Atomistry » Magnesium » PDB 1eo3-1f6t » 1eyz
Atomistry »
  Magnesium »
    PDB 1eo3-1f6t »
      1eyz »

Magnesium in PDB 1eyz: Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp

Protein crystallography data

The structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp, PDB code: 1eyz was solved by J.B.Thoden, S.Firestine, A.Nixon, S.J.Benkovic, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.300, 179.500, 75.700, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1eyz:

The structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp (pdb code 1eyz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp, PDB code: 1eyz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1eyz

Go back to Magnesium Binding Sites List in 1eyz
Magnesium binding site 1 out of 5 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.5
occ:1.00
O3G A:ANP400 1.9 16.7 1.0
O2B A:ANP400 2.0 15.8 1.0
O A:HOH1119 2.1 15.6 1.0
OE1 A:GLU279 2.2 15.6 1.0
OE2 A:GLU279 2.3 16.1 1.0
O A:HOH1131 2.3 23.1 1.0
CD A:GLU279 2.5 15.3 1.0
PG A:ANP400 3.2 18.0 1.0
PB A:ANP400 3.2 16.7 1.0
N3B A:ANP400 3.5 22.2 1.0
O2G A:ANP400 3.6 13.3 1.0
MG A:MG402 3.8 15.4 1.0
O A:HOH1229 3.8 20.0 1.0
O2A A:ANP400 3.9 15.8 1.0
O A:HOH1175 4.0 22.5 1.0
CG A:GLU279 4.0 9.4 1.0
NH1 A:ARG114 4.1 13.8 1.0
O A:HOH1824 4.2 49.4 1.0
O1B A:ANP400 4.2 21.6 1.0
O3A A:ANP400 4.3 13.5 1.0
O A:HOH1149 4.4 15.5 1.0
O A:SER159 4.4 38.3 1.0
NH2 A:ARG114 4.4 16.9 1.0
O1G A:ANP400 4.4 12.6 1.0
OE1 A:GLU84 4.5 28.7 1.0
PA A:ANP400 4.5 13.9 1.0
OE2 A:GLU84 4.5 24.4 1.0
O1A A:ANP400 4.6 13.6 1.0
CZ A:ARG114 4.7 11.7 1.0
CA A:SER160 4.7 30.1 1.0
OE1 A:GLU267 4.8 14.8 1.0
CB A:SER160 4.8 87.5 1.0
CB A:GLU279 4.9 8.6 1.0
CD A:GLU84 5.0 0.0 1.0

Magnesium binding site 2 out of 5 in 1eyz

Go back to Magnesium Binding Sites List in 1eyz
Magnesium binding site 2 out of 5 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:15.4
occ:1.00
O2A A:ANP400 2.0 15.8 1.0
O2G A:ANP400 2.0 13.3 1.0
OE1 A:GLU279 2.1 15.6 1.0
OE2 A:GLU267 2.1 14.1 1.0
O A:HOH1113 2.2 15.1 1.0
OE1 A:GLU267 2.2 14.8 1.0
CD A:GLU267 2.5 10.2 1.0
CD A:GLU279 3.1 15.3 1.0
PG A:ANP400 3.2 18.0 1.0
PA A:ANP400 3.5 13.9 1.0
N3B A:ANP400 3.6 22.2 1.0
CG A:GLU279 3.7 9.4 1.0
O3G A:ANP400 3.7 16.7 1.0
MG A:MG401 3.8 18.5 1.0
CG A:GLU267 4.0 13.1 1.0
O2B A:ANP400 4.0 15.8 1.0
O A:HOH1143 4.2 26.3 1.0
O3A A:ANP400 4.2 13.5 1.0
OE2 A:GLU279 4.2 16.1 1.0
PB A:ANP400 4.2 16.7 1.0
O A:HOH1229 4.2 20.0 1.0
O1A A:ANP400 4.2 13.6 1.0
O A:HOH1331 4.3 41.2 1.0
O A:HOH1174 4.3 15.5 1.0
O5' A:ANP400 4.3 18.3 1.0
O3' A:ANP400 4.4 13.6 1.0
O1G A:ANP400 4.5 12.6 1.0
C5' A:ANP400 4.6 19.4 1.0
O A:HOH1131 4.6 23.1 1.0
O A:HOH1258 4.6 32.7 1.0
NE2 A:HIS285 4.8 17.4 1.0
CB A:GLU267 4.8 10.2 1.0

