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Magnesium in PDB 3vzy: Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168

Protein crystallography data

The structure of Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168, PDB code: 3vzy was solved by F.Ren, X.Feng, T.P.Ko, C.H.Huang, Y.Hu, H.C.Chan, Y.L.Liu, K.Wang, C.C.Chen, X.Pang, M.He, Y.Li, E.Oldfield, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.89 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.919, 55.846, 76.686, 90.00, 108.82, 90.00
R / Rfree (%) 17.5 / 21.5

Other elements in 3vzy:

The structure of Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 (pdb code 3vzy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168, PDB code: 3vzy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3vzy

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Magnesium binding site 1 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:15.5
occ:1.00
 O A:PHE58 2.3 13.3 1.0
O A:HOH830 2.3 19.3 1.0
O A:ARG56 2.4 13.8 1.0
O A:HOH973 2.4 22.3 1.0
O A:HOH831 2.4 15.0 1.0
O A:HOH832 2.5 13.3 1.0
MG A:MG706 3.2 27.0 1.0
C A:ARG56 3.3 14.0 1.0
C A:PHE58 3.4 11.2 1.0
N A:PHE58 3.8 12.1 1.0
O A:HOH1042 3.9 27.8 1.0
CA A:ARG56 3.9 14.5 1.0
OD2 A:ASP77 4.0 16.9 1.0
O A:VAL60 4.1 11.4 1.0
O A:VAL55 4.2 15.0 1.0
CA A:PHE58 4.3 12.4 1.0
C A:ARG57 4.3 13.5 1.0
N A:ARG57 4.3 14.4 1.0
N A:LEU59 4.4 11.2 1.0
CA A:LEU59 4.4 11.7 1.0
O A:HOH829 4.5 21.2 1.0
C A:LEU59 4.5 12.0 1.0
O A:LEU59 4.6 13.8 1.0
CA A:ARG57 4.6 15.2 1.0
OD1 A:ASP77 4.7 16.5 1.0
CG A:ASP77 4.8 16.4 1.0
CB A:ARG56 4.8 13.8 1.0
SG A:CYS62 4.9 13.9 1.0
O A:ARG57 4.9 14.3 1.0
O A:HOH833 4.9 18.4 1.0

Magnesium binding site 2 out of 10 in 3vzy

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Magnesium binding site 2 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:26.3
occ:1.00
 O A:HOH1089 2.2 38.3 1.0
OD1 A:ASP203 2.4 18.4 1.0
O A:HOH816 2.4 20.6 1.0
O A:HOH1012 2.5 28.4 1.0
O A:HOH966 2.5 24.6 1.0
O A:HOH817 2.6 23.8 1.0
CG A:ASP203 3.3 17.0 1.0
MG A:MG705 3.5 26.7 1.0
CB A:ASP203 3.6 13.3 1.0
CA A:ASP203 3.9 13.5 1.0
O A:HOH1010 4.0 40.9 1.0
O A:HOH818 4.0 20.4 1.0
NZ A:LYS175 4.0 26.6 1.0
O A:HOH968 4.2 35.0 1.0
O A:HOH1030 4.2 36.7 1.0
OD2 A:ASP203 4.3 17.7 1.0
O A:HOH967 4.5 41.2 1.0
O A:HOH1057 4.5 36.5 1.0
O A:HOH842 4.5 13.9 1.0
O A:HOH815 4.6 19.8 1.0
O A:ASP203 4.6 14.7 1.0
O A:HOH1040 4.7 36.0 1.0
C A:ASP203 4.8 12.6 1.0
CE A:LYS175 4.9 23.4 1.0
O A:HOH969 5.0 26.7 1.0
N A:ASP203 5.0 13.1 1.0

Magnesium binding site 3 out of 10 in 3vzy

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Magnesium binding site 3 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:26.6
occ:1.00
 O A:HOH1043 2.4 33.3 1.0
O A:HOH972 2.6 24.4 1.0
O A:HOH1078 2.6 31.4 1.0
O A:HOH978 2.7 23.6 1.0
O A:GLY39 2.7 28.4 1.0
O A:HOH870 2.8 24.1 1.0
O A:HOH1013 3.4 30.0 1.0
CB A:SER40 3.8 34.3 1.0
C A:GLY39 3.8 29.3 1.0
O A:HOH1081 3.8 31.1 1.0
O A:HOH1014 3.9 42.2 1.0
CA A:SER40 4.0 33.9 1.0
O A:HOH868 4.2 21.4 1.0
OG A:SER40 4.3 34.1 1.0
O A:HOH869 4.3 33.4 1.0
O A:HOH874 4.3 16.8 1.0
N A:SER40 4.4 31.0 1.0
O A:HOH872 4.4 20.5 1.0
OG A:SER162 4.8 23.9 1.0
OE2 A:GLU160 4.9 28.2 1.0
N A:GLY39 4.9 22.7 1.0
CA A:GLY39 5.0 26.4 1.0

Magnesium binding site 4 out of 10 in 3vzy

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Magnesium binding site 4 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:31.1
occ:1.00
 O A:HOH941 2.3 23.1 1.0
O A:HOH1042 2.3 27.8 1.0
O A:HOH974 2.4 22.9 1.0
O A:HOH1018 2.4 37.2 1.0
O A:HOH975 2.6 32.5 1.0
O A:GLY75 3.8 16.8 1.0
NE A:ARG56 3.9 24.3 1.0
O A:HOH830 3.9 19.3 1.0
NH2 A:ARG56 4.1 28.7 1.0
O A:HOH834 4.2 32.6 1.0
CZ A:ARG56 4.5 26.8 1.0
C A:GLY75 4.7 15.3 1.0
CB A:ARG56 4.7 13.8 1.0
CD A:ARG56 4.9 24.3 1.0
O A:HOH1020 4.9 31.4 1.0
CA A:GLY75 5.0 14.8 1.0

Magnesium binding site 5 out of 10 in 3vzy

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Magnesium binding site 5 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:26.7
occ:1.00
 O A:THR5 2.3 16.5 1.0
O A:HOH819 2.3 37.5 1.0
O A:HOH816 2.4 20.6 1.0
O A:HOH1030 2.4 36.7 1.0
O A:HOH818 2.5 20.4 1.0
O A:HOH966 2.5 24.6 1.0
C A:THR5 3.5 17.1 1.0
MG A:MG702 3.5 26.3 1.0
O A:HOH1029 3.8 45.9 1.0
O A:HOH842 4.0 13.9 1.0
O A:HOH817 4.0 23.8 1.0
O A:HOH1011 4.0 38.1 1.0
O A:HOH1012 4.1 28.4 1.0
CA A:GLU6 4.3 16.6 1.0
N A:GLU6 4.3 14.5 1.0
O A:HOH1057 4.4 36.5 1.0
O A:HOH815 4.4 19.8 1.0
OE1 A:GLU6 4.4 37.4 1.0
CA A:THR5 4.4 14.9 1.0
OE2 A:GLU6 4.5 37.3 1.0
CD A:GLU6 4.6 33.9 1.0
CB A:THR5 4.8 15.8 1.0
C A:GLU6 4.8 15.9 1.0
O A:TRP7 4.9 12.1 1.0

Magnesium binding site 6 out of 10 in 3vzy

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Magnesium binding site 6 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg706

b:27.0
occ:1.00
 O A:HOH973 2.3 22.3 1.0
O A:HOH833 2.3 18.4 1.0
O A:HOH829 2.4 21.2 1.0
O A:HOH830 2.5 19.3 1.0
O A:HOH832 2.5 13.3 1.0
MG A:MG701 3.2 15.5 1.0
OD1 A:ASP77 3.8 16.5 1.0
OH A:TYR2 4.0 15.4 1.0
OD2 A:ASP77 4.3 16.9 1.0
O A:HOH1042 4.3 27.8 1.0
CG A:ASP77 4.5 16.4 1.0
O A:PHE58 4.5 13.3 1.0
O A:ARG56 4.8 13.8 1.0
O A:LEU59 4.9 13.8 1.0
O A:HOH834 5.0 32.6 1.0

Magnesium binding site 7 out of 10 in 3vzy

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Magnesium binding site 7 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:29.0
occ:1.00
 O B:HOH501 2.2 30.2 1.0
O B:PHE58 2.4 21.7 1.0
O B:HOH467 2.4 21.8 1.0
O B:HOH466 2.4 20.8 1.0
O B:ARG56 2.5 27.8 1.0
O B:HOH502 2.5 32.5 1.0
C B:ARG56 3.4 26.9 1.0
C B:PHE58 3.5 21.6 1.0
CA B:ARG56 3.9 27.0 1.0
O B:HOH471 3.9 39.0 1.0
N B:PHE58 4.0 24.6 1.0
O B:VAL60 4.0 15.5 1.0
OD2 B:ASP77 4.1 19.1 1.0
O B:VAL55 4.1 21.4 1.0
CA B:PHE58 4.3 22.1 1.0
C B:ARG57 4.3 28.1 1.0
O B:HOH545 4.3 43.6 1.0
N B:ARG57 4.4 28.3 1.0
N B:LEU59 4.5 21.5 1.0
OD1 B:ASP77 4.6 19.1 1.0
CA B:LEU59 4.6 23.3 1.0
C B:LEU59 4.7 21.5 1.0
O B:LEU59 4.7 21.1 1.0
O B:ARG57 4.8 29.4 1.0
CA B:ARG57 4.8 29.2 1.0
CB B:ARG56 4.8 29.3 1.0
CG B:ASP77 4.8 18.3 1.0
SG B:CYS62 4.9 22.1 1.0
N B:ARG56 5.0 23.9 1.0

Magnesium binding site 8 out of 10 in 3vzy

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Magnesium binding site 8 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


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 Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:32.2
occ:1.00
 O B:THR5 2.2 23.7 1.0
O B:HOH505 2.4 31.6 1.0
O B:HOH438 2.4 26.8 1.0
O B:HOH434 2.5 29.4 1.0
O B:HOH436 2.6 40.2 1.0
C B:THR5 3.4 21.3 1.0
MG B:MG304 3.4 28.0 1.0
O B:HOH506 3.8 25.8 1.0
O B:HOH504 3.9 36.9 1.0
O B:HOH439 4.0 21.7 1.0
CA B:GLU6 4.2 23.3 1.0
N B:GLU6 4.3 20.1 1.0
CA B:THR5 4.4 21.4 1.0
O B:HOH435 4.5 25.2 1.0
O B:HOH437 4.6 37.8 1.0
CB B:THR5 4.7 22.5 1.0
C B:GLU6 4.7 21.2 1.0
O B:TRP7 4.8 15.5 1.0

Magnesium binding site 9 out of 10 in 3vzy

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Magnesium binding site 9 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:28.0
occ:1.00
 O B:HOH506 2.4 25.8 1.0
O B:HOH434 2.4 29.4 1.0
OD1 B:ASP203 2.4 23.5 1.0
O B:HOH565 2.4 37.3 1.0
O B:HOH505 2.5 31.6 1.0
O B:HOH504 2.6 36.9 1.0
CG B:ASP203 3.3 22.3 1.0
MG B:MG303 3.4 32.2 1.0
CB B:ASP203 3.7 17.5 1.0
O B:HOH433 3.7 43.8 1.0
CA B:ASP203 3.9 17.2 1.0
O B:HOH438 4.0 26.8 1.0
NZ B:LYS175 4.1 31.6 1.0
OD2 B:ASP203 4.3 20.7 1.0
O B:HOH439 4.4 21.7 1.0
O B:HOH435 4.6 25.2 1.0
O B:ASP203 4.6 16.9 1.0
O B:HOH547 4.6 46.5 1.0
C B:ASP203 4.7 15.8 1.0

Magnesium binding site 10 out of 10 in 3vzy

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Magnesium binding site 10 out of 10 in the Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Pcrb Complexed with G1P From Bacillus Subtilis Subap. Subtilis Str. 168 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:28.6
occ:1.00
 OD1 B:ASP46 2.1 21.5 1.0
OE1 B:GLU45 2.4 28.3 1.0
O B:HOH486 3.0 30.1 1.0
CG B:ASP46 3.3 21.6 1.0
CD B:GLU45 3.6 25.1 1.0
O B:HOH485 3.8 27.5 1.0
OD2 B:ASP46 3.9 24.1 1.0
OE2 B:GLU45 4.1 28.1 1.0
CB B:ASP46 4.6 17.6 1.0
N B:ASP46 4.6 14.4 1.0
CA B:ASP46 4.7 14.9 1.0
CG B:GLU45 4.7 20.5 1.0
CB B:GLU45 4.9 15.8 1.0

Reference:

F.Ren, X.Feng, T.P.Ko, C.H.Huang, Y.Hu, H.C.Chan, Y.L.Liu, K.Wang, C.C.Chen, X.Pang, M.He, Y.Li, E.Oldfield, R.T.Guo. Insights Into Tim-Barrel Prenyl Transferase Mechanisms: Crystal Structures of Pcrb From Bacillus Subtilis and Staphylococcus Aureus Chembiochem V. 14 195 2013.
ISSN: ISSN 1439-4227
PubMed: 23322418
DOI: 10.1002/CBIC.201200748
Page generated: Thu Aug 15 13:09:37 2024

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