Atomistry » Magnesium » PDB 3p1g-3pio » 3p93
Atomistry »
  Magnesium »
    PDB 3p1g-3pio »
      3p93 »

Magnesium in PDB 3p93: Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate

Protein crystallography data

The structure of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate, PDB code: 3p93 was solved by A.A.Fedorov, E.V.Fedorov, D.Wichelecki, 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) 41.82 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.242, 167.263, 168.863, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate (pdb code 3p93). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate, PDB code: 3p93:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 1 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:17.8
occ:1.00
 OD2 A:ASP213 2.1 15.2 1.0
OE1 A:GLU265 2.1 18.3 1.0
OE1 A:GLU239 2.2 16.9 1.0
O A:HOH1933 2.2 17.6 1.0
O1B A:CS2407 2.3 16.5 1.0
O2 A:CS2407 2.3 20.6 1.0
C1 A:CS2407 3.0 23.8 1.0
CD A:GLU265 3.0 13.8 1.0
CG A:ASP213 3.1 17.0 1.0
C2 A:CS2407 3.1 28.6 1.0
CD A:GLU239 3.2 17.5 1.0
OE2 A:GLU265 3.4 17.4 1.0
OD1 A:ASP213 3.4 14.9 1.0
NH2 A:ARG286 3.8 13.6 1.0
OE2 A:GLU239 3.9 15.3 1.0
O A:HOH442 3.9 16.7 1.0
CD2 A:HIS215 4.0 18.8 1.0
CG A:GLU239 4.1 14.6 1.0
OD2 A:ASP240 4.3 16.6 1.0
NE2 A:HIS215 4.3 22.9 1.0
O A:HOH450 4.3 15.9 1.0
O1A A:CS2407 4.3 27.5 1.0
CB A:ASP213 4.3 19.2 1.0
CG A:GLU265 4.3 13.4 1.0
NH1 A:ARG149 4.4 28.3 1.0
C3 A:CS2407 4.4 27.8 1.0
CG A:ASP240 4.7 16.6 1.0
OH H:TYR77 4.8 15.7 1.0
CZ A:ARG286 4.8 15.3 1.0
NE A:ARG286 4.9 17.3 1.0
CD2 A:HIS315 4.9 16.8 1.0

Magnesium binding site 2 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 2 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:18.8
occ:1.00
 OE1 B:GLU239 2.1 17.5 1.0
OD2 B:ASP213 2.1 18.0 1.0
OE1 B:GLU265 2.2 15.5 1.0
O B:HOH1935 2.2 18.3 1.0
O1B B:CS2407 2.3 15.1 1.0
O2 B:CS2407 2.3 18.8 1.0
C1 B:CS2407 3.0 22.2 1.0
CG B:ASP213 3.0 17.3 1.0
CD B:GLU239 3.1 18.7 1.0
CD B:GLU265 3.1 20.0 1.0
C2 B:CS2407 3.1 26.0 1.0
OE2 B:GLU265 3.3 16.4 1.0
OD1 B:ASP213 3.4 18.4 1.0
OE2 B:GLU239 3.8 18.1 1.0
NH2 B:ARG286 3.8 14.2 1.0
CD2 B:HIS215 4.0 19.4 1.0
O B:HOH412 4.0 17.2 1.0
CG B:GLU239 4.0 15.6 1.0
O B:HOH414 4.0 15.8 1.0
OD2 B:ASP240 4.1 14.7 1.0
CB B:ASP213 4.3 19.8 1.0
O1A B:CS2407 4.3 24.1 1.0
NH1 B:ARG149 4.4 29.8 1.0
CG B:GLU265 4.4 16.8 1.0
C3 B:CS2407 4.4 26.6 1.0
NE2 B:HIS215 4.5 20.5 1.0
CG B:ASP240 4.7 16.9 1.0
OH D:TYR77 4.7 12.3 1.0
CZ B:ARG286 4.8 16.6 1.0
NE B:ARG286 4.8 17.3 1.0
CD2 B:HIS315 5.0 18.6 1.0

Magnesium binding site 3 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 3 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg406

b:18.9
occ:1.00
 OD2 C:ASP213 2.2 19.8 1.0
OE1 C:GLU239 2.2 14.6 1.0
OE1 C:GLU265 2.2 16.9 1.0
O6A C:KDG407 2.3 18.1 1.0
O5 C:KDG407 2.3 15.5 1.0
O C:HOH408 2.4 16.0 1.0
C5 C:KDG407 2.8 25.4 1.0
C6 C:KDG407 2.9 18.9 1.0
CD C:GLU265 3.1 15.8 1.0
CG C:ASP213 3.1 20.7 1.0
CD C:GLU239 3.2 18.3 1.0
OE2 C:GLU265 3.3 15.1 1.0
OD1 C:ASP213 3.4 16.4 1.0
NH2 C:ARG286 3.7 18.7 1.0
OE2 C:GLU239 3.9 18.2 1.0
O C:HOH412 3.9 15.5 1.0
O6B C:KDG407 4.0 28.9 1.0
CD2 C:HIS215 4.1 17.7 1.0
CG C:GLU239 4.2 15.2 1.0
OD2 C:ASP240 4.2 13.0 1.0
O C:HOH420 4.3 17.1 1.0
C4 C:KDG407 4.3 22.6 1.0
NH1 C:ARG149 4.4 25.6 1.0
CB C:ASP213 4.4 19.0 1.0
CG C:GLU265 4.4 12.6 1.0
NE2 C:HIS215 4.5 21.7 1.0
OH G:TYR77 4.6 15.9 1.0
CZ C:ARG286 4.7 18.9 1.0
CG C:ASP240 4.8 17.1 1.0
CD2 C:HIS315 4.8 17.0 1.0
NE C:ARG286 4.9 18.6 1.0
C3 C:KDG407 5.0 22.1 1.0

Magnesium binding site 4 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 4 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg406

b:18.6
occ:1.00
 OD2 D:ASP213 2.1 16.1 1.0
OE1 D:GLU239 2.1 15.8 1.0
OE1 D:GLU265 2.2 16.2 1.0
O D:HOH1934 2.2 14.6 1.0
O6A D:KDG407 2.3 16.1 1.0
O5 D:KDG407 2.4 20.6 1.0
C6 D:KDG407 3.0 25.2 1.0
C5 D:KDG407 3.0 26.2 1.0
CD D:GLU265 3.0 18.6 1.0
CD D:GLU239 3.1 17.8 1.0
CG D:ASP213 3.1 17.6 1.0
OE2 D:GLU265 3.3 14.3 1.0
OD1 D:ASP213 3.5 17.6 1.0
NH2 D:ARG286 3.8 14.4 1.0
OE2 D:GLU239 3.9 18.2 1.0
CD2 D:HIS215 3.9 18.4 1.0
CG D:GLU239 4.0 16.0 1.0
O D:HOH423 4.1 17.9 1.0
OD2 D:ASP240 4.1 14.3 1.0
O D:HOH408 4.1 15.1 1.0
O6B D:KDG407 4.2 30.1 1.0
CB D:ASP213 4.4 16.3 1.0
CG D:GLU265 4.4 16.8 1.0
NE2 D:HIS215 4.4 21.3 1.0
C4 D:KDG407 4.4 28.7 1.0
NH1 D:ARG149 4.5 29.8 1.0
OH B:TYR77 4.6 17.9 1.0
CG D:ASP240 4.7 17.1 1.0
CD2 D:HIS315 4.8 14.8 1.0
CZ D:ARG286 4.8 15.4 1.0
NE D:ARG286 4.9 18.0 1.0
NE2 D:HIS315 4.9 17.6 1.0
C3 D:KDG407 4.9 21.7 1.0

Magnesium binding site 5 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 5 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 5 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg406

b:19.9
occ:1.00
 OE1 E:GLU239 2.1 12.8 1.0
OE1 E:GLU265 2.1 13.8 1.0
O E:HOH1932 2.2 14.2 1.0
OD2 E:ASP213 2.2 15.8 1.0
O1B E:CS2407 2.3 19.2 1.0
O2 E:CS2407 2.3 15.7 1.0
CD E:GLU265 3.0 16.3 1.0
C1 E:CS2407 3.0 23.4 1.0
CD E:GLU239 3.1 15.9 1.0
C2 E:CS2407 3.1 24.4 1.0
CG E:ASP213 3.1 15.4 1.0
OE2 E:GLU265 3.2 17.5 1.0
OD1 E:ASP213 3.4 12.8 1.0
NH2 E:ARG286 3.7 17.0 1.0
OE2 E:GLU239 3.8 14.6 1.0
O E:HOH424 3.9 17.6 1.0
CG E:GLU239 4.0 15.7 1.0
OD2 E:ASP240 4.0 15.9 1.0
O E:HOH425 4.1 14.4 1.0
CD2 E:HIS215 4.2 15.3 1.0
O1A E:CS2407 4.3 27.1 1.0
CG E:GLU265 4.3 14.3 1.0
C3 E:CS2407 4.3 26.2 1.0
CB E:ASP213 4.4 16.3 1.0
NH1 E:ARG149 4.5 22.0 1.0
NE2 E:HIS215 4.6 16.9 1.0
OH F:TYR77 4.7 15.4 1.0
CZ E:ARG286 4.7 15.3 1.0
CG E:ASP240 4.7 16.9 1.0
NE E:ARG286 4.8 15.4 1.0
CD2 E:HIS315 4.9 16.7 1.0
CB E:GLU265 5.0 13.8 1.0
NE2 E:HIS315 5.0 17.6 1.0

Magnesium binding site 6 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 6 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 6 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg406

b:19.2
occ:1.00
 OE1 F:GLU239 2.2 15.8 1.0
O F:HOH1936 2.2 17.5 1.0
OD2 F:ASP213 2.2 16.1 1.0
OE1 F:GLU265 2.2 14.0 1.0
O2 F:CS2407 2.2 19.9 1.0
O1B F:CS2407 2.3 22.6 1.0
C1 F:CS2407 3.0 25.4 1.0
CD F:GLU265 3.1 18.2 1.0
CG F:ASP213 3.1 15.5 1.0
C2 F:CS2407 3.1 26.4 1.0
CD F:GLU239 3.2 17.3 1.0
OE2 F:GLU265 3.3 15.6 1.0
OD1 F:ASP213 3.5 17.9 1.0
NH2 F:ARG286 3.9 15.4 1.0
CD2 F:HIS215 4.0 16.2 1.0
O F:HOH430 4.0 19.1 1.0
OE2 F:GLU239 4.0 17.8 1.0
CG F:GLU239 4.1 14.1 1.0
O F:HOH428 4.1 14.3 1.0
OD2 F:ASP240 4.2 17.4 1.0
O1A F:CS2407 4.3 31.2 1.0
C3 F:CS2407 4.3 26.7 1.0
NE2 F:HIS215 4.4 22.3 1.0
CG F:GLU265 4.4 14.6 1.0
CB F:ASP213 4.4 17.6 1.0
NH1 F:ARG149 4.4 27.3 1.0
OH E:TYR77 4.5 15.6 1.0
CG F:ASP240 4.7 18.5 1.0
CD2 F:HIS315 4.8 15.7 1.0
CZ F:ARG286 4.9 17.0 1.0
NE2 F:HIS315 4.9 20.5 1.0
C4 F:CS2407 5.0 22.6 1.0
NE F:ARG286 5.0 16.3 1.0

