4.5 29.8 1.0
O D:HOH530 4.5 34.0 1.0
O D:HOH538 4.6 34.5 1.0
CG D:ASN193 4.8 30.2 1.0
CB D:ASP191 4.8 26.0 1.0
O D:HOH536 4.9 19.3 1.0

Magnesium binding site 5 out of 8 in 2p88

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Magnesium binding site 5 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:32.7
occ:1.00
 OD2 E:ASP243 2.3 23.4 1.0
OD2 E:ASP191 2.3 30.0 1.0
OE2 E:GLU218 2.4 31.6 1.0
O E:HOH536 2.5 29.3 1.0
CG E:ASP191 3.3 30.4 1.0
OD1 E:ASN193 3.4 39.1 1.0
CG E:ASP243 3.4 27.0 1.0
CD E:GLU218 3.5 32.2 1.0
OD1 E:ASP191 3.6 30.0 1.0
NZ E:LYS163 3.8 51.0 1.0
NZ E:LYS161 3.9 42.9 1.0
CB E:ASP243 4.0 24.7 1.0
OE1 E:GLU244 4.0 33.9 1.0
NZ E:LYS267 4.1 22.6 1.0
OE1 E:GLU218 4.2 32.9 1.0
CG E:GLU218 4.3 29.6 1.0
ND2 E:ASN265 4.4 22.6 1.0
CG E:ASN193 4.4 35.3 1.0
OD1 E:ASP243 4.5 28.2 1.0
CB E:ASP191 4.6 32.1 1.0
CE E:LYS161 4.7 41.5 1.0
CD E:GLU244 4.7 34.8 1.0
O E:HOH537 4.8 30.5 1.0
CE E:LYS267 4.8 22.7 1.0
ND2 E:ASN193 4.9 36.3 1.0
OE2 E:GLU244 4.9 39.5 1.0

Magnesium binding site 6 out of 8 in 2p88

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Magnesium binding site 6 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:41.7
occ:1.00
 OD2 F:ASP191 2.4 31.0 1.0
OD2 F:ASP243 2.4 27.2 1.0
O F:HOH545 2.4 31.4 1.0
OE2 F:GLU218 2.5 37.8 1.0
CG F:ASP191 3.4 31.3 1.0
OD1 F:ASN193 3.4 36.5 1.0
CD F:GLU218 3.5 36.0 1.0
CG F:ASP243 3.5 24.3 1.0
NZ F:LYS163 3.7 46.8 1.0
OD1 F:ASP191 3.8 28.1 1.0
NZ F:LYS161 3.9 40.5 1.0
NZ F:LYS267 3.9 27.4 1.0
CB F:ASP243 4.1 22.3 1.0
OE1 F:GLU244 4.1 37.9 1.0
O F:HOH547 4.2 43.7 1.0
OE1 F:GLU218 4.2 35.7 1.0
ND2 F:ASN265 4.3 23.2 1.0
CG F:GLU218 4.4 31.4 1.0
CG F:ASN193 4.4 34.0 1.0
OD1 F:ASP243 4.5 26.4 1.0
CE F:LYS161 4.6 40.0 1.0
CB F:ASP191 4.7 30.6 1.0
CE F:LYS267 4.7 25.8 1.0
CD F:GLU244 4.8 38.6 1.0
ND2 F:ASN193 4.9 34.4 1.0
OE2 F:GLU244 5.0 42.0 1.0

Magnesium binding site 7 out of 8 in 2p88

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Magnesium binding site 7 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:33.8
occ:1.00
 OD2 G:ASP243 2.3 24.9 1.0
O G:HOH547 2.4 36.6 1.0
OD2 G:ASP191 2.4 31.8 1.0
O G:HOH548 2.4 47.5 1.0
OE2 G:GLU218 2.5 37.0 1.0
OD1 G:ASN193 3.3 35.7 1.0
CG G:ASP191 3.3 31.2 1.0
CG G:ASP243 3.4 21.7 1.0
CD G:GLU218 3.5 35.8 1.0
OD1 G:ASP191 3.5 28.6 1.0
OE1 G:GLU244 3.8 35.5 1.0
NZ G:LYS163 3.9 48.9 1.0
CB G:ASP243 3.9 20.3 1.0
NZ G:LYS267 4.1 30.1 1.0
NZ G:LYS161 4.1 44.1 1.0
CG G:ASN193 4.3 33.2 1.0
CG G:GLU218 4.3 31.1 1.0
OE1 G:GLU218 4.3 36.0 1.0
OD1 G:ASP243 4.5 25.4 1.0
ND2 G:ASN265 4.5 21.4 1.0
CD G:GLU244 4.5 36.2 1.0
CB G:ASP191 4.6 30.9 1.0
O G:HOH550 4.7 43.8 1.0
OE2 G:GLU244 4.7 41.1 1.0
ND2 G:ASN193 4.8 35.2 1.0
CE G:LYS161 4.8 42.8 1.0
CE G:LYS267 4.9 28.1 1.0

Magnesium binding site 8 out of 8 in 2p88

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Magnesium binding site 8 out of 8 in the Crystal Structure of N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579


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 N-Succinyl Arg/Lys Racemase From Bacillus Cereus Atcc 14579 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:37.0
occ:1.00
 OD2 H:ASP191 2.3 31.2 1.0
OD2 H:ASP243 2.3 22.2 1.0
O H:HOH538 2.4 32.0 1.0
OE2 H:GLU218 2.4 36.5 1.0
CG H:ASP191 3.3 30.9 1.0
OD1 H:ASN193 3.4 35.5 1.0
CD H:GLU218 3.4 35.0 1.0
CG H:ASP243 3.4 26.4 1.0
OD1 H:ASP191 3.6 29.9 1.0
NZ H:LYS163 3.8 51.6 1.0
CB H:ASP243 3.9 23.4 1.0
NZ H:LYS161 4.0 40.8 1.0
OE1 H:GLU244 4.0 35.7 1.0
NZ H:LYS267 4.1 22.1 1.0
OE1 H:GLU218 4.2 34.7 1.0
CG H:GLU218 4.2 32.5 1.0
CG H:ASN193 4.4 33.0 1.0
ND2 H:ASN265 4.4 21.2 1.0
OD1 H:ASP243 4.5 27.3 1.0
CB H:ASP191 4.6 31.2 1.0
CE H:LYS161 4.7 39.5 1.0
CD H:GLU244 4.7 35.7 1.0
O H:HOH542 4.7 40.0 1.0
ND2 H:ASN193 4.8 33.2 1.0
OE2 H:GLU244 4.9 39.2 1.0
CE H:LYS267 4.9 21.7 1.0

Reference:

L.Song, C.Kalyanaraman, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, S.Brown, H.J.Imker, P.C.Babbitt, S.C.Almo, M.P.Jacobson, J.A.Gerlt. Prediction and Assignment of Function For A Divergent N-Succinyl Amino Acid Racemase. Nat.Chem.Biol. V. 3 486 2007.
ISSN: ISSN 1552-4450
PubMed: 17603539
DOI: 10.1038/NCHEMBIO.2007.11
Page generated: Mon Dec 14 07:34:18 2020

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