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Magnesium in PDB 2y6p: Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb

Enzymatic activity of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb

All present enzymatic activity of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb:
2.7.7.38;

Protein crystallography data

The structure of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb, PDB code: 2y6p was solved by H.Schmidt, J.R.Mesters, U.Mamat, R.Hilgenfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.35 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.175, 51.175, 107.514, 90.00, 102.68, 90.00
R / Rfree (%) 21.1 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb (pdb code 2y6p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb, PDB code: 2y6p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2y6p

Go back to Magnesium Binding Sites List in 2y6p
Magnesium binding site 1 out of 6 in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1234

b:32.4
occ:1.00
 O A:HOH2056 1.9 26.5 1.0
O A:HOH2015 1.9 28.2 1.0
O A:HOH2014 2.0 15.3 1.0
OD1 A:ASP219 2.0 33.7 1.0
O1A A:CTP1233 2.1 33.6 1.0
OD2 A:ASP95 2.1 33.9 1.0
CG A:ASP219 2.9 35.6 1.0
OD2 A:ASP219 3.1 34.2 1.0
CG A:ASP95 3.1 35.5 1.0
OD1 A:ASP95 3.4 33.7 1.0
NZ A:LYS19 3.4 35.6 1.0
PA A:CTP1233 3.5 33.2 1.0
O2A A:CTP1233 4.1 32.6 1.0
CB A:ASP219 4.3 37.3 1.0
NH2 A:ARG15 4.4 30.7 1.0
O A:HOH2058 4.4 32.7 1.0
C5' A:CTP1233 4.4 34.8 1.0
O A:VAL218 4.4 37.5 1.0
O5' A:CTP1233 4.4 32.7 1.0
O3A A:CTP1233 4.4 31.1 1.0
CB A:ASP95 4.5 35.1 1.0
CA A:ASP219 4.7 38.4 1.0
C A:VAL218 4.7 38.8 1.0
N A:ASP219 4.8 38.4 1.0
CE A:LYS19 4.9 34.6 1.0
N A:VAL218 5.0 40.2 1.0

Magnesium binding site 2 out of 6 in 2y6p

Go back to Magnesium Binding Sites List in 2y6p
Magnesium binding site 2 out of 6 in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1235

b:31.6
occ:1.00
 O1G A:CTP1233 2.0 33.1 1.0
O2A A:CTP1233 2.0 32.6 1.0
O1B A:CTP1233 2.1 30.6 1.0
O A:HOH2061 2.2 23.3 1.0
PB A:CTP1233 3.1 30.5 1.0
PG A:CTP1233 3.2 31.6 1.0
PA A:CTP1233 3.2 33.2 1.0
O3B A:CTP1233 3.4 30.4 1.0
O3A A:CTP1233 3.5 31.1 1.0
O2G A:CTP1233 3.7 33.0 1.0
NH2 A:ARG15 3.8 30.7 1.0
O A:HOH2058 3.9 32.7 1.0
O5' A:CTP1233 3.9 32.7 1.0
NH2 A:ARG10 4.3 33.5 1.0
O1A A:CTP1233 4.4 33.6 1.0
O3G A:CTP1233 4.5 33.1 1.0
O2B A:CTP1233 4.5 30.8 1.0
C6 A:CTP1233 4.7 34.1 1.0
CZ A:ARG15 4.7 34.8 1.0
C5 A:CTP1233 4.7 33.4 1.0
NE A:ARG15 5.0 34.8 1.0

Magnesium binding site 3 out of 6 in 2y6p

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Magnesium binding site 3 out of 6 in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1236

b:31.1
occ:1.00
 OD1 B:ASP219 2.0 33.8 1.0
O B:HOH2095 2.0 20.9 1.0
O1A B:CTP1235 2.1 29.6 1.0
OD2 B:ASP95 2.1 32.5 1.0
O B:HOH2108 2.1 23.6 1.0
O B:HOH2031 2.2 23.2 1.0
CG B:ASP219 2.9 34.5 1.0
OD2 B:ASP219 3.0 38.2 1.0
CG B:ASP95 3.1 31.4 1.0
OD1 B:ASP95 3.5 34.0 1.0
PA B:CTP1235 3.5 33.0 1.0
NZ B:LYS19 3.6 27.8 1.0
C5' B:CTP1235 4.1 30.9 1.0
O2A B:CTP1235 4.2 33.2 1.0
CB B:ASP219 4.3 33.1 1.0
O5' B:CTP1235 4.3 32.5 1.0
CB B:ASP95 4.4 29.9 1.0
O B:VAL218 4.4 32.3 1.0
O3A B:CTP1235 4.5 33.7 1.0
C B:VAL218 4.7 32.5 1.0
CA B:ASP219 4.7 33.3 1.0
NH2 B:ARG15 4.7 34.6 1.0
N B:ASP219 4.9 32.6 1.0
CE B:LYS19 4.9 27.3 1.0
N B:VAL218 4.9 31.2 1.0

Magnesium binding site 4 out of 6 in 2y6p

Go back to Magnesium Binding Sites List in 2y6p
Magnesium binding site 4 out of 6 in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1237

b:38.4
occ:1.00
 O2A B:CTP1235 2.0 33.2 1.0
O1B B:CTP1235 2.0 32.2 1.0
O1G B:CTP1235 2.1 30.3 1.0
O B:HOH2110 2.2 23.3 1.0
O B:HOH2109 2.2 30.1 1.0
O B:HOH2111 2.2 27.3 1.0
PB B:CTP1235 3.1 34.0 1.0
PA B:CTP1235 3.2 33.0 1.0
PG B:CTP1235 3.3 32.9 1.0
O3A B:CTP1235 3.5 33.7 1.0
O3B B:CTP1235 3.6 33.5 1.0
O5' B:CTP1235 3.8 32.5 1.0
NH2 B:ARG15 3.9 34.6 1.0
O2G B:CTP1235 4.0 33.9 1.0
NH2 B:ARG10 4.2 37.8 1.0
O2B B:CTP1235 4.4 36.2 1.0
O1A B:CTP1235 4.4 29.6 1.0
O3G B:CTP1235 4.5 31.4 1.0
C6 B:CTP1235 4.5 29.1 1.0
C5 B:CTP1235 4.6 29.0 1.0
CZ B:ARG15 4.9 35.1 1.0
O B:HOH2027 4.9 22.9 1.0

Magnesium binding site 5 out of 6 in 2y6p

Go back to Magnesium Binding Sites List in 2y6p
Magnesium binding site 5 out of 6 in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1233

b:56.2
occ:1.00
 O1A C:CTP1232 2.1 49.8 1.0
O C:HOH2015 2.4 25.3 1.0
OD2 C:ASP95 2.5 41.0 1.0
OD1 C:ASP219 2.5 51.9 1.0
OD2 C:ASP219 3.0 53.9 1.0
CG C:ASP219 3.1 52.5 1.0
CG C:ASP95 3.4 41.9 1.0
PA C:CTP1232 3.5 48.2 1.0
OD1 C:ASP95 3.5 40.8 1.0
C5' C:CTP1232 3.9 47.5 1.0
NZ C:LYS19 4.0 45.8 1.0
O2A C:CTP1232 4.0 46.4 1.0
O5' C:CTP1232 4.1 48.8 1.0
NH2 C:ARG15 4.6 55.8 1.0
O3A C:CTP1232 4.6 49.7 1.0
CB C:ASP219 4.6 54.6 1.0
CB C:ASP95 4.8 43.6 1.0
O C:VAL218 4.9 50.7 1.0

Magnesium binding site 6 out of 6 in 2y6p

Go back to Magnesium Binding Sites List in 2y6p
Magnesium binding site 6 out of 6 in the Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Evidence For A Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase Kdsb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1234

b:50.1
occ:1.00
 O1G C:CTP1232 1.9 49.5 1.0
O2A C:CTP1232 1.9 46.4 1.0
O C:HOH2018 2.0 42.4 1.0
O C:HOH2017 2.1 28.7 1.0
O1B C:CTP1232 2.1 49.2 1.0
O C:HOH2016 2.4 32.7 1.0
PB C:CTP1232 3.1 49.4 1.0
PG C:CTP1232 3.2 50.8 1.0
PA C:CTP1232 3.2 48.2 1.0
O3B C:CTP1232 3.5 50.9 1.0
O3A C:CTP1232 3.6 49.7 1.0
O2G C:CTP1232 3.8 49.8 1.0
NH2 C:ARG15 3.8 55.8 1.0
O5' C:CTP1232 3.9 48.8 1.0
NH2 C:ARG10 4.3 51.1 1.0
O3G C:CTP1232 4.3 50.2 1.0
O1A C:CTP1232 4.4 49.8 1.0
O2B C:CTP1232 4.5 50.5 1.0
C6 C:CTP1232 4.6 45.6 1.0
C5 C:CTP1232 4.6 46.0 1.0
CZ C:ARG15 4.9 58.4 1.0

Reference:

H.Schmidt, J.R.Mesters, J.Wu, R.W.Woodard, R.Hilgenfeld, U.Mamat. Evidence For A Two-Metal-Ion Mechanism in the Cytidyltransferase Kdsb, An Enzyme Involved in Lipopolysaccharide Biosynthesis. Plos One V. 6 23231 2011.
ISSN: ESSN 1932-6203
PubMed: 21826242
DOI: 10.1371/JOURNAL.PONE.0023231
Page generated: Wed Aug 14 07:27:19 2024

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