Magnesium binding site 7 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 7 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 7 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg406

b:19.2
occ:1.00
 O G:HOH1931 2.2 16.7 1.0
OE1 G:GLU239 2.2 14.5 1.0
OD2 G:ASP213 2.2 18.7 1.0
O5 G:KDG407 2.3 20.6 1.0
OE1 G:GLU265 2.3 17.7 1.0
O6A G:KDG407 2.3 20.1 1.0
C5 G:KDG407 2.9 26.0 1.0
C6 G:KDG407 3.0 22.3 1.0
CD G:GLU265 3.1 17.9 1.0
CG G:ASP213 3.1 20.1 1.0
CD G:GLU239 3.2 15.6 1.0
OE2 G:GLU265 3.3 16.9 1.0
OD1 G:ASP213 3.4 15.7 1.0
NH2 G:ARG286 3.8 14.2 1.0
OE2 G:GLU239 3.9 15.6 1.0
CD2 G:HIS215 3.9 22.7 1.0
O G:HOH409 4.1 13.6 1.0
OD2 G:ASP240 4.1 17.6 1.0
O6B G:KDG407 4.2 26.9 1.0
CG G:GLU239 4.2 14.4 1.0
O G:HOH451 4.3 13.5 1.0
NH1 G:ARG149 4.3 29.1 1.0
NE2 G:HIS215 4.3 19.9 1.0
CB G:ASP213 4.4 17.1 1.0
CG G:GLU265 4.4 17.4 1.0
C4 G:KDG407 4.4 23.5 1.0
OH C:TYR77 4.7 17.6 1.0
CG G:ASP240 4.7 17.0 1.0
CZ G:ARG286 4.9 15.2 1.0
CD2 G:HIS315 5.0 19.2 1.0
C3 G:KDG407 5.0 23.1 1.0

Magnesium binding site 8 out of 8 in 3p93

Go back to Magnesium Binding Sites List in 3p93
Magnesium binding site 8 out of 8 in the Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate 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 8 of Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D- Gluconate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg406

b:17.4
occ:1.00
 OE1 H:GLU265 2.1 15.8 1.0
OE1 H:GLU239 2.1 15.2 1.0
OD2 H:ASP213 2.2 18.7 1.0
O6A H:KDG407 2.2 18.6 1.0
O H:HOH1361 2.3 13.3 1.0
O5 H:KDG407 2.3 14.3 1.0
C6 H:KDG407 2.9 21.4 1.0
C5 H:KDG407 3.0 23.0 1.0
CD H:GLU265 3.0 17.0 1.0
CG H:ASP213 3.1 16.6 1.0
CD H:GLU239 3.1 18.8 1.0
OE2 H:GLU265 3.2 14.4 1.0
OD1 H:ASP213 3.4 14.5 1.0
NH2 H:ARG286 3.8 16.0 1.0
OE2 H:GLU239 3.8 15.4 1.0
O H:HOH411 3.9 15.5 1.0
CG H:GLU239 4.1 15.8 1.0
CD2 H:HIS215 4.1 19.7 1.0
O H:HOH606 4.1 15.8 1.0
O6B H:KDG407 4.1 27.1 1.0
OD2 H:ASP240 4.2 13.6 1.0
CG H:GLU265 4.3 14.8 1.0
CB H:ASP213 4.3 16.4 1.0
C4 H:KDG407 4.4 21.9 1.0
NE2 H:HIS215 4.5 18.0 1.0
NH1 H:ARG149 4.6 23.8 1.0
OH A:TYR77 4.7 12.7 1.0
CG H:ASP240 4.7 18.7 1.0
CZ H:ARG286 4.7 16.3 1.0
NE H:ARG286 4.8 15.6 1.0
CD2 H:HIS315 4.9 20.6 1.0
C3 H:KDG407 5.0 22.4 1.0
CB H:GLU265 5.0 15.8 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.Wichelecki, J.A.Gerlt, S.C.Almo. Crystal Structure of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed with Mg,D-Mannonate and 2-Keto-3-Deoxy-D-Gluconate To Be Published.
Page generated: Mon Aug 11 01:47:08 2025

Last articles

Mg in 7PLH
Mg in 7PJI
Mg in 7PJE
Mg in 7PJF
Mg in 7PH4
Mg in 7PDZ
Mg in 7PH3
Mg in 7PGI
Mg in 7PEM
Mg in 7PDS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy