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Sodium in PDB 4plh: Crystal Structure of Ancestral Apicomplexan Malate Dehydrogenase with Oxamate.

Protein crystallography data

The structure of Crystal Structure of Ancestral Apicomplexan Malate Dehydrogenase with Oxamate., PDB code: 4plh was solved by J.I.Boucher, J.R.Jacobowitz, B.C.Beckett, S.Classen, D.L.Theobald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.14 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.420, 104.570, 142.460, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ancestral Apicomplexan Malate Dehydrogenase with Oxamate. (pdb code 4plh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Ancestral Apicomplexan Malate Dehydrogenase with Oxamate., PDB code: 4plh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4plh

Go back to Sodium Binding Sites List in 4plh
Sodium binding site 1 out of 2 in the Crystal Structure of Ancestral Apicomplexan Malate Dehydrogenase with Oxamate.


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 Ancestral Apicomplexan Malate Dehydrogenase with Oxamate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:31.1
occ:1.00
OG1 A:THR79 2.7 26.4 1.0
O2N A:NAI403 2.7 25.0 1.0
N A:GLY13 2.9 22.4 1.0
N A:GLY16 2.9 22.3 1.0
CA A:GLY13 3.3 26.9 1.0
O5B A:NAI403 3.4 25.6 1.0
C A:GLY13 3.4 27.5 1.0
CB A:THR79 3.4 25.1 1.0
CA A:GLY16 3.6 24.6 1.0
N A:ILE15 3.6 22.6 1.0
N A:ASN14 3.8 22.6 1.0
C A:GLY11 3.8 28.4 1.0
C5B A:NAI403 3.9 31.1 1.0
O A:GLY13 3.9 25.3 1.0
N A:ALA12 3.9 24.7 1.0
C A:ILE15 3.9 28.4 1.0
C A:ALA12 4.0 25.7 1.0
O A:GLY11 4.0 26.4 1.0
C4B A:NAI403 4.1 24.9 1.0
CA A:ILE15 4.1 26.9 1.0
PN A:NAI403 4.1 28.1 1.0
CB A:ILE15 4.1 25.3 1.0
CG2 A:THR79 4.2 20.8 1.0
CA A:ALA12 4.3 23.8 1.0
C5D A:NAI403 4.4 30.3 1.0
O A:THR79 4.4 25.7 1.0
CA A:GLY11 4.4 24.2 1.0
PA A:NAI403 4.4 27.6 1.0
C A:ASN14 4.5 23.9 1.0
O3 A:NAI403 4.5 33.1 1.0
O1A A:NAI403 4.6 26.2 1.0
C A:THR79 4.7 25.7 1.0
CA A:THR79 4.7 23.7 1.0
O5D A:NAI403 4.7 26.7 1.0
CA A:ASN14 4.8 23.6 1.0
O A:HOH607 4.8 25.6 1.0
C A:GLY16 4.8 25.4 1.0
N A:GLY17 5.0 22.4 1.0

Sodium binding site 2 out of 2 in 4plh

Go back to Sodium Binding Sites List in 4plh
Sodium binding site 2 out of 2 in the Crystal Structure of Ancestral Apicomplexan Malate Dehydrogenase with Oxamate.


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 Ancestral Apicomplexan Malate Dehydrogenase with Oxamate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:33.4
occ:1.00
OG1 D:THR79 2.6 28.0 1.0
O2N D:NAI403 2.8 27.2 1.0
N D:GLY13 2.9 20.6 1.0
N D:GLY16 3.0 25.4 1.0
CA D:GLY13 3.3 21.9 1.0
CB D:THR79 3.4 24.1 1.0
O5B D:NAI403 3.5 27.7 1.0
C D:GLY13 3.5 25.9 1.0
CA D:GLY16 3.6 26.7 1.0
C D:GLY11 3.7 28.6 1.0
N D:ILE15 3.8 22.7 1.0
C5B D:NAI403 3.8 30.3 1.0
N D:ALA12 3.9 27.4 1.0
O D:GLY11 3.9 29.9 1.0
O D:GLY13 3.9 24.4 1.0
C D:ALA12 3.9 26.5 1.0
N D:ASN14 4.0 29.4 1.0
C D:ILE15 4.0 28.2 1.0
C4B D:NAI403 4.0 32.5 1.0
PN D:NAI403 4.1 27.9 1.0
O D:THR79 4.2 28.4 1.0
CA D:GLY11 4.2 29.2 1.0
CB D:ILE15 4.2 23.2 1.0
CA D:ILE15 4.2 22.7 1.0
CG2 D:THR79 4.2 22.9 1.0
CA D:ALA12 4.3 25.5 1.0
C5D D:NAI403 4.3 27.6 1.0
C D:THR79 4.5 28.2 1.0
O3 D:NAI403 4.5 29.1 1.0
CA D:THR79 4.6 25.6 1.0
PA D:NAI403 4.6 30.1 1.0
C D:ASN14 4.7 23.9 1.0
O5D D:NAI403 4.7 28.5 1.0
O D:HOH524 4.8 24.4 1.0
O1A D:NAI403 4.8 28.7 1.0
C D:GLY16 4.9 29.0 1.0
O4B D:NAI403 4.9 28.1 1.0
CA D:ASN14 4.9 26.6 1.0
O D:ALA12 5.0 26.5 1.0

Reference:

J.I.Boucher, J.R.Jacobowitz, B.C.Beckett, S.Classen, D.L.Theobald. An Atomic-Resolution View of Neofunctionalization in the Evolution of Apicomplexan Lactate Dehydrogenases. Elife V. 3 02304 2014.
ISSN: ESSN 2050-084X
PubMed: 24966208
DOI: 10.7554/ELIFE.02304
Page generated: Tue Dec 15 06:58:28 2020

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