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Magnesium in PDB 1upb: Carboxyethylarginine Synthase From Streptomyces Clavuligerus

Protein crystallography data

The structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus, PDB code: 1upb was solved by M.E.C.Caines, J.M.Elkins, K.S.Hewitson, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.703, 127.276, 197.091, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus (pdb code 1upb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus, PDB code: 1upb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1upb

Go back to Magnesium Binding Sites List in 1upb
Magnesium binding site 1 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:5.7
occ:1.00
 O3B A:TPP600 2.0 12.8 1.0
OD1 A:ASN490 2.1 15.9 1.0
O A:THR492 2.2 15.1 1.0
O1A A:TPP600 2.2 12.9 1.0
OD1 A:ASP463 2.3 12.3 1.0
PB A:TPP600 3.3 15.1 1.0
CG A:ASN490 3.3 16.4 1.0
PA A:TPP600 3.4 13.3 1.0
CG A:ASP463 3.4 14.3 1.0
C A:THR492 3.4 14.5 1.0
O3A A:TPP600 3.6 13.9 1.0
OD2 A:ASP463 3.8 13.1 1.0
O7 A:TPP600 3.9 14.6 1.0
N A:THR492 4.0 15.4 1.0
O1B A:TPP600 4.0 16.7 1.0
N A:ASP463 4.1 13.4 1.0
N A:ASN490 4.1 16.7 1.0
ND2 A:ASN490 4.1 18.0 1.0
N A:GLY494 4.1 14.4 1.0
CA A:THR492 4.2 15.1 1.0
N A:GLY464 4.3 14.1 1.0
CB A:ASN490 4.4 17.1 1.0
O A:VAL488 4.5 16.3 1.0
N A:ASN493 4.5 14.5 1.0
O2B A:TPP600 4.5 13.3 1.0
CB A:ASP463 4.6 13.8 1.0
CB A:THR492 4.6 15.0 1.0
CA A:ASN490 4.6 16.5 1.0
O2A A:TPP600 4.7 11.9 1.0
CA A:ASN493 4.7 14.2 1.0
CE2 A:TYR561 4.7 28.4 1.0
CA A:ASP463 4.8 13.8 1.0
C A:ASN490 4.8 16.3 1.0
CA A:GLY462 4.8 13.9 1.0
OH A:TYR561 4.8 25.0 1.0
C A:GLY462 4.8 13.9 1.0
N A:ASP491 4.8 16.5 1.0
CA A:GLY494 4.9 15.0 1.0
C A:ASN493 5.0 14.0 1.0

Magnesium binding site 2 out of 4 in 1upb

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Magnesium binding site 2 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:6.9
occ:1.00
 O1A B:TPP600 2.1 12.3 1.0
O3B B:TPP600 2.2 11.8 1.0
OD1 B:ASP463 2.2 14.4 1.0
O B:THR492 2.2 15.5 1.0
OD1 B:ASN490 2.3 16.1 1.0
CG B:ASP463 3.3 14.5 1.0
PA B:TPP600 3.4 12.6 1.0
C B:THR492 3.4 15.1 1.0
PB B:TPP600 3.4 13.5 1.0
CG B:ASN490 3.5 16.4 1.0
O3A B:TPP600 3.7 12.4 1.0
OD2 B:ASP463 3.7 14.8 1.0
N B:ASP463 3.9 14.7 1.0
O7 B:TPP600 4.0 13.5 1.0
N B:THR492 4.0 15.6 1.0
N B:ASN490 4.1 16.9 1.0
N B:GLY494 4.1 15.3 1.0
CA B:THR492 4.2 15.3 1.0
O1B B:TPP600 4.2 14.9 1.0
N B:GLY464 4.3 14.7 1.0
ND2 B:ASN490 4.3 16.6 1.0
CB B:ASP463 4.4 14.7 1.0
O B:VAL488 4.4 16.7 1.0
N B:ASN493 4.4 15.3 1.0
CB B:ASN490 4.5 17.1 1.0
O2B B:TPP600 4.5 13.5 1.0
CB B:THR492 4.5 15.2 1.0
CA B:ASP463 4.6 14.6 1.0
CA B:ASN490 4.6 16.6 1.0
O2A B:TPP600 4.6 13.0 1.0
CA B:ASN493 4.7 15.3 1.0
C B:GLY462 4.7 14.7 1.0
N B:ASP491 4.7 16.8 1.0
C B:ASN490 4.7 16.5 1.0
CA B:GLY462 4.7 14.5 1.0
OH B:TYR561 4.8 26.8 1.0
CA B:GLY494 4.8 15.2 1.0
C B:ASN493 4.9 15.4 1.0
CE2 B:TYR561 4.9 28.8 1.0
C B:ASP463 5.0 14.6 1.0

