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Sodium in PDB 2poc: The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans

Enzymatic activity of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans

All present enzymatic activity of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans:
2.6.1.16;

Protein crystallography data

The structure of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans, PDB code: 2poc was solved by J.Raczynska, J.Olchowy, S.Milewski, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.977, 117.832, 99.711, 90.00, 91.60, 90.00
R / Rfree (%) 17.5 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans (pdb code 2poc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans, PDB code: 2poc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2poc

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Sodium binding site 1 out of 4 in the The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5001

b:26.5
occ:1.00
 O A:THR487 2.3 23.4 1.0
O2 A:UD15002 2.3 22.3 1.0
O A:HOH5004 2.3 27.0 1.0
O A:HOH5005 2.5 24.4 1.0
O A:SER484 2.5 26.7 1.0
O A:ARG485 2.9 26.8 1.0
C2 A:UD15002 3.2 22.8 1.0
C A:THR487 3.4 23.7 1.0
C A:ARG485 3.4 26.8 1.0
C A:SER484 3.7 25.6 1.0
N3 A:UD15002 3.7 20.7 1.0
OG1 A:THR487 3.9 19.9 1.0
CA A:ARG485 3.9 27.1 1.0
N A:THR487 3.9 22.9 1.0
C A:HIS488 4.1 23.8 1.0
CA A:THR487 4.2 22.3 1.0
O A:HOH5144 4.2 16.3 0.5
O A:HIS488 4.2 23.0 1.0
N A:GLN486 4.3 26.1 1.0
N A:ARG485 4.3 26.3 1.0
N1 A:UD15002 4.3 21.9 1.0
N A:HIS488 4.4 22.6 1.0
N A:CYS489 4.4 22.8 1.0
O A:HOH5006 4.4 34.4 1.0
C1B A:UD15002 4.5 21.8 1.0
C A:GLN486 4.5 24.5 1.0
CA A:HIS488 4.5 23.1 1.0
CB A:THR487 4.6 22.7 1.0
CA A:CYS489 4.8 21.3 1.0
CA A:GLN486 4.8 25.8 1.0
CA A:SER484 4.9 25.4 1.0
O A:HOH5087 5.0 36.4 1.0
C4 A:UD15002 5.0 22.1 1.0

Sodium binding site 2 out of 4 in 2poc

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Sodium binding site 2 out of 4 in the The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na5002

b:21.3
occ:1.00
 O B:THR487 2.3 20.7 1.0
O B:SER484 2.4 21.0 1.0
O B:HOH5004 2.4 31.8 1.0
O2 B:UD15003 2.4 21.3 1.0
O B:HOH5005 2.4 24.6 1.0
O B:ARG485 2.7 21.1 1.0
C B:ARG485 3.3 20.9 1.0
C2 B:UD15003 3.3 21.5 1.0
C B:THR487 3.4 20.0 1.0
C B:SER484 3.6 21.1 1.0
CA B:ARG485 3.8 20.6 1.0
N3 B:UD15003 3.8 18.9 1.0
N B:THR487 3.9 19.2 1.0
OG1 B:THR487 4.0 19.4 1.0
N B:GLN486 4.1 19.9 1.0
CA B:THR487 4.1 19.7 1.0
N B:ARG485 4.1 20.8 1.0
O B:HIS488 4.2 22.6 1.0
C B:HIS488 4.3 22.4 1.0
O B:HOH5131 4.4 48.9 1.0
N1 B:UD15003 4.4 20.3 1.0
C B:GLN486 4.4 19.6 1.0
N B:HIS488 4.5 20.3 1.0
O B:HOH5078 4.5 29.7 1.0
CB B:THR487 4.6 18.7 1.0
C1B B:UD15003 4.6 22.7 1.0
N B:CYS489 4.6 21.3 1.0
CA B:HIS488 4.7 20.9 1.0
CA B:GLN486 4.8 19.4 1.0
CA B:SER484 4.8 20.6 1.0
CA B:CYS489 4.9 21.4 1.0

