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Magnesium in PDB 4gyp: Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058)

Enzymatic activity of Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058)

All present enzymatic activity of Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058):
4.2.1.40;

Protein crystallography data

The structure of Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058), PDB code: 4gyp was solved by T.Lukk, S.Ghasempur, H.J.Imker, J.A.Gerlt, S.K.Nair, Enzyme Functioninitiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.470, 113.020, 128.590, 90.00, 105.89, 90.00
R / Rfree (%) 14.9 / 18.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058) (pdb code 4gyp). 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 the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058), PDB code: 4gyp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4gyp

Go back to Magnesium Binding Sites List in 4gyp
Magnesium binding site 1 out of 2 in the Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058)


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 the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.4
occ:1.00
OD1 A:ASN289 2.2 12.2 1.0
OE2 A:GLU260 2.3 14.2 1.0
OD1 A:ASP235 2.5 10.2 1.0
OD2 A:ASP261 2.6 9.5 1.0
OD2 A:ASP235 2.8 8.8 1.0
CG A:ASP235 2.9 12.7 1.0
CD A:GLU260 3.1 14.0 1.0
O A:HOH642 3.2 11.9 1.0
CG A:GLU260 3.3 11.1 1.0
ND2 A:ASN237 3.4 6.3 1.0
CG A:ASN289 3.4 13.2 1.0
CG A:ASP261 3.5 9.2 1.0
CB A:ASP261 3.8 10.1 1.0
O A:HOH629 3.8 13.1 1.0
N A:ASN289 4.1 11.6 1.0
CG A:ASN237 4.1 11.1 1.0
OE1 A:GLU260 4.2 14.7 1.0
CB A:ASN289 4.2 6.0 1.0
CB A:ASP235 4.2 5.3 1.0
ND2 A:ASN289 4.4 6.1 1.0
CA A:ASN237 4.5 6.2 1.0
CB A:GLU260 4.6 8.2 1.0
OD1 A:ASN237 4.7 7.4 1.0
SD A:MET290 4.7 10.6 1.0
CG A:MET290 4.7 15.3 1.0
OD1 A:ASP261 4.7 6.6 1.0
CA A:ASN289 4.7 12.5 1.0
N A:ASN237 4.7 6.1 1.0
NZ A:LYS207 4.8 15.2 1.0
N A:ASP261 4.9 6.6 1.0
C A:GLU260 4.9 6.7 1.0
CB A:ASN237 4.9 7.9 1.0
C A:THR288 5.0 11.8 1.0
CA A:ASP261 5.0 14.2 1.0

Magnesium binding site 2 out of 2 in 4gyp

Go back to Magnesium Binding Sites List in 4gyp
Magnesium binding site 2 out of 2 in the Crystal Structure of the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058)


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 the Heterotetrameric Complex of Glucd and Glucdrp From E. Coli K-12 MG1655 (Efi Target Efi-506058) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:19.2
occ:1.00
OD1 B:ASN289 2.2 13.1 1.0
OE2 B:GLU260 2.4 16.8 1.0
OD2 B:ASP261 2.4 11.9 1.0
OD1 B:ASP235 2.5 10.1 1.0
OD2 B:ASP235 2.8 12.5 1.0
CG B:ASP235 2.9 10.4 1.0
CD B:GLU260 3.1 14.6 1.0
ND2 B:ASN237 3.3 11.7 1.0
CG B:GLU260 3.3 10.7 1.0
CG B:ASP261 3.4 11.1 1.0
CG B:ASN289 3.4 8.4 1.0
O B:HOH677 3.6 25.5 1.0
CB B:ASP261 3.7 10.3 1.0
O B:HOH676 3.9 13.7 1.0
N B:ASN289 4.0 11.6 1.0
CG B:ASN237 4.1 13.3 1.0
CB B:ASN289 4.1 7.4 1.0
OE1 B:GLU260 4.2 17.4 1.0
CB B:ASP235 4.3 8.0 1.0
ND2 B:ASN289 4.4 7.5 1.0
CA B:ASN237 4.5 8.7 1.0
OD1 B:ASP261 4.5 8.0 1.0
CB B:GLU260 4.6 11.4 1.0
SD B:MET290 4.6 13.0 1.0
CA B:ASN289 4.6 8.9 1.0
CG B:MET290 4.6 14.7 1.0
N B:ASN237 4.7 7.8 1.0
OD1 B:ASN237 4.7 8.5 1.0
N B:ASP261 4.8 9.6 1.0
C B:GLU260 4.8 13.2 1.0
C B:THR288 4.9 12.4 1.0
CB B:ASN237 4.9 10.2 1.0
CA B:ASP261 4.9 10.8 1.0
O B:GLU260 4.9 12.1 1.0
NZ B:LYS207 5.0 17.7 1.0

Reference:

T.Lukk, S.Ghasempur, H.J.Imker, S.K.Nair, J.A.Gerlt. Glucarate Dehydratase and Its Related Protein From Escherichia Coli Form A Heterotetrameric Complex. To Be Published.
Page generated: Mon Dec 14 16:56:06 2020

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