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Magnesium in PDB 1upa: Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure)

Protein crystallography data

The structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure), PDB code: 1upa 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) 35.14 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.690, 127.270, 196.770, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure) (pdb code 1upa). 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 (Semet Structure), PDB code: 1upa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1upa

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Magnesium binding site 1 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure)


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 (Semet Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:6.6
occ:1.00
 O3B A:TPP600 2.0 14.8 1.0
OD1 A:ASN490 2.2 20.6 1.0
O1A A:TPP600 2.2 17.0 1.0
O A:THR492 2.3 18.8 1.0
OD1 A:ASP463 2.3 16.2 1.0
O A:HOH2210 2.3 16.8 1.0
PB A:TPP600 3.3 19.3 1.0
CG A:ASP463 3.3 17.4 1.0
PA A:TPP600 3.4 15.6 1.0
CG A:ASN490 3.4 21.5 1.0
C A:THR492 3.4 19.0 1.0
O3A A:TPP600 3.6 17.3 1.0
OD2 A:ASP463 3.7 16.4 1.0
O1B A:TPP600 3.9 20.0 1.0
O7 A:TPP600 3.9 17.9 1.0
N A:ASN490 4.0 20.9 1.0
N A:THR492 4.0 19.9 1.0
N A:GLY494 4.1 18.7 1.0
N A:ASP463 4.1 16.7 1.0
ND2 A:ASN490 4.2 21.1 1.0
CA A:THR492 4.2 19.6 1.0
N A:GLY464 4.3 17.1 1.0
O2B A:TPP600 4.4 16.9 1.0
CB A:ASN490 4.4 21.2 1.0
O A:VAL488 4.4 18.8 1.0
N A:ASN493 4.5 18.8 1.0
CB A:ASP463 4.6 17.4 1.0
CA A:ASN490 4.6 20.9 1.0
CB A:THR492 4.6 19.6 1.0
O2A A:TPP600 4.7 16.1 1.0
CA A:ASN493 4.7 18.5 1.0
CA A:GLY494 4.7 18.8 1.0
OH A:TYR561 4.7 30.0 1.0
C A:ASN490 4.7 21.1 1.0
CA A:ASP463 4.8 17.0 1.0
N A:ASP491 4.8 21.3 1.0
CE2 A:TYR561 4.8 33.6 1.0
CA A:GLY462 4.8 16.6 1.0
C A:GLY462 4.9 16.7 1.0
C A:ASN493 4.9 18.4 1.0

Magnesium binding site 2 out of 4 in 1upa

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Magnesium binding site 2 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure)


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 (Semet Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:7.4
occ:1.00
 O3B B:TPP600 2.0 17.3 1.0
O B:HOH2278 2.1 15.6 1.0
O1A B:TPP600 2.2 18.5 1.0
OD1 B:ASP463 2.2 17.8 1.0
OD1 B:ASN490 2.2 21.5 1.0
O B:THR492 2.3 20.0 1.0
CG B:ASP463 3.3 17.4 1.0
PB B:TPP600 3.3 20.1 1.0
PA B:TPP600 3.3 15.7 1.0
CG B:ASN490 3.4 21.8 1.0
C B:THR492 3.4 19.8 1.0
O3A B:TPP600 3.6 17.9 1.0
OD2 B:ASP463 3.8 18.1 1.0
O7 B:TPP600 3.9 17.6 1.0
N B:ASP463 3.9 17.8 1.0
O1B B:TPP600 4.0 21.1 1.0
N B:GLY494 4.0 18.8 1.0
N B:THR492 4.1 20.9 1.0
N B:ASN490 4.1 21.2 1.0
ND2 B:ASN490 4.1 21.8 1.0
CA B:THR492 4.2 20.4 1.0
N B:GLY464 4.2 17.5 1.0
O2B B:TPP600 4.4 16.1 1.0
O B:VAL488 4.4 19.4 1.0
N B:ASN493 4.4 19.8 1.0
CB B:ASP463 4.4 17.9 1.0
CB B:ASN490 4.5 21.3 1.0
CB B:THR492 4.6 20.4 1.0
CA B:ASP463 4.6 17.7 1.0
CA B:ASN493 4.6 19.5 1.0
O2A B:TPP600 4.6 17.2 1.0
CA B:ASN490 4.6 21.2 1.0
C B:GLY462 4.7 17.6 1.0
CA B:GLY462 4.7 17.5 1.0
C B:ASN490 4.8 21.2 1.0
CA B:GLY494 4.8 18.9 1.0
OH B:TYR561 4.8 31.6 1.0
N B:ASP491 4.8 21.7 1.0
C B:ASN493 4.9 19.0 1.0
CE2 B:TYR561 4.9 33.6 1.0
C B:ASP463 5.0 17.2 1.0

Magnesium binding site 3 out of 4 in 1upa

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Magnesium binding site 3 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure)


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 (Semet Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:9.9
occ:1.00
 O1A C:TPP600 2.1 19.0 1.0
O C:HOH2170 2.2 20.0 1.0
O C:THR492 2.2 20.1 1.0
OD1 C:ASN490 2.2 22.6 1.0
O3B C:TPP600 2.2 15.5 1.0
OD1 C:ASP463 2.2 17.6 1.0
CG C:ASP463 3.2 17.9 1.0
PA C:TPP600 3.3 17.6 1.0
C C:THR492 3.3 20.4 1.0
CG C:ASN490 3.4 22.8 1.0
PB C:TPP600 3.4 21.8 1.0
O3A C:TPP600 3.6 19.0 1.0
OD2 C:ASP463 3.7 18.5 1.0
O7 C:TPP600 3.8 18.6 1.0
N C:ASP463 3.9 17.1 1.0
N C:THR492 3.9 21.8 1.0
N C:GLY494 4.0 19.7 1.0
N C:ASN490 4.0 21.4 1.0
ND2 C:ASN490 4.1 24.0 1.0
CA C:THR492 4.1 21.0 1.0
O1B C:TPP600 4.2 22.1 1.0
N C:GLY464 4.3 17.8 1.0
N C:ASN493 4.4 19.7 1.0
CB C:ASP463 4.4 17.4 1.0
O C:VAL488 4.5 19.7 1.0
CB C:THR492 4.5 21.1 1.0
CB C:ASN490 4.5 21.9 1.0
O2B C:TPP600 4.6 17.9 1.0
CA C:ASP463 4.6 17.4 1.0
O2A C:TPP600 4.6 17.3 1.0
CA C:ASN490 4.6 21.5 1.0
CA C:ASN493 4.6 19.4 1.0
C C:ASN490 4.7 21.9 1.0
N C:ASP491 4.7 22.4 1.0
CA C:GLY494 4.7 19.9 1.0
C C:GLY462 4.7 17.5 1.0
OH C:TYR561 4.8 31.5 1.0
CA C:GLY462 4.8 17.4 1.0
C C:ASN493 4.9 19.5 1.0
CE2 C:TYR561 4.9 33.8 1.0
C C:ASP463 5.0 17.6 1.0

Magnesium binding site 4 out of 4 in 1upa

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Magnesium binding site 4 out of 4 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus (Semet Structure)


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 (Semet Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:7.6
occ:1.00
 O3B D:TPP600 2.1 16.2 1.0
OD1 D:ASN490 2.1 22.8 1.0
O1A D:TPP600 2.1 18.2 1.0
O D:THR492 2.2 19.3 1.0
O D:HOH2188 2.2 17.7 1.0
OD1 D:ASP463 2.2 18.9 1.0
CG D:ASN490 3.3 23.1 1.0
PA D:TPP600 3.3 15.5 1.0
CG D:ASP463 3.3 17.9 1.0
PB D:TPP600 3.3 19.9 1.0
C D:THR492 3.4 19.7 1.0
O3A D:TPP600 3.6 17.5 1.0
OD2 D:ASP463 3.7 17.1 1.0
O7 D:TPP600 3.9 18.4 1.0
ND2 D:ASN490 3.9 24.5 1.0
N D:THR492 4.0 20.8 1.0
N D:ASN490 4.1 20.7 1.0
N D:ASP463 4.1 17.4 1.0
O1B D:TPP600 4.1 20.6 1.0
N D:GLY494 4.1 19.1 1.0
CA D:THR492 4.2 20.2 1.0
N D:GLY464 4.3 18.0 1.0
N D:ASN493 4.4 19.3 1.0
CB D:ASN490 4.4 21.6 1.0
O D:VAL488 4.4 17.8 1.0
O2B D:TPP600 4.5 18.0 1.0
CB D:ASP463 4.5 17.4 1.0
O2A D:TPP600 4.6 17.2 1.0
CB D:THR492 4.6 20.0 1.0
CA D:ASN490 4.6 21.5 1.0
CA D:ASN493 4.6 19.1 1.0
CA D:ASP463 4.7 17.6 1.0
CA D:GLY462 4.7 17.5 1.0
C D:ASN490 4.7 21.3 1.0
C D:GLY462 4.8 17.7 1.0
CA D:GLY494 4.8 19.3 1.0
N D:ASP491 4.8 21.6 1.0
OH D:TYR561 4.8 30.6 1.0
C D:ASN493 4.9 19.1 1.0
CE2 D:TYR561 4.9 33.0 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 14:52:41 2024

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