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Magnesium in PDB 2eb5: Crystal Structure of Hpcg Complexed with Oxalate

Protein crystallography data

The structure of Crystal Structure of Hpcg Complexed with Oxalate, PDB code: 2eb5 was solved by A.Izumi, D.Rea, T.Adachi, S.Unzai, S.Y.Park, D.I.Roper, J.R.H.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.541, 136.541, 192.397, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hpcg Complexed with Oxalate (pdb code 2eb5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Hpcg Complexed with Oxalate, PDB code: 2eb5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2eb5

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Magnesium binding site 1 out of 5 in the Crystal Structure of Hpcg Complexed with Oxalate


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 Hpcg Complexed with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:16.6
occ:1.00
 OE2 A:GLU108 2.0 15.0 1.0
OE1 A:GLU139 2.0 18.6 1.0
O A:HOH3008 2.1 12.2 1.0
OE2 A:GLU106 2.1 18.9 1.0
O2 A:OXL2001 2.1 16.6 1.0
O3 A:OXL2001 2.1 17.7 1.0
C1 A:OXL2001 2.8 19.1 1.0
C2 A:OXL2001 2.8 18.2 1.0
CD A:GLU108 3.0 15.8 1.0
CD A:GLU106 3.3 22.6 1.0
CD A:GLU139 3.3 17.3 1.0
OE1 A:GLU108 3.4 17.4 1.0
NZ A:LYS61 3.9 15.2 1.0
CB A:GLU139 4.0 14.6 1.0
CG A:GLU106 4.0 17.2 1.0
O1 A:OXL2001 4.0 20.1 1.0
CE A:LYS61 4.1 15.8 1.0
O4 A:OXL2001 4.1 17.5 1.0
OE2 A:GLU139 4.1 15.8 1.0
OE1 A:GLU106 4.2 25.1 1.0
CG A:GLU139 4.2 14.5 1.0
N A:SER239 4.2 16.2 1.0
CG A:GLU108 4.3 13.5 1.0
O A:ILE62 4.4 16.8 1.0
CB A:SER239 4.5 16.9 1.0
CG2 A:ILE141 4.5 14.7 1.0
CA A:GLY238 4.6 14.9 1.0
C A:GLY238 4.7 15.9 1.0
CA A:GLY63 4.9 17.3 1.0
CA A:SER239 4.9 16.3 1.0

Magnesium binding site 2 out of 5 in 2eb5

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Magnesium binding site 2 out of 5 in the Crystal Structure of Hpcg Complexed with Oxalate


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 Hpcg Complexed with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:16.9
occ:1.00
 OE1 B:GLU139 2.0 18.0 1.0
OE2 B:GLU108 2.0 13.8 1.0
OE2 B:GLU106 2.0 20.1 1.0
O4 B:OXL2002 2.1 15.3 1.0
O1 B:OXL2002 2.2 17.1 1.0
O B:HOH3003 2.2 15.0 1.0
C2 B:OXL2002 2.9 19.9 1.0
C1 B:OXL2002 2.9 20.2 1.0
CD B:GLU108 3.0 14.4 1.0
CD B:GLU106 3.1 24.0 1.0
CD B:GLU139 3.3 17.5 1.0
OE1 B:GLU108 3.4 14.0 1.0
NZ B:LYS61 3.9 19.7 1.0
CG B:GLU106 3.9 19.4 1.0
CB B:GLU139 3.9 15.5 1.0
OE1 B:GLU106 4.0 27.9 1.0
O2 B:OXL2002 4.1 19.7 1.0
CG B:GLU139 4.1 17.0 1.0
O3 B:OXL2002 4.1 19.2 1.0
OE2 B:GLU139 4.2 18.8 1.0
N B:SER239 4.2 15.4 1.0
CE B:LYS61 4.3 21.8 1.0
CG B:GLU108 4.3 14.7 1.0
CB B:SER239 4.4 15.8 1.0
O B:ILE62 4.4 16.7 1.0
CG2 B:ILE141 4.5 14.7 1.0
CA B:GLY238 4.6 15.1 1.0
C B:GLY238 4.7 15.4 1.0
CA B:SER239 4.9 15.6 1.0
CA B:GLY63 4.9 16.6 1.0

Magnesium binding site 3 out of 5 in 2eb5

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Magnesium binding site 3 out of 5 in the Crystal Structure of Hpcg Complexed with Oxalate


