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Magnesium in PDB 2qjj: Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans, PDB code: 2qjj 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) 23.16 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 117.465, 167.711, 166.441, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans (pdb code 2qjj). 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, PDB code: 2qjj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2qjj

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Magnesium binding site 1 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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

b:19.8
occ:1.00
OD2 A:ASP210 2.2 5.9 1.0
O A:HOH1219 2.3 8.9 1.0
OE1 A:GLU262 2.3 7.0 1.0
O A:HOH1220 2.3 13.4 1.0
OE1 A:GLU236 2.3 7.1 1.0
O A:HOH1221 2.4 19.3 1.0
CD A:GLU262 3.0 7.5 1.0
CG A:ASP210 3.2 8.2 1.0
OE2 A:GLU262 3.2 8.4 1.0
CD A:GLU236 3.3 9.3 1.0
OD1 A:ASP210 3.5 6.9 1.0
CD2 A:HIS212 3.9 18.4 1.0
NH2 A:ARG283 3.9 8.6 1.0
O A:HOH1020 3.9 6.9 1.0
OE2 A:GLU236 4.0 6.5 1.0
NE2 A:HIS212 4.1 19.5 1.0
OD2 A:ASP237 4.1 7.6 1.0
CG A:GLU236 4.2 7.2 1.0
O A:HOH1083 4.2 11.9 1.0
OH A:TYR159 4.3 23.6 1.0
O A:HOH1018 4.3 6.1 1.0
CG A:GLU262 4.4 6.8 1.0
CB A:ASP210 4.5 6.7 1.0
OH B:TYR75 4.5 8.3 1.0
NH1 A:ARG147 4.5 14.8 1.0
CG A:ASP237 4.8 7.1 1.0
CZ A:TYR159 4.8 22.5 1.0
CZ A:ARG283 4.9 10.3 1.0
CG A:HIS212 5.0 17.2 1.0

Magnesium binding site 2 out of 4 in 2qjj

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Magnesium binding site 2 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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

b:17.0
occ:1.00
OD2 B:ASP210 2.2 8.0 1.0
OE1 B:GLU262 2.2 6.6 1.0
O B:HOH1218 2.3 11.6 1.0
OE1 B:GLU236 2.3 9.8 1.0
O B:HOH1217 2.3 14.2 1.0
O B:HOH1219 2.4 14.7 1.0
CD B:GLU262 3.0 8.4 1.0
CG B:ASP210 3.2 9.3 1.0
OE2 B:GLU262 3.2 9.6 1.0
CD B:GLU236 3.2 10.0 1.0
OD1 B:ASP210 3.5 7.5 1.0
NH2 B:ARG283 3.9 8.5 1.0
CD2 B:HIS212 3.9 19.4 1.0
OE2 B:GLU236 3.9 8.7 1.0
O B:HOH1018 4.0 7.3 1.0
NE2 B:HIS212 4.1 19.6 1.0
OD2 B:ASP237 4.1 6.6 1.0
CG B:GLU236 4.2 7.2 1.0
OH B:TYR159 4.2 24.5 1.0
O B:HOH1015 4.2 6.3 1.0
O B:HOH1073 4.3 12.3 1.0
CG B:GLU262 4.4 7.2 1.0
CB B:ASP210 4.5 9.1 1.0
OH A:TYR75 4.6 10.4 1.0
NH1 B:ARG147 4.6 16.1 1.0
CZ B:TYR159 4.7 21.9 1.0
CG B:ASP237 4.7 6.4 1.0
CZ B:ARG283 4.9 7.7 1.0
CE2 B:TYR159 4.9 20.6 1.0
NE B:ARG283 5.0 9.0 1.0

Magnesium binding site 3 out of 4 in 2qjj

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Magnesium binding site 3 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:16.6
occ:1.00
O C:HOH1213 2.2 10.5 1.0
OD2 C:ASP210 2.2 6.0 1.0
OE1 C:GLU262 2.2 6.6 1.0
OE1 C:GLU236 2.3 8.1 1.0
O C:HOH1214 2.3 11.2 1.0
O C:HOH1212 2.3 10.4 1.0
CD C:GLU262 3.0 8.1 1.0
CG C:ASP210 3.1 9.7 1.0
OE2 C:GLU262 3.2 10.1 1.0
CD C:GLU236 3.3 9.6 1.0
OD1 C:ASP210 3.4 8.2 1.0
OE2 C:GLU236 3.9 7.2 1.0
NH2 C:ARG283 4.0 8.3 1.0
O C:HOH1013 4.1 7.0 1.0
OD2 C:ASP237 4.1 6.2 1.0
NE2 C:HIS212 4.1 22.5 1.0
CG C:GLU236 4.1 8.2 1.0
CD2 C:HIS212 4.2 20.3 1.0
O C:HOH1017 4.3 5.8 1.0
CG C:GLU262 4.4 6.9 1.0
O C:HOH1044 4.4 8.8 1.0
NH1 C:ARG147 4.5 16.8 1.0
CB C:ASP210 4.5 7.8 1.0
OH D:TYR75 4.5 8.9 1.0
CG C:ASP237 4.7 8.3 1.0
CE1 C:HIS212 4.8 22.3 1.0
O C:HOH1206 4.9 23.6 1.0
CZ C:ARG283 5.0 9.4 1.0

Magnesium binding site 4 out of 4 in 2qjj

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Magnesium binding site 4 out of 4 in the Crystal Structure of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:20.7
occ:1.00
OD2 D:ASP210 2.2 5.7 1.0
OE1 D:GLU262 2.2 8.9 1.0
O D:HOH1212 2.2 8.3 1.0
O D:HOH1211 2.3 9.1 1.0
OE1 D:GLU236 2.3 6.0 1.0
O D:HOH1213 2.4 14.2 1.0
CD D:GLU262 3.0 10.4 1.0
CG D:ASP210 3.1 7.8 1.0
OE2 D:GLU262 3.2 10.9 1.0
CD D:GLU236 3.3 6.6 1.0
OD1 D:ASP210 3.4 7.5 1.0
NH2 D:ARG283 4.0 8.9 1.0
OE2 D:GLU236 4.0 5.3 1.0
O D:HOH1005 4.1 5.5 1.0
OD2 D:ASP237 4.1 6.2 1.0
O D:HOH1025 4.2 7.3 1.0
CG D:GLU236 4.2 6.1 1.0
CD2 D:HIS212 4.3 18.6 1.0
NE2 D:HIS212 4.3 22.8 1.0
O D:HOH1161 4.4 15.0 1.0
CG D:GLU262 4.4 7.0 1.0
OH C:TYR75 4.5 9.1 1.0
NH1 D:ARG147 4.5 15.2 1.0
CB D:ASP210 4.5 7.2 1.0
CG D:ASP237 4.7 6.4 1.0
CZ D:ARG283 5.0 10.4 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 02:45:16 2024

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