Sodium binding site 3 out of 4 in 2poc

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Sodium binding site 3 out of 4 in the The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na5003

b:21.9
occ:1.00
 O C:HOH5006 2.3 33.6 1.0
O C:THR487 2.3 18.8 1.0
O2 C:UD15004 2.4 20.7 1.0
O C:SER484 2.4 19.0 1.0
O C:HOH5005 2.5 27.4 1.0
O C:ARG485 2.8 21.4 1.0
C2 C:UD15004 3.3 20.7 1.0
C C:ARG485 3.3 19.8 1.0
C C:THR487 3.5 18.8 1.0
C C:SER484 3.6 18.3 1.0
CA C:ARG485 3.8 19.3 1.0
N3 C:UD15004 3.8 18.6 1.0
N C:THR487 3.9 18.3 1.0
OG1 C:THR487 3.9 17.9 1.0
CA C:THR487 4.1 18.2 1.0
N C:ARG485 4.2 18.6 1.0
N C:GLN486 4.2 20.1 1.0
O C:HOH5224 4.2 46.5 1.0
O C:HIS488 4.3 20.7 1.0
N1 C:UD15004 4.3 21.2 1.0
C C:HIS488 4.4 20.8 1.0
C C:GLN486 4.4 19.0 1.0
N C:HIS488 4.5 19.1 1.0
C1B C:UD15004 4.6 21.1 1.0
O C:HOH5009 4.6 27.0 1.0
CB C:THR487 4.6 18.1 1.0
N C:CYS489 4.7 19.2 1.0
CA C:HIS488 4.7 19.4 1.0
CA C:GLN486 4.8 19.6 1.0
CA C:SER484 4.8 18.4 1.0

Sodium binding site 4 out of 4 in 2poc

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Sodium binding site 4 out of 4 in the The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Isomerase Domain of Glucosamine-6-Phosphate Synthase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na5004

b:27.0
occ:1.00
 O2 D:UD15005 2.4 21.6 1.0
O D:THR487 2.4 24.9 1.0
O D:SER484 2.5 24.5 1.0
O D:ARG485 2.7 29.2 1.0
C2 D:UD15005 3.2 24.1 1.0
C D:ARG485 3.3 27.8 1.0
C D:THR487 3.5 23.6 1.0
C D:SER484 3.6 25.6 1.0
N3 D:UD15005 3.8 22.1 1.0
CA D:ARG485 3.8 27.9 1.0
OG1 D:THR487 3.9 22.7 1.0
N D:THR487 4.0 24.2 1.0
N D:ARG485 4.2 26.9 1.0
N D:GLN486 4.2 26.4 1.0
CA D:THR487 4.2 23.9 1.0
N1 D:UD15005 4.2 22.1 1.0
O D:HOH5114 4.3 32.3 1.0
O D:HIS488 4.3 22.0 1.0
C D:HIS488 4.3 23.4 1.0
C1B D:UD15005 4.5 23.5 1.0
N D:HIS488 4.5 22.6 1.0
C D:GLN486 4.6 25.7 1.0
N D:CYS489 4.6 21.9 1.0
CB D:THR487 4.6 23.1 1.0
CA D:HIS488 4.7 22.2 1.0
CA D:GLN486 4.8 26.6 1.0
CA D:SER484 4.9 25.1 1.0
CA D:CYS489 4.9 22.2 1.0
C4 D:UD15005 5.0 24.2 1.0

Reference:

J.Raczynska, J.Olchowy, P.V.Konariev, D.I.Svergun, S.Milewski, W.Rypniewski. The Crystal and Solution Studies of Glucosamine-6-Phosphate Synthase From Candida Albicans J.Mol.Biol. V. 372 672 2007.
ISSN: ISSN 0022-2836
PubMed: 17681543
DOI: 10.1016/J.JMB.2007.07.002
Page generated: Sun Aug 17 11:21:21 2025

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