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Sodium in PDB 3oq8: Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate

Enzymatic activity of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate

All present enzymatic activity of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate, PDB code: 3oq8 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.20 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.500, 136.030, 181.770, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 19.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate (pdb code 3oq8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate, PDB code: 3oq8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3oq8

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Sodium binding site 1 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na460

b:15.5
occ:1.00
 O D:HOH917 2.1 13.1 1.0
O D:SER103 2.3 12.9 1.0
OD1 A:ASP157 2.4 13.8 1.0
O D:HOH534 2.5 16.8 1.0
OD2 A:ASP157 2.8 13.8 1.0
CG A:ASP157 2.9 10.2 1.0
O A:HOH613 3.1 23.9 1.0
C D:SER103 3.4 12.2 1.0
CB D:SER103 3.8 12.6 1.0
O D:GLN102 3.9 12.3 1.0
O A:PHE152 4.0 14.7 1.0
O D:ALA180 4.2 10.2 1.0
CA D:SER103 4.2 12.4 1.0
N D:LEU104 4.3 12.0 1.0
CB A:ASP157 4.3 10.6 1.0
CA D:LEU104 4.3 11.1 1.0
O D:HOH530 4.4 10.6 1.0
CA D:SER181 4.7 12.5 1.0
O D:HOH585 4.7 18.7 1.0
CD2 D:LEU104 4.8 11.8 1.0
C D:GLN102 4.9 12.2 1.0
C D:ALA180 4.9 11.3 1.0
CA A:GLY153 4.9 14.4 1.0
O D:SER181 5.0 14.4 1.0

Sodium binding site 2 out of 9 in 3oq8

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Sodium binding site 2 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:14.1
occ:1.00
 OD2 A:ASP147 2.2 11.6 1.0
O A:HOH949 2.2 4.8 1.0
O A:HOH430 2.3 10.1 1.0
O A:HOH945 2.4 7.2 1.0
O A:HOH580 2.6 10.7 1.0
O A:HOH464 2.8 12.9 1.0
CG A:ASP147 3.2 10.9 1.0
OD1 A:ASP147 3.6 10.6 1.0
OD2 A:ASP101 4.0 11.9 1.0
O3B A:MLA440 4.0 19.7 1.0
O3A A:MLA440 4.0 20.0 1.0
NH1 A:ARG222 4.1 13.6 1.0
NZ A:LYS183 4.1 13.8 1.0
N A:TRP86 4.3 10.3 1.0
N A:GLY85 4.3 9.6 1.0
CE1 A:HIS174 4.3 8.3 1.0
OD1 A:ASP101 4.4 11.6 1.0
CE A:LYS183 4.4 13.7 1.0
C3 A:MLA440 4.5 18.6 1.0
OH A:TYR82 4.5 11.6 1.0
CB A:ASP147 4.5 9.8 1.0
CA A:GLY85 4.5 9.8 1.0
O A:HOH560 4.6 11.8 1.0
CG A:ASP101 4.6 12.9 1.0
CG A:GLU149 4.7 11.0 1.0
OE1 A:GLU176 4.8 11.8 1.0
C A:GLY85 4.8 10.2 1.0
OE2 A:GLU149 4.9 9.6 1.0
CB A:TRP86 4.9 11.2 1.0
NE2 A:HIS174 5.0 6.5 1.0

Sodium binding site 3 out of 9 in 3oq8

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Sodium binding site 3 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na460

b:17.8
occ:1.00
 O C:SER103 2.3 11.2 1.0
O C:HOH537 2.4 11.1 1.0
O B:HOH1117 2.5 19.5 1.0
OD1 B:ASP157 2.5 13.1 1.0
OD2 B:ASP157 2.6 13.2 1.0
O B:HOH1118 2.8 28.2 1.0
CG B:ASP157 2.8 11.5 1.0
C C:SER103 3.4 11.3 1.0
CB C:SER103 3.9 12.2 1.0
O B:PHE152 4.0 14.3 1.0
O B:HOH1170 4.1 26.8 1.0
O C:GLN102 4.2 13.4 1.0
O C:ALA180 4.2 10.3 1.0
O C:HOH444 4.2 5.4 1.0
CA C:SER103 4.2 11.8 1.0
CB B:ASP157 4.3 11.7 1.0
N C:LEU104 4.3 11.1 1.0
CA C:LEU104 4.4 10.3 1.0
CA C:SER181 4.8 13.0 1.0
CA B:GLY153 4.8 14.5 1.0
CD2 C:LEU104 4.9 10.4 1.0
O C:HOH569 5.0 27.9 1.0

Sodium binding site 4 out of 9 in 3oq8

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Sodium binding site 4 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:13.8
occ:1.00
 OD2 B:ASP147 2.3 11.5 1.0
O B:HOH434 2.3 10.8 1.0
O B:HOH431 2.3 11.8 1.0
O B:HOH432 2.4 7.4 1.0
O B:HOH430 2.5 7.9 1.0
O B:HOH542 2.9 11.9 1.0
CG B:ASP147 3.3 12.1 1.0
OD1 B:ASP147 3.6 10.0 1.0
O3B B:MLA440 3.9 20.2 1.0
O3A B:MLA440 4.0 19.3 1.0
NZ B:LYS183 4.0 15.4 1.0
NH1 B:ARG222 4.1 13.4 1.0
OD2 B:ASP101 4.2 13.7 1.0
N B:TRP86 4.2 10.7 1.0
N B:GLY85 4.2 10.5 1.0
CE1 B:HIS174 4.3 9.5 1.0
C3 B:MLA440 4.3 18.9 1.0
OH B:TYR82 4.3 15.1 1.0
CE B:LYS183 4.4 16.2 1.0
OD1 B:ASP101 4.5 13.7 1.0
CA B:GLY85 4.5 10.2 1.0
CB B:ASP147 4.6 10.2 1.0
O B:HOH473 4.7 11.2 1.0
CG B:ASP101 4.8 11.5 1.0
C B:GLY85 4.8 11.2 1.0
OE2 B:GLU149 4.8 12.2 1.0
OE1 B:GLU176 4.8 14.5 1.0
CG B:GLU149 4.8 12.1 1.0
NE2 B:HIS174 4.9 9.8 1.0
CB B:TRP86 5.0 10.8 1.0

Sodium binding site 5 out of 9 in 3oq8

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Sodium binding site 5 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na460

b:18.9
occ:1.00
 O B:HOH697 2.2 14.3 1.0
O B:SER103 2.4 12.8 1.0
O B:HOH961 2.4 22.5 1.0
OD1 C:ASP157 2.5 8.6 1.0
OD2 C:ASP157 2.8 13.0 1.0
CG C:ASP157 2.9 10.7 1.0
O C:HOH643 3.1 16.0 1.0
C B:SER103 3.5 12.2 1.0
O C:PHE152 3.9 14.3 1.0
CB B:SER103 3.9 12.9 1.0
O C:HOH1224 4.1 31.8 1.0
O B:GLN102 4.1 10.6 1.0
O B:ALA180 4.2 11.2 1.0
O C:HOH802 4.3 17.3 1.0
O B:HOH910 4.3 5.8 1.0
CA B:SER103 4.4 12.9 1.0
CB C:ASP157 4.4 10.7 1.0
N B:LEU104 4.4 11.4 1.0
CA B:LEU104 4.5 10.5 1.0
CA C:GLY153 4.7 13.3 1.0
CA B:SER181 4.7 13.1 1.0
C C:PHE152 4.9 12.4 1.0

Sodium binding site 6 out of 9 in 3oq8

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Sodium binding site 6 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:12.4
occ:1.00
 O C:HOH947 2.2 6.3 1.0
OD2 C:ASP147 2.3 11.5 1.0
O C:HOH946 2.3 8.9 1.0
O C:HOH635 2.3 5.5 1.0
O C:HOH527 2.6 10.6 1.0
O C:HOH431 2.9 9.8 1.0
CG C:ASP147 3.2 10.9 1.0
OD1 C:ASP147 3.5 10.7 1.0
O3A C:MLA440 3.9 17.8 1.0
OD2 C:ASP101 4.0 11.1 1.0
NZ C:LYS183 4.0 11.8 1.0
O3B C:MLA440 4.0 19.1 1.0
NH1 C:ARG222 4.1 13.5 1.0
N C:TRP86 4.1 10.1 1.0
CE C:LYS183 4.3 14.1 1.0
OD1 C:ASP101 4.3 10.8 1.0
N C:GLY85 4.3 9.7 1.0
C3 C:MLA440 4.4 17.8 1.0
CE1 C:HIS174 4.4 10.6 1.0
CA C:GLY85 4.5 9.3 1.0
OH C:TYR82 4.5 10.1 1.0
CG C:GLU149 4.5 12.2 1.0
O C:HOH550 4.5 13.6 1.0
CG C:ASP101 4.6 10.7 1.0
CB C:ASP147 4.6 9.5 1.0
OE2 C:GLU149 4.6 11.2 1.0
C C:GLY85 4.7 10.2 1.0
CB C:TRP86 4.8 10.4 1.0
OE2 C:GLU176 4.9 10.0 1.0
CD C:GLU149 5.0 13.4 1.0
CA C:TRP86 5.0 10.1 1.0

Sodium binding site 7 out of 9 in 3oq8

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Sodium binding site 7 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na430

b:29.2
occ:1.00
 O C:HOH1093 2.1 15.5 1.0
O C:HOH580 2.3 9.1 1.0
O C:VAL243 2.5 14.8 1.0
O C:HOH666 2.8 15.2 1.0
O C:HOH1120 3.0 24.8 1.0
C C:VAL243 3.7 15.3 1.0
O C:PRO241 4.2 15.2 1.0
O C:HOH520 4.2 10.5 1.0
O C:GLN240 4.3 14.7 1.0
CD2 C:TYR245 4.4 15.9 1.0
O C:HOH1094 4.5 23.7 1.0
CA C:ASP244 4.5 16.4 1.0
N C:ASP244 4.5 15.6 1.0
N C:VAL243 4.5 14.8 1.0
N C:TYR245 4.6 16.9 1.0
C C:PRO241 4.6 15.0 1.0
CA C:VAL243 4.7 14.4 1.0
CE2 C:TYR245 4.9 16.7 1.0
C C:PHE242 5.0 14.1 1.0

Sodium binding site 8 out of 9 in 3oq8

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Sodium binding site 8 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na460

b:20.7
occ:1.00
 O A:HOH742 2.2 17.0 1.0
O A:SER103 2.4 13.1 1.0
OD1 D:ASP157 2.4 16.3 1.0
O A:HOH1146 2.6 21.9 1.0
OD2 D:ASP157 2.7 14.2 1.0
CG D:ASP157 2.8 14.0 1.0
O D:HOH1013 3.2 28.7 1.0
C A:SER103 3.4 12.2 1.0
O D:PHE152 3.9 13.6 1.0
O A:GLN102 4.0 12.8 1.0
CB A:SER103 4.0 13.2 1.0
CB D:ASP157 4.2 12.5 1.0
O D:HOH795 4.2 34.8 1.0
N A:LEU104 4.3 12.1 1.0
CA A:SER103 4.3 12.9 1.0
O A:HOH469 4.3 5.5 1.0
CA A:LEU104 4.3 11.3 1.0
O A:ALA180 4.4 13.8 1.0
CA A:SER181 4.8 15.2 1.0
CA D:GLY153 4.8 13.8 1.0
CD2 A:LEU104 4.8 10.6 1.0
C D:PHE152 5.0 12.5 1.0
C A:GLN102 5.0 13.3 1.0

Sodium binding site 9 out of 9 in 3oq8

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Sodium binding site 9 out of 9 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:15.5
occ:1.00
 OD2 D:ASP147 2.3 11.6 1.0
O D:HOH948 2.3 6.7 1.0
O D:HOH431 2.3 6.1 1.0
O D:HOH919 2.4 14.3 1.0
O D:HOH448 2.6 11.9 1.0
O D:HOH430 2.9 11.4 1.0
CG D:ASP147 3.2 11.3 1.0
OD1 D:ASP147 3.5 10.5 1.0
NZ D:LYS183 3.9 12.8 1.0
O3A D:MLA440 4.1 17.8 1.0
N D:TRP86 4.1 11.3 1.0
NH1 D:ARG222 4.1 14.3 1.0
OD2 D:ASP101 4.2 13.2 1.0
N D:GLY85 4.2 10.8 1.0
O3B D:MLA440 4.2 18.1 1.0
CE D:LYS183 4.4 14.4 1.0
CA D:GLY85 4.4 11.2 1.0
CE1 D:HIS174 4.4 9.5 1.0
OD1 D:ASP101 4.4 13.5 1.0
OH D:TYR82 4.5 11.7 1.0
CG D:GLU149 4.5 11.6 1.0
CB D:ASP147 4.5 10.1 1.0
C3 D:MLA440 4.6 17.9 1.0
O D:HOH529 4.6 11.5 1.0
C D:GLY85 4.7 10.8 1.0
CG D:ASP101 4.7 12.7 1.0
OE2 D:GLU149 4.7 14.1 1.0
OE1 D:GLU176 4.8 12.4 1.0
CB D:TRP86 5.0 12.2 1.0

Reference:

Ssgcid, A.Gardberg, T.Edwards, B.Staker, L.Stewart. Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to the Product Mimic Malonate To Be Published.
Page generated: Mon Oct 7 12:05:23 2024

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