Magnesium binding site 3 out of 4 in 1upb

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Magnesium binding site 3 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:6.0
occ:1.00
 O C:THR492 2.1 15.7 1.0
O1A C:TPP600 2.1 13.7 1.0
OD1 C:ASN490 2.2 17.4 1.0
O3B C:TPP600 2.3 13.3 1.0
OD1 C:ASP463 2.3 13.5 1.0
PA C:TPP600 3.3 13.1 1.0
C C:THR492 3.3 15.1 1.0
CG C:ASP463 3.3 13.9 1.0
CG C:ASN490 3.4 17.4 1.0
PB C:TPP600 3.5 15.2 1.0
O3A C:TPP600 3.6 14.3 1.0
OD2 C:ASP463 3.8 14.4 1.0
O7 C:TPP600 3.8 14.3 1.0
N C:THR492 3.9 16.5 1.0
N C:ASP463 4.0 14.2 1.0
N C:GLY494 4.0 15.5 1.0
N C:ASN490 4.1 17.1 1.0
CA C:THR492 4.1 15.8 1.0
ND2 C:ASN490 4.1 19.6 1.0
N C:GLY464 4.3 14.4 1.0
O1B C:TPP600 4.3 16.8 1.0
N C:ASN493 4.4 14.7 1.0
CB C:ASN490 4.4 17.2 1.0
CB C:THR492 4.5 15.7 1.0
CB C:ASP463 4.5 14.1 1.0
O C:VAL488 4.5 16.8 1.0
CA C:ASN490 4.6 16.9 1.0
O2A C:TPP600 4.6 12.1 1.0
O2B C:TPP600 4.6 14.2 1.0
CA C:ASN493 4.6 14.7 1.0
CA C:ASP463 4.7 14.1 1.0
C C:ASN490 4.7 17.1 1.0
OH C:TYR561 4.7 24.4 1.0
N C:ASP491 4.7 17.5 1.0
CA C:GLY494 4.8 15.8 1.0
C C:GLY462 4.8 14.3 1.0
CA C:GLY462 4.8 14.2 1.0
CE2 C:TYR561 4.8 27.2 1.0
C C:ASN493 4.9 15.2 1.0

Magnesium binding site 4 out of 4 in 1upb

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Magnesium binding site 4 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:4.9
occ:1.00
 OD1 D:ASN490 2.1 18.9 1.0
O3B D:TPP600 2.1 12.2 1.0
O D:THR492 2.1 15.3 1.0
O1A D:TPP600 2.2 13.1 1.0
OD1 D:ASP463 2.3 15.1 1.0
CG D:ASN490 3.2 19.0 1.0
C D:THR492 3.3 15.2 1.0
PA D:TPP600 3.4 12.2 1.0
PB D:TPP600 3.4 14.4 1.0
CG D:ASP463 3.4 15.3 1.0
O3A D:TPP600 3.6 13.1 1.0
OD2 D:ASP463 3.9 14.7 1.0
O7 D:TPP600 3.9 15.5 1.0
N D:THR492 3.9 16.0 1.0
ND2 D:ASN490 4.0 20.1 1.0
N D:ASN490 4.0 16.8 1.0
N D:GLY494 4.0 15.4 1.0
CA D:THR492 4.1 15.4 1.0
N D:ASP463 4.1 14.7 1.0
O1B D:TPP600 4.1 13.6 1.0
CB D:ASN490 4.3 17.3 1.0
N D:ASN493 4.4 15.2 1.0
N D:GLY464 4.4 15.0 1.0
CB D:THR492 4.5 15.5 1.0
O2B D:TPP600 4.5 13.2 1.0
O D:VAL488 4.5 14.7 1.0
CA D:ASN490 4.5 17.1 1.0
CB D:ASP463 4.6 14.9 1.0
CA D:ASN493 4.6 14.8 1.0
C D:ASN490 4.7 16.7 1.0
O2A D:TPP600 4.7 13.5 1.0
OH D:TYR561 4.7 23.8 1.0
CA D:GLY494 4.7 15.4 1.0
N D:ASP491 4.8 16.8 1.0
CE2 D:TYR561 4.8 27.7 1.0
CA D:ASP463 4.8 14.9 1.0
C D:ASN493 4.9 14.9 1.0
CA D:GLY462 4.9 14.7 1.0
C D:GLY462 4.9 14.8 1.0

Reference:

M.E.C.Caines, J.M.Elkins, K.S.Hewitson, C.J.Schofield. Crystal Structure and Mechanistic Implications of N2-(2-Carboxyethyl)Arginine Synthase, the First Enzyme in the Clavulanic Acid Biosynthesis Pathway J.Biol.Chem. V. 279 5685 2004.
ISSN: ISSN 0021-9258
PubMed: 14623876
DOI: 10.1074/JBC.M310803200
Page generated: Tue Aug 13 14:53:04 2024

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