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Magnesium in PDB 3n6q: Crystal Structure of Yghz From E. Coli

Protein crystallography data

The structure of Crystal Structure of Yghz From E. Coli, PDB code: 3n6q was solved by C.Zubieta, M.Totir, N.Echols, A.May, T.Alber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.07 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 91.700, 98.056, 98.257, 90.27, 92.97, 106.12
R / Rfree (%) 16.9 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yghz From E. Coli (pdb code 3n6q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Yghz From E. Coli, PDB code: 3n6q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3n6q

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Magnesium binding site 1 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:12.0
occ:1.00
 OE1 A:GLU83 2.1 33.0 1.0
O A:HOH922 2.1 35.2 1.0
NH2 A:ARG79 2.1 25.0 0.3
CD A:GLU83 3.0 34.4 1.0
CZ A:ARG79 3.0 26.5 0.3
OE2 A:GLU83 3.2 28.9 1.0
NH1 A:ARG79 3.5 26.8 0.3
NE A:ARG79 4.0 22.7 0.3
NH2 A:ARG46 4.1 27.1 1.0
O A:HOH760 4.2 48.3 1.0
CG A:GLU83 4.4 26.7 1.0
NH2 A:ARG79 4.5 37.7 0.7

Magnesium binding site 2 out of 9 in 3n6q

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Magnesium binding site 2 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:12.6
occ:1.00
 OE2 B:GLU83 1.8 32.4 1.0
CD B:GLU83 2.8 35.6 1.0
O B:HOH821 3.1 34.9 1.0
OE1 B:GLU83 3.1 30.6 1.0
CG B:GLU83 4.2 24.1 1.0
NH2 B:ARG46 4.2 27.9 1.0
O B:HOH834 4.3 44.3 1.0
NH2 B:ARG79 4.3 58.3 1.0

Magnesium binding site 3 out of 9 in 3n6q

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Magnesium binding site 3 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:19.4
occ:1.00
 OE1 C:GLU83 2.0 43.6 1.0
O C:HOH770 2.7 41.8 1.0
CD C:GLU83 3.0 35.1 1.0
OE2 C:GLU83 3.2 35.7 1.0
NH2 C:ARG46 4.1 32.2 1.0
CG C:GLU83 4.4 31.4 1.0
NH1 C:ARG79 4.5 30.3 0.5
CD C:ARG79 4.8 34.6 0.5

Magnesium binding site 4 out of 9 in 3n6q

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Magnesium binding site 4 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:17.1
occ:1.00
 O D:HOH772 2.2 36.8 1.0
OE1 D:GLU83 2.2 37.9 1.0
CD D:GLU83 3.0 37.8 1.0
OE2 D:GLU83 3.1 33.5 1.0
O D:HOH822 4.0 59.2 1.0
NH2 D:ARG46 4.1 29.7 1.0
O D:HOH729 4.2 51.5 1.0
CG D:GLU83 4.4 26.7 1.0
CD D:ARG79 4.7 47.9 1.0
NH1 D:ARG79 4.8 55.5 1.0

Magnesium binding site 5 out of 9 in 3n6q

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Magnesium binding site 5 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:54.0
occ:1.00
 OE1 D:GLU75 2.5 30.6 1.0
NE2 D:HIS38 2.8 25.5 1.0
CD D:GLU75 3.2 33.6 1.0
OE2 D:GLU75 3.3 35.9 1.0
O D:HOH577 3.3 36.2 1.0
CD2 D:HIS38 3.4 24.5 1.0
CE1 D:HIS38 4.0 24.4 1.0
CB D:SER72 4.5 20.1 1.0
CG D:GLU75 4.5 21.1 1.0
CG D:HIS38 4.7 21.9 1.0
CA D:SER72 4.7 19.4 1.0
ND1 D:HIS38 4.9 24.4 1.0
O D:HOH699 4.9 46.6 1.0

Magnesium binding site 6 out of 9 in 3n6q

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Magnesium binding site 6 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:15.6
occ:1.00
 OE1 E:GLU83 1.9 35.6 1.0
CD E:GLU83 2.9 37.9 1.0
O E:HOH616 3.1 43.1 1.0
OE2 E:GLU83 3.2 39.2 1.0
NH2 E:ARG79 4.2 36.4 0.5
NH2 E:ARG46 4.2 29.8 1.0
NH2 E:ARG79 4.3 34.8 0.5
CG E:GLU83 4.3 31.8 1.0
NE E:ARG79 4.4 33.7 0.5
NE E:ARG79 4.6 39.1 0.5
CZ E:ARG79 4.7 38.8 0.5
CZ E:ARG79 4.8 29.7 0.5

Magnesium binding site 7 out of 9 in 3n6q

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Magnesium binding site 7 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:10.5
occ:1.00
 OE1 F:GLU83 1.9 32.1 1.0
CD F:GLU83 2.8 34.5 1.0
OE2 F:GLU83 3.1 31.9 1.0
NH2 F:ARG46 4.2 24.4 1.0
CG F:GLU83 4.2 27.3 1.0
NH2 F:ARG79 4.3 27.6 0.5

Magnesium binding site 8 out of 9 in 3n6q

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Magnesium binding site 8 out of 9 in the Crystal Structure of Yghz From E. Coli


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 Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:12.7
occ:1.00
 OE1 G:GLU83 2.2 35.5 1.0
CD G:GLU83 3.0 33.8 1.0
OE2 G:GLU83 3.1 29.0 1.0
NH2 G:ARG46 4.1 22.8 1.0
NH2 G:ARG79 4.2 32.8 0.5
CG G:GLU83 4.4 29.3 1.0
O G:HOH716 4.5 51.4 1.0
NE G:ARG79 4.6 40.7 0.5
CD G:ARG79 5.0 24.9 0.5
CZ G:ARG79 5.0 25.4 0.5

Magnesium binding site 9 out of 9 in 3n6q

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Magnesium binding site 9 out of 9 in the Crystal Structure of Yghz From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Yghz From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:14.0
occ:1.00
 OE1 H:GLU83 2.0 39.2 1.0
CD H:GLU83 2.8 37.0 1.0
OE2 H:GLU83 3.1 33.5 1.0
NH2 H:ARG46 4.1 31.5 1.0
CG H:GLU83 4.2 29.9 1.0
O H:HOH632 4.2 44.9 1.0
NH1 H:ARG79 4.3 58.3 1.0
O H:HOH670 4.6 49.0 1.0
CD H:ARG79 4.9 49.6 1.0

Reference:

M.Totir, N.Echols, M.Nanao, C.L.Gee, A.Moskaleva, S.Gradia, A.T.Iavarone, J.M.Berger, A.P.May, C.Zubieta, T.Alber. Macro-to-Micro Structural Proteomics: Native Source Proteins For High-Throughput Crystallization. Plos One V. 7 32498 2012.
ISSN: ESSN 1932-6203
PubMed: 22393408
DOI: 10.1371/JOURNAL.PONE.0032498
Page generated: Mon Dec 14 08:27:45 2020

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