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Magnesium in PDB 2qjn: Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate, PDB code: 2qjn was solved by A.A.Fedorov, E.V.Fedorov, J.F.Rakus, J.E.Vick, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.89 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 116.269, 165.241, 167.039, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate (pdb code 2qjn). 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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate, PDB code: 2qjn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2qjn

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Magnesium binding site 1 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:28.9
occ:1.00
OD2 A:ASP210 2.2 19.5 1.0
OE1 A:GLU236 2.2 18.8 1.0
OE1 A:GLU262 2.3 23.5 1.0
O A:HOH2154 2.3 18.6 1.0
O5 A:KDG2001 2.5 33.3 1.0
O6A A:KDG2001 2.5 28.8 1.0
CD A:GLU262 3.1 21.3 1.0
CG A:ASP210 3.1 21.2 1.0
CD A:GLU236 3.2 22.0 1.0
C5 A:KDG2001 3.2 33.5 1.0
C6 A:KDG2001 3.2 32.4 1.0
OE2 A:GLU262 3.3 21.3 1.0
OD1 A:ASP210 3.4 17.9 1.0
NH2 A:ARG283 3.8 16.5 1.0
OE2 A:GLU236 3.9 16.7 1.0
O A:HOH2054 4.0 18.2 1.0
OD2 A:ASP237 4.0 20.1 1.0
CD2 A:HIS212 4.0 27.4 1.0
CG A:GLU236 4.0 20.3 1.0
O A:HOH2007 4.2 15.5 1.0
NE2 A:HIS212 4.3 28.2 1.0
CG A:GLU262 4.4 21.0 1.0
O6B A:KDG2001 4.4 31.9 1.0
CB A:ASP210 4.4 18.6 1.0
OH B:TYR75 4.5 20.5 1.0
NH1 A:ARG147 4.5 34.2 1.0
C4 A:KDG2001 4.6 33.8 1.0
CG A:ASP237 4.7 20.9 1.0
CZ A:ARG283 4.9 19.4 1.0
NE A:ARG283 5.0 18.5 1.0
CG A:HIS212 5.0 27.1 1.0

Magnesium binding site 2 out of 4 in 2qjn

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Magnesium binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:26.6
occ:1.00
O B:HOH2173 2.2 19.4 1.0
OE1 B:GLU262 2.2 21.8 1.0
OD2 B:ASP210 2.2 20.5 1.0
OE1 B:GLU236 2.3 21.0 1.0
O5 B:KDG2002 2.5 27.5 1.0
O6A B:KDG2002 2.5 26.8 1.0
CD B:GLU262 3.1 22.1 1.0
CG B:ASP210 3.1 21.3 1.0
C5 B:KDG2002 3.2 30.2 1.0
CD B:GLU236 3.2 22.2 1.0
C6 B:KDG2002 3.3 30.1 1.0
OE2 B:GLU262 3.3 22.7 1.0
OD1 B:ASP210 3.4 19.0 1.0
NH2 B:ARG283 3.9 17.0 1.0
OE2 B:GLU236 3.9 21.5 1.0
OD2 B:ASP237 4.0 24.3 1.0
CD2 B:HIS212 4.0 30.1 1.0
O B:HOH2028 4.0 19.1 1.0
CG B:GLU236 4.1 20.4 1.0
O B:HOH2026 4.1 18.0 1.0
NE2 B:HIS212 4.1 31.4 1.0
CG B:GLU262 4.4 19.9 1.0
O6B B:KDG2002 4.5 31.1 1.0
CB B:ASP210 4.5 20.0 1.0
OH A:TYR75 4.5 23.1 1.0
C4 B:KDG2002 4.6 30.5 1.0
CG B:ASP237 4.6 22.2 1.0
NH1 B:ARG147 4.8 34.0 1.0
CZ B:ARG283 4.9 17.9 1.0
NE B:ARG283 4.9 18.2 1.0

