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Magnesium in PDB 3cfx: Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate

Protein crystallography data

The structure of Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate, PDB code: 3cfx was solved by M.Comellas-Bigler, K.Hollenstein, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.500, 51.860, 124.048, 90.00, 116.93, 90.00
R / Rfree (%) 21 / 23.5

Other elements in 3cfx:

The structure of Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate also contains other interesting chemical elements:

Tungsten (W) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate (pdb code 3cfx). 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 M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate, PDB code: 3cfx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3cfx

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Magnesium binding site 1 out of 4 in the Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate


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 M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:26.5
occ:1.00
OD1 A:ASP185 2.0 22.2 1.0
O A:ASP181 2.1 25.4 1.0
O A:HOH1046 2.1 25.9 1.0
O A:HOH902 2.1 27.7 1.0
OE2 A:GLU175 2.2 22.4 1.0
OE1 A:GLU175 2.2 25.0 1.0
CD A:GLU175 2.5 24.3 1.0
C A:ASP181 3.1 25.2 1.0
CG A:ASP185 3.1 20.5 1.0
OD2 A:ASP185 3.7 23.8 1.0
O A:HOH913 3.9 25.0 1.0
N A:MET182 3.9 23.9 1.0
CA A:ASP181 3.9 26.9 1.0
CG A:GLU175 4.0 23.1 1.0
CA A:MET182 4.0 21.9 1.0
O A:HOH1106 4.2 37.5 1.0
N A:ASP185 4.2 20.3 1.0
CB A:ASP181 4.3 29.6 1.0
NE2 A:GLN172 4.4 23.0 1.0
CB A:ASP185 4.4 21.3 1.0
O A:HOH1000 4.4 34.0 1.0
CB A:TYR184 4.5 18.5 1.0
C A:MET182 4.5 20.4 1.0
N A:TYR184 4.6 18.7 1.0
N A:ILE183 4.7 19.9 1.0
CB A:GLU175 4.8 24.8 1.0
CA A:ASP185 4.9 19.1 1.0
CA A:TYR184 5.0 18.8 1.0
SD A:MET182 5.0 27.8 1.0

Magnesium binding site 2 out of 4 in 3cfx

Go back to Magnesium Binding Sites List in 3cfx
Magnesium binding site 2 out of 4 in the Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate


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 M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:32.0
occ:1.00
O A:HOH1036 2.1 33.2 1.0
O A:VAL71 2.1 27.8 1.0
O A:HOH1025 2.1 34.7 1.0
OE2 A:GLU63 2.2 31.6 1.0
OD1 A:ASP70 2.2 35.0 1.0
OE1 A:GLU59 2.3 31.5 1.0
C A:VAL71 3.1 26.5 1.0
CD A:GLU59 3.2 30.1 1.0
CD A:GLU63 3.3 31.9 1.0
N A:VAL71 3.4 27.9 1.0
CG A:ASP70 3.4 35.4 1.0
OE1 A:GLU63 3.7 32.9 1.0
CA A:VAL71 3.8 26.8 1.0
CG A:GLU59 3.9 29.4 1.0
C A:ASP70 3.9 28.6 1.0
OE2 A:GLU59 4.0 28.3 1.0
O A:HOH1064 4.1 42.3 1.0
O A:HOH1047 4.1 26.1 1.0
N A:GLN72 4.2 25.3 1.0
OD2 A:ASP70 4.2 34.8 1.0
CA A:ASP70 4.2 30.1 1.0
CB A:VAL71 4.2 26.6 1.0
CB A:ASP70 4.4 31.4 1.0
CA A:GLN72 4.5 25.8 1.0
CG A:GLU63 4.6 30.6 1.0
CG A:GLN72 4.7 30.3 1.0
O A:ASP70 4.8 27.5 1.0

Magnesium binding site 3 out of 4 in 3cfx

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Magnesium binding site 3 out of 4 in the Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate


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 M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:24.0
occ:1.00
OD1 B:ASP185 2.0 20.7 1.0
O B:HOH905 2.0 29.0 1.0
O B:ASP181 2.1 22.3 1.0
OE1 B:GLU175 2.1 24.2 1.0
OE2 B:GLU175 2.2 22.1 1.0
O B:HOH910 2.2 21.2 1.0
CD B:GLU175 2.4 24.1 1.0
C B:ASP181 3.1 23.5 1.0
CG B:ASP185 3.1 21.3 1.0
OD2 B:ASP185 3.7 23.5 1.0
O B:HOH1082 3.9 24.1 1.0
N B:MET182 3.9 23.7 1.0
CA B:ASP181 4.0 25.3 1.0
CG B:GLU175 4.0 22.8 1.0
CA B:MET182 4.0 22.7 1.0
O B:HOH1084 4.1 42.4 1.0
N B:ASP185 4.2 19.8 1.0
O B:HOH918 4.2 35.4 1.0
O B:HOH1043 4.3 42.3 1.0
OE1 B:GLN172 4.3 21.6 1.0
CB B:ASP181 4.3 28.5 1.0
CB B:ASP185 4.3 20.2 1.0
C B:MET182 4.5 22.6 1.0
CB B:TYR184 4.6 20.3 1.0
N B:TYR184 4.6 20.7 1.0
N B:ILE183 4.7 21.4 1.0
O B:HOH987 4.8 39.4 1.0
CB B:GLU175 4.8 23.4 1.0
CA B:ASP185 4.9 19.2 1.0
SD B:MET182 5.0 28.7 1.0

Magnesium binding site 4 out of 4 in 3cfx

Go back to Magnesium Binding Sites List in 3cfx
Magnesium binding site 4 out of 4 in the Crystal Structure of M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate


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 M. Acetivorans Periplasmic Binding Protein Moda/Wtpa with Bound Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:40.8
occ:1.00
OD2 B:ASP70 2.0 39.7 1.0
OE1 B:GLU59 2.2 37.7 1.0
O B:VAL71 2.2 32.3 1.0
O B:HOH982 2.3 40.4 1.0
O B:HOH944 2.3 37.0 1.0
OE2 B:GLU63 2.3 39.8 1.0
C B:VAL71 3.1 30.9 1.0
N B:VAL71 3.3 32.7 1.0
CG B:ASP70 3.3 39.2 1.0
CD B:GLU59 3.3 39.4 1.0
CD B:GLU63 3.4 40.7 1.0
CA B:VAL71 3.7 32.2 1.0
C B:ASP70 3.8 33.2 1.0
OE1 B:GLU63 3.9 41.1 1.0
CG B:GLU59 3.9 37.6 1.0
OD1 B:ASP70 4.0 41.0 1.0
CA B:ASP70 4.1 36.0 1.0
N B:GLN72 4.2 30.0 1.0
O B:HOH1037 4.2 39.3 1.0
CB B:VAL71 4.2 31.5 1.0
OE2 B:GLU59 4.3 38.3 1.0
O B:HOH1030 4.3 35.2 1.0
CB B:ASP70 4.3 37.2 1.0
CA B:GLN72 4.5 30.0 1.0
CG B:GLU63 4.6 40.4 1.0
O B:ASP70 4.7 32.9 1.0
CG B:GLN72 5.0 31.6 1.0

Reference:

K.Hollenstein, M.Comellas-Bigler, L.E.Bevers, M.C.Feiters, W.Meyer-Klaucke, P.L.Hagedoorn, K.P.Locher. Distorted Octahedral Coordination of Tungstate in A Subfamily of Specific Binding Proteins. J.Biol.Inorg.Chem. V. 14 663 2009.
ISSN: ISSN 0949-8257
PubMed: 19234723
DOI: 10.1007/S00775-009-0479-7
Page generated: Mon Dec 14 08:00:48 2020

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