Atomistry » Sodium » PDB 2ply-2qd6 » 2puv
Atomistry »
  Sodium »
    PDB 2ply-2qd6 »
      2puv »

Sodium in PDB 2puv: 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: 2puv 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) 19.93 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.121, 118.167, 100.137, 90.00, 91.87, 90.00
R / Rfree (%) 17.1 / 21.2

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 2puv). 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: 2puv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2puv

Go back to Sodium Binding Sites List in 2puv
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:24.9
occ:1.00
 O2 A:UD15002 2.3 23.2 1.0
O A:THR487 2.3 20.7 1.0
O A:HOH5013 2.4 23.3 1.0
O A:HOH5012 2.4 25.6 1.0
O A:SER484 2.5 24.3 1.0
O A:ARG485 2.8 22.7 1.0
C2 A:UD15002 3.2 22.9 1.0
C A:ARG485 3.3 23.2 1.0
C A:THR487 3.5 21.3 1.0
C A:SER484 3.7 23.9 1.0
N3 A:UD15002 3.7 21.0 1.0
CA A:ARG485 3.8 24.2 1.0
OG1 A:THR487 3.9 18.4 1.0
N A:THR487 4.0 20.8 1.0
C A:HIS488 4.2 21.4 1.0
O A:HIS488 4.2 21.6 1.0
N A:GLN486 4.2 22.1 1.0
CA A:THR487 4.2 20.3 1.0
N A:ARG485 4.2 23.4 1.0
N1 A:UD15002 4.3 21.8 1.0
O A:HOH5014 4.4 30.5 1.0
N A:CYS489 4.4 20.5 1.0
N A:HIS488 4.4 20.2 1.0
C1B A:UD15002 4.5 22.3 1.0
C A:GLN486 4.5 21.5 1.0
CB A:THR487 4.6 20.4 1.0
CA A:HIS488 4.6 21.2 1.0
CA A:GLN486 4.8 22.3 1.0
CA A:CYS489 4.8 19.1 1.0
CA A:SER484 4.9 23.6 1.0
O A:HOH5248 5.0 29.1 1.0
C4 A:UD15002 5.0 21.4 1.0

Sodium binding site 2 out of 4 in 2puv

Go back to Sodium Binding Sites List in 2puv
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:19.4
occ:1.00
 O B:THR487 2.3 19.1 1.0
O B:HOH5008 2.3 28.5 1.0
O B:SER484 2.4 20.3 1.0
O2 B:UD15003 2.4 19.5 1.0
O B:HOH5009 2.5 26.9 1.0
O B:ARG485 2.6 18.4 1.0
C B:ARG485 3.3 17.7 1.0
C2 B:UD15003 3.4 17.6 1.0
C B:THR487 3.4 17.8 1.0
C B:SER484 3.6 18.6 1.0
CA B:ARG485 3.8 17.3 1.0
N3 B:UD15003 3.8 15.7 1.0
N B:THR487 3.8 17.2 1.0
OG1 B:THR487 4.0 16.9 1.0
N B:GLN486 4.1 17.6 1.0
CA B:THR487 4.1 17.7 1.0
N B:ARG485 4.2 17.7 1.0
O B:HIS488 4.3 19.9 1.0
C B:HIS488 4.3 19.4 1.0
C B:GLN486 4.4 17.9 1.0
N1 B:UD15003 4.4 17.4 1.0
N B:HIS488 4.4 17.1 1.0
O B:HOH5346 4.5 25.1 1.0
CB B:THR487 4.6 16.8 1.0
C1B B:UD15003 4.6 20.9 1.0
N B:CYS489 4.6 17.9 1.0
CA B:HIS488 4.7 18.5 1.0
CA B:GLN486 4.7 17.7 1.0
CA B:SER484 4.8 18.5 1.0
CA B:CYS489 4.9 19.1 1.0
O B:HOH5349 5.0 29.1 1.0

Sodium binding site 3 out of 4 in 2puv

Go back to Sodium Binding Sites List in 2puv
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:20.2
occ:1.00
 O2 C:UD15004 2.3 18.1 1.0
O C:THR487 2.3 17.2 1.0
O C:HOH5011 2.3 30.1 1.0
O C:SER484 2.4 19.2 1.0
O C:HOH5010 2.6 26.4 1.0
O C:ARG485 2.9 19.6 1.0
C2 C:UD15004 3.2 17.1 1.0
C C:THR487 3.4 16.8 1.0
C C:ARG485 3.4 17.0 1.0
C C:SER484 3.6 17.2 1.0
N3 C:UD15004 3.8 16.9 1.0
N C:THR487 3.9 14.9 1.0
CA C:ARG485 3.9 16.0 1.0
OG1 C:THR487 4.0 17.3 1.0
CA C:THR487 4.1 15.7 1.0
O C:HOH5733 4.2 42.3 1.0
O C:HIS488 4.2 16.3 1.0
C C:HIS488 4.2 17.5 1.0
N C:GLN486 4.2 16.6 1.0
N C:ARG485 4.3 16.7 1.0
N1 C:UD15004 4.3 20.0 1.0
N C:HIS488 4.4 15.4 1.0
O C:HOH5021 4.4 25.7 1.0
C C:GLN486 4.5 16.9 1.0
C1B C:UD15004 4.5 18.6 1.0
CA C:HIS488 4.6 16.3 1.0
N C:CYS489 4.6 16.2 1.0
CB C:THR487 4.6 15.6 1.0
CA C:SER484 4.8 17.3 1.0
CA C:GLN486 4.8 16.1 1.0
CA C:CYS489 4.9 16.5 1.0

Sodium binding site 4 out of 4 in 2puv

Go back to Sodium Binding Sites List in 2puv
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:23.3
occ:1.00
 O D:SER484 2.4 22.8 1.0
O2 D:UD15005 2.4 17.6 1.0
O D:THR487 2.4 21.3 1.0
O D:ARG485 2.6 24.2 1.0
C D:ARG485 3.2 22.3 1.0
C2 D:UD15005 3.3 18.1 1.0
C D:SER484 3.5 21.9 1.0
C D:THR487 3.5 20.1 1.0
CA D:ARG485 3.7 24.0 1.0
N3 D:UD15005 3.8 18.8 1.0
OG1 D:THR487 3.8 20.1 1.0
N D:THR487 4.0 20.0 1.0
N D:ARG485 4.1 22.8 1.0
N D:GLN486 4.1 22.1 1.0
CA D:THR487 4.2 20.5 1.0
N1 D:UD15005 4.2 20.7 1.0
C D:HIS488 4.3 21.3 1.0
O D:HIS488 4.3 20.8 1.0
O D:HOH5105 4.4 28.1 1.0
C1B D:UD15005 4.4 21.8 1.0
C D:GLN486 4.5 21.3 1.0
N D:HIS488 4.5 19.9 1.0
N D:CYS489 4.6 20.0 1.0
CB D:THR487 4.6 19.7 1.0
CA D:HIS488 4.7 20.3 1.0
CA D:GLN486 4.8 21.1 1.0
CA D:SER484 4.8 21.5 1.0
CA D:CYS489 4.9 20.4 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: Mon Oct 7 03:45:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy