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Magnesium in PDB 1r2r: Crystal Structure of Rabbit Muscle Triosephosphate Isomerase

Enzymatic activity of Crystal Structure of Rabbit Muscle Triosephosphate Isomerase

All present enzymatic activity of Crystal Structure of Rabbit Muscle Triosephosphate Isomerase:
5.3.1.1;

Protein crystallography data

The structure of Crystal Structure of Rabbit Muscle Triosephosphate Isomerase, PDB code: 1r2r was solved by R.Aparicio, S.T.Ferreira, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.79 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.550, 75.952, 166.010, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase (pdb code 1r2r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase, PDB code: 1r2r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1r2r

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Magnesium binding site 1 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg257

b:35.8
occ:1.00
 O B:HOH822 2.2 39.8 1.0
O B:HOH538 2.2 35.6 1.0
NE2 B:GLN146 2.9 11.0 1.0
O B:HOH586 3.1 21.6 1.0
O B:HOH855 3.2 28.7 1.0
NH1 B:ARG99 3.3 11.4 1.0
OD2 B:ASP106 3.6 27.3 1.0
OD1 B:ASP106 3.6 21.9 1.0
CG B:GLN146 3.7 8.8 1.0
CD B:GLN146 3.8 9.7 1.0
CG B:ASP106 3.9 18.4 1.0
CD B:ARG99 4.1 8.8 1.0
CZ B:ARG99 4.2 9.1 1.0
O B:HOH833 4.3 23.3 1.0
O B:HOH1167 4.4 34.0 1.0
O D:HOH1371 4.6 39.3 1.0
NE B:ARG99 4.6 8.2 1.0
CE1 B:HIS100 4.8 15.2 1.0
O B:HOH859 4.8 34.1 1.0
CG B:ARG99 4.9 7.7 1.0
OE1 B:GLN146 4.9 9.9 1.0
O B:HOH587 5.0 20.4 1.0

Magnesium binding site 2 out of 9 in 1r2r

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Magnesium binding site 2 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg261

b:35.4
occ:1.00
 O B:HOH1156 2.2 35.8 1.0
O C:HOH836 2.2 38.6 1.0
O C:HOH834 2.2 37.5 1.0
O C:HOH832 2.2 36.7 1.0
O B:HOH838 2.2 36.4 1.0
O B:HOH840 2.2 36.7 1.0
OE2 C:GLU135 4.2 19.2 1.0
OD2 B:ASP198 4.3 12.6 1.0
O B:HOH717 4.3 31.1 1.0
O C:HOH874 4.3 45.2 1.0
OD1 B:ASP198 4.3 15.8 1.0
O B:HOH793 4.3 42.4 1.0
CG B:ASP198 4.8 12.5 1.0

Magnesium binding site 3 out of 9 in 1r2r

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Magnesium binding site 3 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg260

b:29.7
occ:1.00
 O C:HOH824 2.2 28.6 1.0
O C:HOH826 2.2 31.2 1.0
O C:HOH540 2.2 29.9 1.0
O C:HOH830 2.2 31.1 1.0
O C:HOH542 2.2 31.2 1.0
O C:HOH828 2.2 29.8 1.0
O C:SER222 4.4 10.7 1.0
O C:HOH1068 4.4 45.0 1.0
CB C:SER222 4.5 10.6 0.5
CB C:SER222 4.5 10.3 0.5

Magnesium binding site 4 out of 9 in 1r2r

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Magnesium binding site 4 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg263

b:42.8
occ:1.00
 O C:HOH848 2.2 36.4 1.0
O C:HOH846 2.2 42.7 1.0
O B:HOH825 3.5 19.6 1.0
O B:HOH680 3.6 15.0 1.0
O B:HOH719 3.6 24.6 1.0
O B:GLU135 3.9 9.1 1.0
O B:ALA136 4.1 7.6 1.0
O C:HOH1114 4.1 26.3 1.0
CA B:ALA136 4.2 7.4 1.0
O B:HOH866 4.3 19.7 1.0
O C:HOH918 4.3 21.1 1.0
C B:ALA136 4.4 7.3 1.0
O B:HOH818 4.5 38.0 1.0
O C:HOH951 4.5 43.0 1.0
NZ C:LYS68 4.6 16.2 1.0
O B:HOH740 4.6 50.4 1.0
O C:HOH1122 4.8 28.0 1.0
C B:GLU135 4.8 9.6 1.0
O B:HOH741 4.8 37.6 1.0
N B:ALA136 5.0 7.7 1.0

Magnesium binding site 5 out of 9 in 1r2r

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Magnesium binding site 5 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg262

b:41.8
occ:1.00
 O C:HOH844 2.2 44.0 1.0
O C:HOH842 2.2 41.8 1.0
O C:SER96 3.5 8.5 1.0
C C:SER96 3.7 8.6 1.0
OG C:SER96 3.9 14.0 1.0
CA C:GLU97 3.9 8.5 1.0
N C:GLU97 4.0 8.5 1.0
O C:HOH1113 4.0 28.8 1.0
CG2 C:VAL101 4.0 12.0 1.0
CG C:GLU97 4.0 10.3 1.0
CB C:HIS100 4.1 10.8 1.0
CB C:SER96 4.1 9.9 1.0
CG1 C:VAL167 4.5 13.6 1.0
CA C:SER96 4.6 8.6 1.0
CB C:GLU97 4.6 9.0 1.0
N C:VAL101 4.7 10.0 1.0
O C:HOH880 4.7 50.2 1.0
CD2 C:HIS100 4.8 11.9 1.0
C C:HIS100 4.8 11.4 1.0
CG C:HIS100 4.8 11.1 1.0
CG2 C:ILE170 4.8 29.2 1.0
CA C:HIS100 4.9 10.6 1.0