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 Hpcg Complexed with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:17.3
occ:1.00
 OE2 C:GLU108 2.0 17.1 1.0
OE1 C:GLU139 2.1 17.3 1.0
OE2 C:GLU106 2.1 18.5 1.0
O1 C:OXL2003 2.2 15.8 1.0
O4 C:OXL2003 2.2 14.6 1.0
O C:HOH3007 2.2 12.2 1.0
C1 C:OXL2003 2.9 17.3 1.0
C2 C:OXL2003 2.9 15.7 1.0
CD C:GLU108 3.1 13.2 1.0
CD C:GLU106 3.2 21.5 1.0
CD C:GLU139 3.3 17.4 1.0
OE1 C:GLU108 3.5 12.7 1.0
CG C:GLU106 4.0 19.4 1.0
CB C:GLU139 4.0 15.2 1.0
NZ C:LYS61 4.0 14.5 1.0
OE1 C:GLU106 4.1 23.2 1.0
CE C:LYS61 4.1 15.9 1.0
O3 C:OXL2003 4.2 17.5 1.0
OE2 C:GLU139 4.2 20.3 1.0
O2 C:OXL2003 4.2 18.9 1.0
N C:SER239 4.2 14.6 1.0
CG C:GLU139 4.2 15.4 1.0
CG C:GLU108 4.4 11.7 1.0
CB C:SER239 4.4 15.4 1.0
CG2 C:ILE141 4.4 14.8 1.0
O C:ILE62 4.4 14.3 1.0
CA C:GLY238 4.6 14.5 1.0
C C:GLY238 4.7 14.8 1.0
CA C:SER239 4.8 15.1 1.0
CA C:GLY63 5.0 14.3 1.0

Magnesium binding site 4 out of 5 in 2eb5

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Magnesium binding site 4 out of 5 in the Crystal Structure of Hpcg Complexed with Oxalate


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 Hpcg Complexed with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:21.6
occ:1.00
 OE2 D:GLU108 2.0 18.3 1.0
OE1 D:GLU139 2.0 21.0 1.0
O2 D:OXL2004 2.1 21.4 1.0
O D:HOH3009 2.1 19.8 1.0
OE2 D:GLU106 2.1 25.7 1.0
O3 D:OXL2004 2.2 22.0 1.0
C2 D:OXL2004 2.9 21.8 1.0
C1 D:OXL2004 2.9 22.1 1.0
CD D:GLU108 3.0 19.2 1.0
CD D:GLU106 3.3 29.2 1.0
CD D:GLU139 3.3 20.5 1.0
OE1 D:GLU108 3.4 17.0 1.0
CB D:GLU139 4.0 17.7 1.0
CG D:GLU106 4.0 24.6 1.0
NZ D:LYS61 4.0 18.8 1.0
O4 D:OXL2004 4.1 22.6 1.0
CE D:LYS61 4.1 22.3 1.0
OE2 D:GLU139 4.1 22.3 1.0
O1 D:OXL2004 4.2 21.9 1.0
CG D:GLU139 4.2 19.4 1.0
OE1 D:GLU106 4.2 33.2 1.0
N D:SER239 4.2 18.9 1.0
CG D:GLU108 4.3 15.9 1.0
O D:ILE62 4.4 20.7 1.0
CB D:SER239 4.4 20.1 1.0
CG2 D:ILE141 4.6 20.4 1.0
CA D:GLY238 4.6 18.2 1.0
C D:GLY238 4.7 19.0 1.0
CA D:SER239 4.9 19.4 1.0
CA D:GLY63 4.9 21.9 1.0

Magnesium binding site 5 out of 5 in 2eb5

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Magnesium binding site 5 out of 5 in the Crystal Structure of Hpcg Complexed with Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Hpcg Complexed with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1005

b:20.1
occ:1.00
 OE2 E:GLU108 2.1 14.5 1.0
OE1 E:GLU139 2.1 22.5 1.0
O4 E:OXL2005 2.1 18.2 1.0
O1 E:OXL2005 2.1 18.9 1.0
OE1 E:GLU106 2.1 22.6 1.0
O E:HOH3007 2.2 17.3 1.0
C2 E:OXL2005 2.9 20.6 1.0
C1 E:OXL2005 2.9 20.4 1.0
CD E:GLU108 3.1 17.0 1.0
CD E:GLU139 3.3 20.8 1.0
CD E:GLU106 3.3 28.1 1.0
OE1 E:GLU108 3.4 16.1 1.0
OE2 E:GLU106 3.9 30.8 1.0
CB E:GLU139 4.0 16.8 1.0
NZ E:LYS61 4.1 17.6 1.0
O2 E:OXL2005 4.1 21.0 1.0
N E:SER239 4.1 18.1 1.0
O3 E:OXL2005 4.1 20.3 1.0
CE E:LYS61 4.1 21.2 1.0
OE2 E:GLU139 4.2 21.4 1.0
CG E:GLU139 4.2 19.0 1.0
CG E:GLU108 4.4 15.7 1.0
CB E:SER239 4.4 19.2 1.0
O E:ILE62 4.4 19.7 1.0
CG E:GLU106 4.5 24.7 1.0
CG2 E:ILE141 4.5 18.7 1.0
CA E:GLY238 4.6 18.0 1.0
C E:GLY238 4.7 18.7 1.0
CB E:GLU106 4.7 21.6 1.0
CA E:SER239 4.8 19.0 1.0
CA E:GLY63 4.9 20.8 1.0

Reference:

A.Izumi, D.Rea, T.Adachi, S.Unzai, S.Y.Park, D.I.Roper, J.R.H.Tame. Structure and Mechanism of Hpcg, A Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia Coli J.Mol.Biol. V. 370 899 2007.
ISSN: ISSN 0022-2836
PubMed: 17559873
DOI: 10.1016/J.JMB.2007.05.006
Page generated: Sun Aug 10 10:36:44 2025

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