Magnesium binding site 3 out of 5 in 1eyz

Go back to Magnesium Binding Sites List in 1eyz
Magnesium binding site 3 out of 5 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:29.6
occ:1.00
O A:HOH1143 2.1 26.3 1.0
O A:HOH1792 2.2 29.5 1.0
O A:HOH1794 2.3 30.6 1.0
O1G A:ANP400 2.3 12.6 1.0
OD2 A:ASP286 2.6 31.0 1.0
O A:HOH1258 3.0 32.7 1.0
CG A:ASP286 3.2 14.2 1.0
OD1 A:ASP286 3.3 14.8 1.0
PG A:ANP400 3.4 18.0 1.0
O2G A:ANP400 3.5 13.3 1.0
O A:HOH1394 3.6 38.0 1.0
O A:HOH1144 3.8 19.3 1.0
OG A:SER161 4.0 63.2 1.0
O A:HOH1175 4.2 22.5 1.0
O A:HOH1331 4.3 41.2 1.0
O3G A:ANP400 4.4 16.7 1.0
O A:HOH1173 4.5 23.6 1.0
CB A:ASP286 4.5 15.2 1.0
N3B A:ANP400 4.6 22.2 1.0
NH2 A:ARG363 4.6 23.8 1.0
CA A:SER161 4.8 26.4 1.0
O A:HOH1138 4.8 33.7 1.0
CB A:SER161 4.9 71.4 1.0
N A:SER161 4.9 27.6 1.0

Magnesium binding site 4 out of 5 in 1eyz

Go back to Magnesium Binding Sites List in 1eyz
Magnesium binding site 4 out of 5 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:25.1
occ:1.00
O B:HOH1615 1.9 31.6 1.0
O2B B:ANP961 2.0 35.7 1.0
O3G B:ANP961 2.0 24.7 1.0
OE2 B:GLU279 2.2 22.4 1.0
OE1 B:GLU279 2.4 28.1 1.0
O B:HOH1885 2.5 32.5 1.0
CD B:GLU279 2.6 25.1 1.0
PB B:ANP961 3.3 37.8 1.0
PG B:ANP961 3.3 36.6 1.0
N3B B:ANP961 3.7 36.3 1.0
O B:HOH1626 3.8 49.8 1.0
OE1 B:GLU84 3.8 47.9 1.0
O B:HOH1542 3.8 27.1 1.0
NH2 B:ARG114 3.8 40.0 1.0
MG B:MG402 3.9 23.9 1.0
O2G B:ANP961 3.9 23.7 1.0
NH1 B:ARG114 4.1 25.6 1.0
O2A B:ANP961 4.1 33.2 1.0
CG B:GLU279 4.1 19.3 1.0
O3A B:ANP961 4.2 18.6 1.0
O B:HOH1661 4.2 34.6 1.0
O B:SER159 4.3 87.0 1.0
O1B B:ANP961 4.3 36.9 1.0
CZ B:ARG114 4.3 26.9 1.0
O1G B:ANP961 4.5 50.7 1.0
PA B:ANP961 4.6 27.9 1.0
O B:HOH1528 4.6 30.4 1.0
O1A B:ANP961 4.7 20.2 1.0
CA B:SER160 4.8 75.9 1.0
CD B:GLU84 4.9 21.3 1.0
CB B:SER160 4.9 41.5 1.0
O B:HOH1505 4.9 24.4 1.0
CB B:GLU279 4.9 13.3 1.0

Magnesium binding site 5 out of 5 in 1eyz

Go back to Magnesium Binding Sites List in 1eyz
Magnesium binding site 5 out of 5 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:23.9
occ:1.00
O2G B:ANP961 1.8 23.7 1.0
O2A B:ANP961 2.0 33.2 1.0
OE1 B:GLU279 2.0 28.1 1.0
O B:HOH1473 2.0 21.5 1.0
OE2 B:GLU267 2.1 23.1 1.0
OE1 B:GLU267 2.4 24.2 1.0
CD B:GLU267 2.6 30.1 1.0
PG B:ANP961 3.0 36.6 1.0
CD B:GLU279 3.1 25.1 1.0
PA B:ANP961 3.4 27.9 1.0
O3G B:ANP961 3.4 24.7 1.0
N3B B:ANP961 3.5 36.3 1.0
CG B:GLU279 3.7 19.3 1.0
O B:HOH1542 3.8 27.1 1.0
MG B:MG401 3.9 25.1 1.0
O B:HOH2064 4.1 60.4 1.0
O3A B:ANP961 4.1 18.6 1.0
PB B:ANP961 4.1 37.8 1.0
O2B B:ANP961 4.1 35.7 1.0
CG B:GLU267 4.1 21.7 1.0
OE2 B:GLU279 4.2 22.4 1.0
O1G B:ANP961 4.2 50.7 1.0
O B:HOH1555 4.3 22.5 1.0
O5' B:ANP961 4.3 28.7 1.0
O1A B:ANP961 4.3 20.2 1.0
C5' B:ANP961 4.4 20.1 1.0
O3' B:ANP961 4.4 26.7 1.0
NE2 B:HIS285 4.8 16.5 1.0
C3' B:ANP961 4.8 29.8 1.0
O B:HOH1885 4.9 32.5 1.0
CB B:GLU267 4.9 14.7 1.0
O B:HOH1579 5.0 38.6 1.0

Reference:

J.B.Thoden, S.Firestine, A.Nixon, S.J.Benkovic, H.M.Holden. Molecular Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase. Biochemistry V. 39 8791 2000.
ISSN: ISSN 0006-2960
PubMed: 10913290
DOI: 10.1021/BI000926J
Page generated: Mon Dec 14 05:52:57 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