Magnesium in PDB 4jiw: C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Enzymatic activity of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

All present enzymatic activity of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5:
3.2.1.17;

Protein crystallography data

The structure of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiw was solved by S.A.Buth, P.G.Leiman, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 3.40
Space group P 61 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.157, 184.157, 238.893, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 24.3

Other elements in 4jiw:

The structure of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 (pdb code 4jiw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jiw

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Magnesium binding site 1 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.3
occ:1.00
O A:HOH602 2.1 85.3 1.0
O B:HOH702 2.1 0.3 1.0
O A:HOH601 2.1 0.5 1.0
O C:HOH602 2.1 0.4 1.0
O C:HOH601 2.1 88.8 1.0
O B:HOH701 2.1 0.5 1.0
OE1 C:GLU552 3.6 0.2 1.0
OE2 A:GLU552 3.9 1.0 1.0
OE1 B:GLU552 4.1 0.7 1.0
OE2 C:GLU552 4.2 0.1 1.0
CD C:GLU552 4.3 0.7 1.0
OE2 B:GLU552 4.6 0.3 1.0
CD B:GLU552 4.8 0.6 1.0
CD A:GLU552 4.8 0.8 1.0
OE1 A:GLU552 4.8 0.9 1.0
CE B:MET557 4.8 0.2 1.0
CE C:MET557 4.9 0.9 1.0

Magnesium binding site 2 out of 4 in 4jiw

Go back to Magnesium Binding Sites List in 4jiw
Magnesium binding site 2 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:0.5
occ:1.00
O G:HOH602 2.1 0.6 1.0
O F:HOH701 2.1 0.1 1.0
O E:HOH701 2.1 0.8 1.0
O F:HOH702 2.1 99.0 1.0
O E:HOH702 2.1 0.7 1.0
O G:HOH601 2.1 0.4 1.0
OE2 F:GLU552 3.7 0.1 1.0
OE1 G:GLU552 3.8 0.3 1.0
OE2 G:GLU552 4.3 0.7 1.0
OE1 E:GLU552 4.4 0.9 1.0
CD G:GLU552 4.4 0.6 1.0
OE1 F:GLU552 4.5 0.4 1.0
CE E:MET557 4.5 0.8 1.0
CD F:GLU552 4.5 0.3 1.0
CE F:MET557 4.6 0.7 1.0
OE2 E:GLU552 4.8 0.7 1.0
CE G:MET557 4.9 0.4 1.0

Magnesium binding site 3 out of 4 in 4jiw

Go back to Magnesium Binding Sites List in 4jiw
Magnesium binding site 3 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:0.1
occ:1.00
O I:HOH702 2.1 88.2 1.0
O J:HOH602 2.1 82.4 1.0
O I:HOH701 2.1 0.3 1.0
O K:HOH601 2.1 85.1 1.0
O K:HOH602 2.1 0.3 1.0
O J:HOH601 2.1 0.6 1.0
OE1 I:GLU552 3.9 0.5 1.0
OE1 K:GLU552 3.9 0.2 1.0
OE2 J:GLU552 4.3 0.5 1.0
OE2 I:GLU552 4.5 0.3 1.0
OE2 K:GLU552 4.5 0.4 1.0
CE K:MET557 4.6 0.6 1.0
OE1 J:GLU552 4.6 0.2 1.0
CD I:GLU552 4.6 0.8 1.0
CD K:GLU552 4.6 0.0 1.0
CD J:GLU552 4.9 0.8 1.0
CE I:MET557 4.9 0.8 1.0

Magnesium binding site 4 out of 4 in 4jiw

Go back to Magnesium Binding Sites List in 4jiw
Magnesium binding site 4 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg601

b:0.0
occ:1.00
O O:HOH701 2.1 0.3 1.0
O N:HOH601 2.1 1.0 1.0
O O:HOH703 2.1 0.8 1.0
O M:HOH701 2.1 0.7 1.0
O N:HOH602 2.1 79.0 1.0
O O:HOH702 2.1 0.6 1.0
OE2 O:GLU552 3.4 0.7 1.0
OE1 O:GLU552 4.2 0.7 1.0
CE O:MET557 4.2 0.4 1.0
OE2 M:GLU552 4.2 0.3 1.0
CD O:GLU552 4.2 0.8 1.0
OE1 N:GLU552 4.3 0.2 1.0
OE1 M:GLU552 4.6 0.4 1.0
OE2 N:GLU552 4.8 0.8 1.0
CD M:GLU552 4.8 1.0 1.0
CD N:GLU552 4.9 0.7 1.0

Reference:

M.M.Shneider, S.A.Buth, B.T.Ho, M.Basler, J.J.Mekalanos, P.G.Leiman. Paar-Repeat Proteins Sharpen and Diversify the Type VI Secretion System Spike. Nature V. 500 350 2013.
ISSN: ISSN 0028-0836
PubMed: 23925114
DOI: 10.1038/NATURE12453
Page generated: Mon Dec 14 19:00:15 2020

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