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Magnesium in PDB 5guf: Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis

Enzymatic activity of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis

All present enzymatic activity of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis:
2.7.7.67;

Protein crystallography data

The structure of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis, PDB code: 5guf was solved by W.Cheng, S.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.63 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 56.505, 89.249, 98.876, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.9

Other elements in 5guf:

The structure of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis (pdb code 5guf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis, PDB code: 5guf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5guf

Go back to Magnesium Binding Sites List in 5guf
Magnesium binding site 1 out of 3 in the Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:55.2
occ:1.00
 O2B A:CTP201 2.1 47.8 1.0
O1A A:CTP201 2.2 42.8 1.0
O A:HOH325 2.3 54.4 1.0
O A:HOH313 2.3 54.2 1.0
O A:HOH302 2.4 50.3 1.0
PA A:CTP201 3.5 51.6 1.0
PB A:CTP201 3.5 56.1 1.0
O3G A:CTP201 3.8 46.7 1.0
O3A A:CTP201 3.9 54.5 1.0
O2A A:CTP201 4.1 57.5 1.0
OD2 A:ASP122 4.1 45.8 1.0
CG A:ASP122 4.3 49.0 1.0
O1B A:CTP201 4.4 53.3 1.0
K A:K205 4.5 64.4 1.0
NZ A:LYS107 4.5 36.1 1.0
O3B A:CTP201 4.5 48.7 1.0
OD1 A:ASP122 4.6 43.2 1.0
O A:GLY115 4.6 46.7 1.0
PG A:CTP201 4.6 36.1 1.0
O5' A:CTP201 4.7 60.3 1.0
CA A:GLY115 4.7 42.9 1.0
O1G A:CTP201 4.8 39.6 1.0
C5' A:CTP201 4.9 59.0 1.0
C A:GLY115 4.9 43.0 1.0
CB A:ASP122 4.9 37.7 1.0
O A:HOH332 5.0 57.1 1.0

Magnesium binding site 2 out of 3 in 5guf

Go back to Magnesium Binding Sites List in 5guf
Magnesium binding site 2 out of 3 in the Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:18.5
occ:1.00
 O A:HOH307 1.8 41.2 1.0
O A:ARG10 2.2 33.1 1.0
OE2 A:GLU16 2.2 32.1 1.0
OD1 A:ASP8 2.4 35.8 1.0
O A:HOH304 2.5 31.2 1.0
OD1 A:ASP12 2.5 37.5 1.0
OD2 A:ASP8 2.6 35.8 1.0
OE1 A:GLU16 2.7 33.2 1.0
CG A:ASP8 2.8 36.6 1.0
CD A:GLU16 2.8 39.2 1.0
CG A:ASP12 3.3 40.5 1.0
C A:ARG10 3.4 31.5 1.0
OD2 A:ASP12 3.5 46.7 1.0
N A:ASP12 4.0 31.8 1.0
CA A:ARG10 4.2 31.8 1.0
CB A:ASP8 4.3 25.8 1.0
O A:HOH346 4.3 48.9 1.0
N A:ILE11 4.3 31.7 1.0
CB A:ARG10 4.3 27.7 1.0
CG A:GLU16 4.3 34.8 1.0
N A:ARG10 4.4 31.6 1.0
CA A:ILE11 4.4 36.5 1.0
CB A:ASP12 4.5 36.8 1.0
N A:ASP8 4.5 31.3 1.0
ND2 A:ASN13 4.7 39.4 1.0
C A:ILE11 4.7 31.9 1.0
CA A:ASP12 4.8 32.4 1.0
CA A:ASP8 4.8 31.6 1.0
CG A:ARG10 4.9 31.2 1.0
C A:ASP8 4.9 32.8 1.0

Magnesium binding site 3 out of 3 in 5guf

Go back to Magnesium Binding Sites List in 5guf
Magnesium binding site 3 out of 3 in the Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Insight Into An Intramembrane Enzyme For Archaeal Membrane Lipids Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:39.6
occ:1.00
 O A:HOH355 2.0 45.2 1.0
N A:ARG51 3.2 34.8 1.0
CD A:ARG50 3.6 48.3 1.0
CG A:ARG51 3.8 33.8 1.0
CB A:ARG51 3.8 35.2 1.0
CD A:ARG108 3.8 31.0 1.0
CA A:ARG50 3.9 33.8 1.0
CB A:ARG50 4.1 42.4 1.0
C A:ARG50 4.1 34.1 1.0
CA A:ARG51 4.1 32.9 1.0
CG A:ARG50 4.5 38.6 1.0
NE A:ARG108 4.6 37.3 1.0
NE A:ARG50 4.8 58.0 1.0
O A:HOH323 4.8 43.7 1.0
NH1 A:ARG50 4.9 47.3 1.0
CG A:ARG108 4.9 32.7 1.0
O A:ARG51 5.0 35.6 1.0

Reference:

S.Ren, A.Caforio, Q.Yang, B.Sun, F.Yu, X.Zhu, J.Wang, C.Dou, Q.Fu, N.Huang, Q.Sun, C.Nie, S.Qi, X.Gong, J.He, Y.Wei, A.J.Driessen, W.Cheng. Structural and Mechanistic Insights Into the Biosynthesis of Cdp-Archaeol in Membranes. Cell Res. V. 27 1378 2017.
ISSN: ISSN 1748-7838
PubMed: 28961231
DOI: 10.1038/CR.2017.122
Page generated: Mon Dec 14 20:25:22 2020

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