Magnesium binding site 6 out of 9 in 1r2r

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Magnesium binding site 6 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg249

b:25.7
occ:1.00
 O D:HOH1158 2.2 24.8 1.0
O D:HOH850 2.2 22.7 1.0
O B:HOH1160 2.2 27.9 1.0
O D:HOH1164 2.2 28.6 1.0
O B:HOH1166 2.2 29.0 1.0
O D:HOH1162 2.2 27.8 1.0
O B:HOH835 2.7 36.7 1.0
O D:HOH1188 3.9 17.0 1.0
O B:HOH859 3.9 34.1 1.0
O D:HOH1314 3.9 33.4 1.0
O D:HOH1341 4.1 46.0 1.0
O D:HOH1159 4.1 27.4 1.0
O D:HOH1371 4.2 39.3 1.0
O D:ARG99 4.2 9.8 1.0
O D:HOH1134 4.3 38.4 1.0
OD2 D:ASP106 4.3 17.7 0.5
O D:HOH1273 4.4 18.6 0.5
O D:GLU104 4.4 10.8 1.0
O D:HOH1131 4.4 32.7 1.0
ND1 D:HIS100 4.7 14.8 1.0
CE1 D:HIS100 4.8 16.2 1.0
C D:ARG99 5.0 8.9 1.0

Magnesium binding site 7 out of 9 in 1r2r

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Magnesium binding site 7 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg255

b:38.7
occ:1.00
 O D:HOH854 2.2 39.3 1.0
O D:HOH852 2.2 33.4 1.0
O D:HOH1172 3.1 45.6 1.0
NE1 D:TRP191 3.2 13.0 1.0
O D:PHE144 3.7 8.5 1.0
CE2 D:TRP191 4.0 12.0 1.0
CB D:PHE144 4.0 8.1 1.0
CB D:LYS148 4.0 9.0 1.0
C D:PHE144 4.1 7.9 1.0
CZ2 D:TRP191 4.1 12.2 1.0
O D:HOH1135 4.1 49.2 1.0
CD D:LYS148 4.2 15.3 1.0
CD1 D:TRP191 4.2 12.8 1.0
CG D:LYS148 4.4 11.8 1.0
O D:HOH1285 4.4 29.1 1.0
O D:HOH1266 4.5 21.9 1.0
N D:GLU145 4.6 8.0 1.0
CA D:PHE144 4.7 7.9 1.0
CA D:GLU145 4.8 8.5 1.0
O D:HOH1129 4.8 51.5 1.0
OE1 D:GLU145 4.8 16.7 1.0

Magnesium binding site 8 out of 9 in 1r2r

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Magnesium binding site 8 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg256

b:46.3
occ:1.00
 O D:HOH544 2.2 46.4 1.0
O D:HOH546 2.2 40.9 1.0
CG2 D:THR177 3.4 14.8 1.0
O D:THR175 3.8 17.4 1.0
OE1 D:GLN180 3.9 14.2 1.0
O D:HOH1173 4.2 43.1 1.0
CD D:GLN180 4.5 14.7 1.0
NE2 D:GLN180 4.5 18.6 1.0
O D:HOH1388 4.7 57.8 1.0
CB D:THR177 4.8 13.8 1.0
N D:THR177 4.8 13.8 1.0

Magnesium binding site 9 out of 9 in 1r2r

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Magnesium binding site 9 out of 9 in the Crystal Structure of Rabbit Muscle Triosephosphate Isomerase


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 Rabbit Muscle Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg257

b:43.9
occ:1.00
 O D:HOH1168 2.2 44.4 1.0
O D:HOH856 2.2 43.8 1.0
OG D:SER96 3.1 14.6 0.5
O D:SER96 3.6 9.4 1.0
C D:SER96 3.8 7.8 1.0
CG D:GLU97 3.9 9.4 1.0
N D:GLU97 3.9 7.6 1.0
CA D:GLU97 3.9 7.6 1.0
OG D:SER96 4.0 3.7 0.5
O D:HOH1171 4.0 46.7 1.0
O D:HOH1143 4.1 26.1 1.0
CB D:SER96 4.2 9.2 0.5
CB D:SER96 4.2 8.2 0.5
CB D:HIS100 4.2 10.7 1.0
CG2 D:VAL101 4.2 11.7 1.0
CB D:GLU97 4.6 8.1 1.0
CD2 D:HIS100 4.6 11.9 1.0
CA D:SER96 4.6 8.1 1.0
CG D:HIS100 4.8 11.9 1.0
O C:HOH1112 4.9 23.2 1.0
N D:VAL101 4.9 9.5 1.0
CG1 D:VAL167 4.9 10.1 1.0

Reference:

R.Aparicio, S.T.Ferreira, I.Polikarpov. Closed Conformation of the Active Site Loop of Rabbit Muscle Triosephosphate Isomerase in the Absence of Substrate: Evidence of Conformational Heterogeneity. J.Mol.Biol. V. 334 1023 2003.
ISSN: ISSN 0022-2836
PubMed: 14643664
DOI: 10.1016/J.JMB.2003.10.022
Page generated: Tue Aug 13 12:01:44 2024

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