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Magnesium in PDB 1gqc: The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K

Enzymatic activity of The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K

All present enzymatic activity of The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K:
2.7.7.38;

Protein crystallography data

The structure of The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K, PDB code: 1gqc was solved by S.Jelakovic, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.44 / 2.6
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.944, 130.996, 48.148, 90.00, 102.31, 90.00
R / Rfree (%) 17.8 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K (pdb code 1gqc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K, PDB code: 1gqc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1gqc

Go back to Magnesium Binding Sites List in 1gqc
Magnesium binding site 1 out of 2 in the The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1243

b:26.3
occ:1.00
O A:HOH2109 2.3 31.4 1.0
O1A A:CMK1244 2.5 23.9 1.0
O A:HOH2115 2.6 28.8 1.0
OE1 A:GLN96 2.6 53.0 1.0
OD1 A:ASP98 2.6 48.7 1.0
OD2 A:ASP98 2.8 51.0 1.0
CG A:ASP98 3.1 48.1 1.0
OE1 A:GLU99 3.5 61.6 1.0
PA A:CMK1244 3.7 22.0 1.0
OD1 A:ASP225 3.8 82.5 1.0
CD A:GLN96 3.8 51.0 1.0
O2 A:CMK1244 3.8 20.0 1.0
OD2 A:ASP225 4.0 83.5 1.0
CD A:GLU99 4.3 59.5 1.0
OE2 A:GLU99 4.3 61.7 1.0
CG A:ASP225 4.3 82.3 1.0
NE2 A:GLN96 4.5 52.4 1.0
O1X A:CMK1244 4.6 14.8 1.0
CB A:ASP98 4.6 45.7 1.0
O2A A:CMK1244 4.7 22.2 1.0
O5' A:CMK1244 4.7 23.6 1.0
O A:HOH2114 4.7 38.6 1.0
O A:HOH2022 4.8 24.1 1.0
CG A:GLN96 4.9 46.3 1.0
CB A:GLN96 5.0 38.4 1.0

Magnesium binding site 2 out of 2 in 1gqc

Go back to Magnesium Binding Sites List in 1gqc
Magnesium binding site 2 out of 2 in the The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase Complexed with Cmp-Kdo at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1242

b:33.0
occ:1.00
O2P B:C5P1243 2.2 48.7 1.0
O B:HOH2148 2.3 30.0 1.0
OD2 B:ASP225 2.6 52.3 1.0
OD2 B:ASP98 2.7 28.3 1.0
P B:C5P1243 3.5 49.3 1.0
CG B:ASP98 3.5 27.6 1.0
CG B:ASP225 3.7 51.0 1.0
OD1 B:ASP98 3.8 28.6 1.0
C5' B:C5P1243 3.8 39.5 1.0
O5' B:C5P1243 3.9 44.2 1.0
O1P B:C5P1243 3.9 51.0 1.0
NZ B:LYS19 4.1 26.2 1.0
CB B:ASP225 4.5 47.2 1.0
OD1 B:ASP225 4.5 53.5 1.0
O3P B:C5P1243 4.7 46.2 1.0
CB B:ASP98 4.8 27.8 1.0

Reference:

S.Jelakovic, G.E.Schulz. Catalytic Mechanism of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase As Derived From Complexes with Reaction Educt and Product. Biochemistry V. 41 1174 2002.
ISSN: ISSN 0006-2960
PubMed: 11802716
DOI: 10.1021/BI0119060
Page generated: Mon Dec 14 05:58:11 2020

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