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Magnesium in PDB 1kof: Crystal Structure of Gluconate Kinase

Enzymatic activity of Crystal Structure of Gluconate Kinase

All present enzymatic activity of Crystal Structure of Gluconate Kinase:
2.7.1.12;

Protein crystallography data

The structure of Crystal Structure of Gluconate Kinase, PDB code: 1kof was solved by L.Kraft, G.A.Sprenger, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.740, 88.410, 51.480, 90.00, 105.76, 90.00
R / Rfree (%) 25.2 / 31.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Gluconate Kinase (pdb code 1kof). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Gluconate Kinase, PDB code: 1kof:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1kof

Go back to Magnesium Binding Sites List in 1kof
Magnesium binding site 1 out of 2 in the Crystal Structure of Gluconate Kinase


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 Gluconate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:60.3
occ:1.00
O2G A:ACP500 2.2 57.6 1.0
O A:HOH1023 2.3 69.4 1.0
O1B A:ACP500 2.6 58.1 1.0
OG A:SER22 2.8 61.7 1.0
CB A:SER22 3.2 59.8 1.0
PG A:ACP500 3.3 58.8 1.0
C3B A:ACP500 3.6 57.3 1.0
PB A:ACP500 3.6 60.7 1.0
O1G A:ACP500 3.8 59.1 1.0
O1A A:ACP500 3.9 65.8 1.0
N A:SER22 3.9 59.0 1.0
CA A:SER22 4.2 59.5 1.0
O3G A:ACP500 4.5 51.7 1.0
O2B A:ACP500 4.6 55.5 1.0
O3A A:ACP500 4.6 62.3 1.0
CG1 A:VAL86 4.7 50.2 1.0
PA A:ACP500 4.7 64.9 1.0
CB A:LYS21 4.8 56.8 1.0
OD2 A:ASP38 4.9 57.1 1.0
C A:LYS21 5.0 57.3 1.0
O2A A:ACP500 5.0 63.1 1.0

Magnesium binding site 2 out of 2 in 1kof

Go back to Magnesium Binding Sites List in 1kof
Magnesium binding site 2 out of 2 in the Crystal Structure of Gluconate Kinase


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 Gluconate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:51.0
occ:1.00
OG B:SER22 2.2 64.7 1.0
O2G B:ACP501 2.2 68.6 1.0
O1B B:ACP501 2.4 52.4 1.0
CB B:SER22 3.2 61.3 1.0
O1G B:ACP501 3.3 66.7 1.0
PG B:ACP501 3.3 68.5 1.0
PB B:ACP501 3.8 58.4 1.0
N B:SER22 4.1 60.9 1.0
CA B:SER22 4.2 61.2 1.0
CG1 B:VAL86 4.2 50.4 1.0
C3B B:ACP501 4.3 61.3 1.0
O2B B:ACP501 4.4 56.7 1.0
OD2 B:ASP38 4.4 53.7 1.0
O3G B:ACP501 4.5 65.8 1.0
O1A B:ACP501 4.7 64.2 1.0
CE B:LYS21 4.8 42.7 1.0
CB B:LYS21 4.9 58.2 1.0
O3A B:ACP501 5.0 59.5 1.0

Reference:

L.Kraft, G.A.Sprenger, Y.Lindqvist. Conformational Changes During the Catalytic Cycle of Gluconate Kinase As Revealed By X-Ray Crystallography. J.Mol.Biol. V. 318 1057 2002.
ISSN: ISSN 0022-2836
PubMed: 12054802
DOI: 10.1016/S0022-2836(02)00215-2
Page generated: Mon Dec 14 06:22:06 2020

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