Magnesium in PDB 6mxc: Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp, PDB code: 6mxc was solved by D.Teran, L.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.74 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.021, 107.321, 117.214, 90.00, 96.93, 90.00
R / Rfree (%) 15.2 / 20

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp (pdb code 6mxc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp, PDB code: 6mxc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 6mxc

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Magnesium binding site 1 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:32.0
occ:1.00
 OE2 A:GLU147 2.6 20.5 1.0
O A:VAL85 3.0 13.5 1.0
O A:HOH406 3.0 17.1 0.5
O A:HOH406 3.1 16.2 0.5
O A:HOH556 3.3 50.4 1.0
OD1 A:ASP148 3.4 22.4 1.0
CG A:ASP148 3.4 15.9 1.0
N A:GLY88 3.4 18.9 1.0
CA A:GLY88 3.5 11.1 1.0
OD2 A:ASP148 3.5 17.2 1.0
N A:SER89 3.5 11.8 1.0
CG1 A:VAL85 3.5 13.9 1.0
CD A:GLU147 3.6 18.5 1.0
C A:GLY88 3.7 12.2 1.0
CB A:VAL85 3.8 16.9 1.0
C A:VAL85 3.8 11.9 1.0
OE1 A:GLU147 3.9 22.1 1.0
CB A:SER89 4.2 13.4 1.0
CB A:ASP148 4.2 12.7 1.0
N A:ASP148 4.3 13.3 1.0
C A:LEU86 4.3 19.9 1.0
O A:LEU86 4.3 22.1 1.0
CA A:VAL85 4.4 14.3 1.0
CA A:SER89 4.4 12.1 1.0
O3' A:5GP301 4.5 23.1 1.0
C A:LYS87 4.5 18.3 1.0
N A:LYS87 4.5 15.8 1.0
N A:LEU86 4.6 12.4 1.0
O A:GLY88 4.6 18.1 1.0
CA A:LEU86 4.8 13.6 1.0
CA A:ASP148 4.9 13.1 1.0

Magnesium binding site 2 out of 11 in 6mxc

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Magnesium binding site 2 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:39.3
occ:1.00
 O A:HOH556 2.4 50.4 1.0
O A:HOH545 2.5 37.0 1.0
O A:HOH413 2.7 36.2 1.0
O A:HOH406 3.2 17.1 0.5
NH1 A:ARG214 3.5 16.1 1.0
N A:GLY88 3.6 18.9 1.0
NH2 A:ARG214 3.7 18.0 1.0
OE2 A:GLU208 3.7 24.6 1.0
O A:HOH403 3.8 3.9 0.5
CA A:GLY88 3.8 11.1 1.0
CZ A:ARG214 4.1 20.9 1.0
O A:HOH403 4.2 3.2 0.5
N A:LYS87 4.3 15.8 1.0
C A:LYS87 4.4 18.3 1.0
CD A:GLU208 4.5 22.0 1.0
CB A:LYS87 4.5 13.0 1.0
O2' A:5GP301 4.6 23.0 1.0
CA A:LYS87 4.6 12.9 1.0
OD1 A:ASP148 4.7 22.4 1.0
CG A:GLU208 4.8 18.0 1.0
O A:HOH404 4.9 49.8 1.0

Magnesium binding site 3 out of 11 in 6mxc

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Magnesium binding site 3 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:41.2
occ:1.00
 O B:HOH467 2.2 34.5 1.0
O B:HOH450 2.8 38.0 1.0
N B:LYS87 3.1 10.8 1.0
O B:HOH495 3.3 40.9 1.0
O B:HOH516 3.5 25.0 1.0
CB B:LYS87 3.7 11.8 1.0
CG B:LYS87 3.8 16.4 1.0
CA B:LYS87 3.9 11.3 1.0
C B:LEU86 4.0 16.7 1.0
O B:LEU86 4.0 17.9 1.0
NH2 B:ARG113 4.3 42.8 1.0
N B:GLY88 4.4 10.5 1.0
CE B:LYS87 4.4 15.8 1.0
NH2 B:ARG214 4.5 17.7 1.0
O B:ILE114 4.5 55.4 1.0
NE B:ARG113 4.6 43.6 1.0
C B:LYS87 4.6 15.8 1.0
CD B:LYS87 4.7 17.9 1.0
CZ B:ARG113 4.8 43.7 1.0
O B:HOH412 4.9 2.7 0.4

Magnesium binding site 4 out of 11 in 6mxc

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Magnesium binding site 4 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:32.7
occ:1.00
 OE2 B:GLU147 2.4 17.7 1.0
O B:VAL85 2.9 10.2 1.0
O B:HOH495 3.1 40.9 1.0
O B:HOH412 3.2 6.7 0.6
O B:HOH412 3.3 2.7 0.4
CG1 B:VAL85 3.4 12.2 1.0
OD1 B:ASP148 3.4 15.9 1.0
CG B:ASP148 3.4 18.6 1.0
CD B:GLU147 3.4 19.0 1.0
N B:GLY88 3.5 10.5 1.0
OD2 B:ASP148 3.5 21.3 1.0
CA B:GLY88 3.5 13.6 1.0
CB B:VAL85 3.6 12.6 1.0
N B:SER89 3.6 12.2 1.0
OE1 B:GLU147 3.7 19.5 1.0
C B:VAL85 3.7 13.2 1.0
C B:GLY88 3.8 10.8 1.0
CB B:ASP148 4.2 12.4 1.0
CB B:SER89 4.2 17.4 1.0
O3' B:5GP301 4.2 28.9 1.0
N B:ASP148 4.2 10.7 1.0
CA B:VAL85 4.3 13.4 1.0
O B:LEU86 4.4 17.9 1.0
C B:LEU86 4.4 16.7 1.0
CA B:SER89 4.5 13.6 1.0
C B:LYS87 4.6 15.8 1.0
N B:LEU86 4.6 12.1 1.0
N B:LYS87 4.7 10.8 1.0
CG B:GLU147 4.8 14.2 1.0
O B:GLY88 4.8 13.8 1.0
CG2 B:VAL85 4.8 11.3 1.0
CA B:ASP148 4.9 12.0 1.0
CA B:LEU86 4.9 18.0 1.0

Magnesium binding site 5 out of 11 in 6mxc

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Magnesium binding site 5 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:31.8
occ:1.00
 OE2 C:GLU147 2.6 22.6 1.0
O C:HOH423 2.7 18.0 0.4
O C:VAL85 2.9 10.6 1.0
OG C:SER89 3.1 14.5 0.5
O C:HOH423 3.1 15.2 0.6
OD1 C:ASP148 3.4 24.5 1.0
N C:GLY88 3.4 17.0 1.0
OD2 C:ASP148 3.4 34.0 1.0
CG C:ASP148 3.4 26.0 1.0
N C:SER89 3.4 13.9 0.5
N C:SER89 3.4 13.9 0.5
CA C:GLY88 3.6 16.8 1.0
CG1 C:VAL85 3.6 15.7 1.0
CD C:GLU147 3.6 23.5 1.0
C C:VAL85 3.7 12.1 1.0
C C:GLY88 3.8 16.0 1.0
CB C:VAL85 3.9 13.4 1.0
OE1 C:GLU147 3.9 20.9 1.0
CB C:SER89 4.1 13.6 0.5
CB C:SER89 4.1 13.4 0.5
O C:LEU86 4.1 19.3 1.0
C C:LEU86 4.2 17.2 1.0
CB C:ASP148 4.3 17.6 1.0
N C:ASP148 4.3 13.8 1.0
CA C:SER89 4.3 13.1 0.5
CA C:SER89 4.3 13.0 0.5
CA C:VAL85 4.4 12.6 1.0
C C:LYS87 4.4 16.9 1.0
N C:LYS87 4.5 12.1 1.0
N C:LEU86 4.6 14.4 1.0
CA C:LEU86 4.7 17.0 1.0
O2' C:5GP301 4.8 33.9 1.0
O C:GLY88 4.9 20.3 1.0
O C:HOH415 4.9 5.8 0.3
CA C:ASP148 4.9 15.8 1.0
CG C:GLU147 5.0 18.2 1.0

Magnesium binding site 6 out of 11 in 6mxc

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Magnesium binding site 6 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:51.0
occ:1.00
 O D:HOH525 1.8 43.1 1.0
O D:HOH555 2.5 45.2 1.0
O D:HOH484 3.1 28.1 1.0
O D:HOH465 3.2 37.8 1.0
O D:HOH536 3.6 41.6 1.0
N D:LYS87 3.9 11.1 1.0
O D:HOH414 4.0 1.8 0.3
CB D:LYS87 4.4 13.2 1.0
N D:GLY88 4.5 15.8 1.0
O D:LEU86 4.6 19.0 1.0
O D:ILE114 4.6 51.5 1.0
CA D:LYS87 4.7 14.2 1.0
C D:LEU86 4.7 18.2 1.0
CG D:LYS87 4.7 13.2 1.0
NH2 D:ARG214 4.9 18.6 1.0
OE1 D:GLU208 5.0 16.6 1.0

Magnesium binding site 7 out of 11 in 6mxc

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Magnesium binding site 7 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:36.3
occ:1.00
 OE2 D:GLU147 2.5 22.9 1.0
O D:VAL85 3.0 11.1 1.0
O D:HOH465 3.0 37.8 1.0
O D:HOH414 3.1 16.7 0.7
O D:HOH414 3.3 1.8 0.3
OD1 D:ASP148 3.3 15.8 1.0
CG1 D:VAL85 3.4 15.7 1.0
CG D:ASP148 3.4 16.2 1.0
CD D:GLU147 3.5 22.1 1.0
N D:GLY88 3.5 15.8 1.0
OD2 D:ASP148 3.5 17.0 1.0
CA D:GLY88 3.5 16.5 1.0
CB D:VAL85 3.6 16.7 1.0
N D:SER89 3.6 10.9 1.0
C D:VAL85 3.8 16.0 1.0
OE1 D:GLU147 3.8 25.8 1.0
C D:GLY88 3.8 16.1 1.0
CB D:ASP148 4.2 11.8 1.0
CB D:SER89 4.3 15.1 1.0
N D:ASP148 4.3 15.9 1.0
CA D:VAL85 4.3 15.8 1.0
O D:LEU86 4.3 19.0 1.0
O3' D:5GP301 4.4 20.6 1.0
C D:LEU86 4.4 18.2 1.0
CA D:SER89 4.5 13.9 1.0
C D:LYS87 4.6 15.8 1.0
N D:LEU86 4.6 11.9 1.0
N D:LYS87 4.7 11.1 1.0
O D:GLY88 4.8 14.0 1.0
CA D:LEU86 4.8 18.5 1.0
CG D:GLU147 4.8 19.5 1.0
CG2 D:VAL85 4.9 13.6 1.0
CA D:ASP148 4.9 14.4 1.0

Magnesium binding site 8 out of 11 in 6mxc

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Magnesium binding site 8 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:44.0
occ:1.00
 O E:HOH519 2.4 42.0 1.0
O E:HOH524 3.0 34.8 1.0
N E:LYS87 3.1 13.1 1.0
O E:HOH490 3.3 35.6 1.0
O E:HOH539 3.4 48.7 1.0
CB E:LYS87 3.6 12.8 1.0
CA E:LYS87 3.9 15.1 1.0
CG E:LYS87 4.0 12.8 1.0
C E:LEU86 4.1 15.2 1.0
O E:LEU86 4.1 15.6 1.0
N E:GLY88 4.2 13.5 1.0
O E:ILE114 4.4 32.8 1.0
CE E:LYS87 4.4 17.2 1.0
O E:HOH431 4.5 7.8 0.5
C E:LYS87 4.5 13.8 1.0
NH2 E:ARG113 4.5 28.5 1.0
NH2 E:ARG214 4.7 25.9 1.0
NE E:ARG113 4.8 29.4 1.0
CD E:LYS87 4.9 13.9 1.0
O E:HOH582 4.9 46.3 1.0

Magnesium binding site 9 out of 11 in 6mxc

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Magnesium binding site 9 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:34.7
occ:1.00
 OE2 E:GLU147 2.4 24.3 1.0
O E:VAL85 2.9 13.4 1.0
O E:HOH539 3.1 48.7 1.0
CG1 E:VAL85 3.2 15.2 1.0
OG E:SER89 3.4 16.6 0.5
N E:GLY88 3.5 13.5 1.0
CB E:VAL85 3.5 15.4 1.0
CD E:GLU147 3.5 28.9 1.0
O E:HOH431 3.5 17.0 0.5
CA E:GLY88 3.5 12.4 1.0
O E:HOH431 3.5 7.8 0.5
OD1 E:ASP148 3.5 17.8 1.0
CG E:ASP148 3.6 19.7 1.0
N E:SER89 3.6 13.0 0.5
N E:SER89 3.6 13.0 0.5
C E:VAL85 3.6 15.1 1.0
OD2 E:ASP148 3.7 22.9 1.0
OE1 E:GLU147 3.8 31.2 1.0
C E:GLY88 3.9 13.7 1.0
CA E:VAL85 4.2 13.5 1.0
CB E:SER89 4.2 13.6 0.5
N E:ASP148 4.2 17.0 1.0
CB E:SER89 4.3 13.5 0.5
CB E:ASP148 4.3 16.8 1.0
O E:LEU86 4.4 15.6 1.0
C E:LEU86 4.4 15.2 1.0
CA E:SER89 4.5 13.1 0.5
O3' E:5GP301 4.5 19.9 1.0
N E:LEU86 4.5 14.1 1.0
CA E:SER89 4.5 13.0 0.5
C E:LYS87 4.6 13.8 1.0
N E:LYS87 4.7 13.1 1.0
CG2 E:VAL85 4.8 14.9 1.0
CA E:LEU86 4.8 15.3 1.0
CG E:GLU147 4.8 28.0 1.0
O E:GLY88 4.8 15.1 1.0
CA E:ASP148 4.9 14.8 1.0
CA E:GLU147 4.9 20.5 1.0
N E:VAL85 5.0 12.9 1.0

Magnesium binding site 10 out of 11 in 6mxc

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Magnesium binding site 10 out of 11 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp


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 Trypanosoma Brucei Hypoxanthine-Guanine-Xanthine Phosphoribosyltranferase in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:53.0
occ:1.00
 O F:HOH556 2.2 39.6 1.0
O F:HOH511 2.4 27.2 1.0
O F:HOH410 2.7 12.1 0.6
N F:GLY88 3.1 12.8 1.0
N F:LYS87 3.1 13.1 1.0
O F:HOH540 3.2 37.4 1.0
CA F:GLY88 3.8 12.8 1.0
C F:LEU86 3.9 15.6 1.0
CA F:LYS87 3.9 12.6 1.0
C F:LYS87 3.9 15.9 1.0
O F:LEU86 3.9 17.7 1.0
MG F:MG303 4.2 34.2 1.0
CB F:LYS87 4.2 13.7 1.0
NH1 F:ARG214 4.6 19.7 1.0
OD2 F:ASP148 4.7 24.3 1.0
O F:HOH418 4.7 37.9 1.0
O F:HOH456 4.7 2.4 0.5
O F:HOH410 4.8 10.9 0.5
O2' F:5GP301 4.8 22.7 1.0
NH2 F:ARG214 4.9 20.1 1.0
CG F:LYS87 4.9 13.7 1.0

Reference:

D.Teran, E.Dolezelova, D.T.Keough, D.Hockova, A.Zikova, L.W.Guddat. Crystal Structures of Trypanosoma Brucei Hypoxanthine - Guanine - Xanthine Phosphoribosyltransferase in Complex with Imp, Gmp and Xmp. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31287615
DOI: 10.1111/FEBS.14987
Page generated: Mon Dec 14 23:38:35 2020

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