Magnesium binding site 3 out of 4 in 2qjn

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Magnesium binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:28.2
occ:1.00
OD2 C:ASP210 2.2 20.8 1.0
OE1 C:GLU236 2.3 21.6 1.0
OE1 C:GLU262 2.3 21.1 1.0
O C:HOH2157 2.3 23.0 1.0
O6A C:KDG2003 2.5 29.1 1.0
O5 C:KDG2003 2.5 31.7 1.0
CG C:ASP210 3.1 22.6 1.0
CD C:GLU262 3.1 22.9 1.0
C5 C:KDG2003 3.2 32.8 1.0
CD C:GLU236 3.2 22.8 1.0
C6 C:KDG2003 3.2 32.0 1.0
OE2 C:GLU262 3.3 22.2 1.0
OD1 C:ASP210 3.4 20.2 1.0
NH2 C:ARG283 3.9 18.2 1.0
OE2 C:GLU236 3.9 22.5 1.0
CG C:GLU236 4.0 21.6 1.0
OD2 C:ASP237 4.0 23.2 1.0
O C:HOH2007 4.1 20.2 1.0
CD2 C:HIS212 4.1 31.2 1.0
O C:HOH2005 4.2 19.6 1.0
NE2 C:HIS212 4.3 32.8 1.0
O6B C:KDG2003 4.4 33.7 1.0
CB C:ASP210 4.4 19.8 1.0
CG C:GLU262 4.4 20.1 1.0
OH D:TYR75 4.5 22.2 1.0
CG C:ASP237 4.6 22.5 1.0
NH1 C:ARG147 4.6 34.3 1.0
C4 C:KDG2003 4.6 33.0 1.0
CZ C:ARG283 4.9 20.4 1.0
NE C:ARG283 4.9 20.2 1.0

Magnesium binding site 4 out of 4 in 2qjn

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Magnesium binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate


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 D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed with Mg and 2-Keto-3-Deoxy-D-Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:28.4
occ:1.00
OD2 D:ASP210 2.2 22.7 1.0
O D:HOH2139 2.2 18.8 1.0
OE1 D:GLU262 2.3 22.7 1.0
OE1 D:GLU236 2.3 20.9 1.0
O6A D:KDG2004 2.5 29.6 1.0
O5 D:KDG2004 2.5 32.6 1.0
CD D:GLU262 3.1 23.1 1.0
CG D:ASP210 3.1 23.3 1.0
CD D:GLU236 3.2 21.4 1.0
C5 D:KDG2004 3.2 33.9 1.0
C6 D:KDG2004 3.2 32.1 1.0
OE2 D:GLU262 3.3 22.2 1.0
OD1 D:ASP210 3.4 20.7 1.0
NH2 D:ARG283 3.8 19.9 1.0
OE2 D:GLU236 3.9 18.9 1.0
CG D:GLU236 4.0 20.3 1.0
O D:HOH2013 4.0 19.4 1.0
OD2 D:ASP237 4.1 25.6 1.0
O D:HOH2008 4.2 20.1 1.0
CD2 D:HIS212 4.3 32.7 1.0
NE2 D:HIS212 4.4 35.4 1.0
CG D:GLU262 4.4 20.4 1.0
CB D:ASP210 4.4 21.8 1.0
O6B D:KDG2004 4.4 32.0 1.0
OH C:TYR75 4.6 23.7 1.0
NH1 D:ARG147 4.6 33.2 1.0
C4 D:KDG2004 4.6 33.7 1.0
CG D:ASP237 4.7 24.1 1.0
CZ D:ARG283 4.8 21.5 1.0
NE D:ARG283 4.9 19.9 1.0

Reference:

J.F.Rakus, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, J.E.Vick, P.C.Babbitt, S.C.Almo, J.A.Gerlt. Evolution of Enzymatic Activities in the Enolase Superfamily: D-Mannonate Dehydratase From Novosphingobium Aromaticivorans. Biochemistry V. 46 12896 2007.
ISSN: ISSN 0006-2960
PubMed: 17944491
DOI: 10.1021/BI701703W
Page generated: Wed Aug 14 02:45:54 2024

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