Atomistry » Magnesium » PDB 1ueu-1v5f » 1upb
Atomistry »
  Magnesium »
    PDB 1ueu-1v5f »
      1upb »

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

Go back to Magnesium Binding Sites List in 1upb
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

Go back to Magnesium Binding Sites List in 1upb
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

Go back to Magnesium Binding Sites List in 1upb
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: Mon Dec 14 06:53:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy