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Magnesium in PDB 3k8d: Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo

Enzymatic activity of Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo

All present enzymatic activity of Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo:
2.7.7.38;

Protein crystallography data

The structure of Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo, PDB code: 3k8d was solved by D.J.Heyes, C.W.Levy, P.Lafite, N.S.Scrutton, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.27 / 1.90
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 94.770, 94.770, 153.140, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 18.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo (pdb code 3k8d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo, PDB code: 3k8d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3k8d

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Magnesium binding site 1 out of 4 in the Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo


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 E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1242

b:29.5
occ:1.00
O1A A:CTP1243 2.2 18.6 1.0
O1B A:CTP1243 2.3 17.0 1.0
O A:HOH282 2.3 25.5 1.0
O A:HOH250 2.3 14.2 1.0
O3G A:CTP1243 2.4 22.6 1.0
O A:HOH257 2.4 17.8 1.0
PB A:CTP1243 3.2 20.8 1.0
PA A:CTP1243 3.3 17.4 1.0
PG A:CTP1243 3.4 21.9 1.0
O3B A:CTP1243 3.6 24.0 1.0
O3A A:CTP1243 3.6 21.2 1.0
O5' A:CTP1243 3.8 15.0 1.0
O A:HOH269 3.9 24.2 1.0
NH1 D:ARG164 3.9 22.0 1.0
NH2 A:ARG15 4.1 18.2 1.0
O1G A:CTP1243 4.1 20.9 1.0
O1A A:KDO1244 4.1 20.5 1.0
O A:HOH294 4.3 33.0 1.0
C3 A:KDO1244 4.3 15.4 1.0
C6 A:CTP1243 4.5 17.1 1.0
C5 A:CTP1243 4.5 16.2 1.0
O2B A:CTP1243 4.6 20.3 1.0
NH1 A:ARG10 4.6 21.0 1.0
O2A A:CTP1243 4.7 16.7 1.0
O2G A:CTP1243 4.7 20.5 1.0
O A:HOH253 4.8 16.3 1.0
C1 A:KDO1244 4.9 14.5 1.0
O A:HOH526 4.9 37.8 1.0
CZ D:ARG164 5.0 29.9 1.0
C2 A:KDO1244 5.0 16.4 1.0

Magnesium binding site 2 out of 4 in 3k8d

Go back to Magnesium Binding Sites List in 3k8d
Magnesium binding site 2 out of 4 in the Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo


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 E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1242

b:29.6
occ:1.00
O1A B:CTP1243 2.2 18.1 1.0
O1B B:CTP1243 2.2 16.2 1.0
O B:HOH279 2.3 23.7 1.0
O3G B:CTP1243 2.3 21.1 1.0
O B:HOH251 2.3 14.5 1.0
O B:HOH253 2.4 16.2 1.0
PB B:CTP1243 3.2 21.1 1.0
PA B:CTP1243 3.3 16.9 1.0
PG B:CTP1243 3.4 20.8 1.0
O3B B:CTP1243 3.6 23.6 1.0
O3A B:CTP1243 3.6 22.0 1.0
O5' B:CTP1243 3.8 14.1 1.0
O B:HOH262 3.9 23.8 1.0
NH1 C:ARG164 3.9 21.0 1.0
O1G B:CTP1243 4.1 21.1 1.0
NH2 B:ARG15 4.1 18.0 1.0
O1A B:KDO1244 4.1 20.7 1.0
O B:HOH294 4.2 33.8 1.0
C3 B:KDO1244 4.3 13.4 1.0
C6 B:CTP1243 4.4 15.5 1.0
C5 B:CTP1243 4.5 17.3 1.0
O2B B:CTP1243 4.6 20.0 1.0
NH1 B:ARG10 4.6 21.7 1.0
O2G B:CTP1243 4.7 18.6 1.0
O2A B:CTP1243 4.7 16.8 1.0
O B:HOH254 4.8 16.8 1.0
C1 B:KDO1244 4.9 15.8 1.0
O B:HOH536 4.9 35.9 1.0
CZ C:ARG164 5.0 32.4 1.0

Magnesium binding site 3 out of 4 in 3k8d

Go back to Magnesium Binding Sites List in 3k8d
Magnesium binding site 3 out of 4 in the Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo


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 E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1242

b:13.7
occ:1.00
O1A C:CTP1243 2.2 16.6 1.0
O1B C:CTP1243 2.2 17.4 1.0
O3G C:CTP1243 2.3 20.4 1.0
O C:HOH252 2.4 17.9 1.0
O C:HOH257 2.4 21.8 1.0
O C:HOH273 2.4 30.9 1.0
PB C:CTP1243 3.2 19.3 1.0
PA C:CTP1243 3.3 17.4 1.0
PG C:CTP1243 3.4 18.8 1.0
O3B C:CTP1243 3.6 19.1 1.0
O3A C:CTP1243 3.6 22.0 1.0
O5' C:CTP1243 3.8 15.2 1.0
NH1 B:ARG164 3.9 20.7 1.0
O C:HOH263 4.0 21.0 1.0
O1G C:CTP1243 4.1 21.2 1.0
NH2 C:ARG15 4.1 16.1 1.0
O1A C:KDO1244 4.1 16.6 1.0
C3 C:KDO1244 4.2 14.4 1.0
O C:HOH325 4.3 31.4 1.0
C6 C:CTP1243 4.5 13.4 1.0
O2B C:CTP1243 4.6 21.4 1.0
C5 C:CTP1243 4.6 21.1 1.0
O2A C:CTP1243 4.6 18.3 1.0
O2G C:CTP1243 4.7 16.0 1.0
NH1 C:ARG10 4.7 24.2 1.0
O C:HOH261 4.8 17.7 1.0
C1 C:KDO1244 4.9 25.8 1.0
C2 C:KDO1244 5.0 18.7 1.0

Magnesium binding site 4 out of 4 in 3k8d

Go back to Magnesium Binding Sites List in 3k8d
Magnesium binding site 4 out of 4 in the Crystal Structure of E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo


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 E. Coli Lipopolysaccharide Specific Cmp-Kdo Synthetase in Complex with Ctp and 2-Deoxy-Kdo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1242

b:13.6
occ:1.00
O1A D:CTP1243 2.2 16.4 1.0
O1B D:CTP1243 2.2 16.6 1.0
O3G D:CTP1243 2.4 21.1 1.0
O D:HOH257 2.4 20.9 1.0
O D:HOH258 2.4 18.6 1.0
O D:HOH275 2.4 29.3 1.0
PB D:CTP1243 3.2 19.1 1.0
PA D:CTP1243 3.3 18.1 1.0
PG D:CTP1243 3.4 19.3 1.0
O3B D:CTP1243 3.5 18.6 1.0
O3A D:CTP1243 3.6 22.4 1.0
O5' D:CTP1243 3.7 14.5 1.0
O D:HOH265 3.9 21.6 1.0
NH1 A:ARG164 4.0 19.0 1.0
O1G D:CTP1243 4.1 22.4 1.0
NH2 D:ARG15 4.1 17.9 1.0
O1A D:KDO1244 4.1 16.1 1.0
C3 D:KDO1244 4.2 14.2 1.0
O D:HOH342 4.4 29.8 1.0
C6 D:CTP1243 4.5 12.4 1.0
O2B D:CTP1243 4.5 18.8 1.0
C5 D:CTP1243 4.6 19.4 1.0
O2A D:CTP1243 4.6 17.9 1.0
O2G D:CTP1243 4.7 18.9 1.0
NH1 D:ARG10 4.7 23.9 1.0
O D:HOH264 4.8 17.6 1.0
C1 D:KDO1244 4.9 22.7 1.0
C2 D:KDO1244 5.0 22.5 1.0

Reference:

D.J.Heyes, C.Levy, P.Lafite, I.S.Roberts, M.Goldrick, A.V.Stachulski, S.B.Rossington, D.Stanford, S.E.J.Rigby, N.S.Scrutton, D.Leys. Structure-Based Mechanism of Cmp-2-Keto-3-Deoxymanno-Octulonic Acid Synthetase: Convergent Evolution of A Sugar-Activating Enzyme with Dna/Rna Polymerases J.Biol.Chem. V. 284 35514 2009.
ISSN: ISSN 0021-9258
PubMed: 19815542
DOI: 10.1074/JBC.M109.056630
Page generated: Mon Dec 14 08:21:35 2020

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