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Sodium in PDB 5gu8: Structure of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshi OT3 (Delta N79) Wild Type

Protein crystallography data

The structure of Structure of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshi OT3 (Delta N79) Wild Type, PDB code: 5gu8 was solved by K.Yamada, N.Kunishima, Y.Matsuura, K.Nakai, H.Naitow, Y.Fukasawa, K.Tomii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.20 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 26.861, 39.954, 59.641, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshi OT3 (Delta N79) Wild Type (pdb code 5gu8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshi OT3 (Delta N79) Wild Type, PDB code: 5gu8:

Sodium binding site 1 out of 1 in 5gu8

Go back to Sodium Binding Sites List in 5gu8
Sodium binding site 1 out of 1 in the Structure of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshi OT3 (Delta N79) Wild Type


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshi OT3 (Delta N79) Wild Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:39.9
occ:1.00
O A:HOH302 2.4 25.6 1.0
O A:HOH337 2.4 23.9 1.0
O A:ALA138 2.5 17.8 1.0
C A:ALA138 3.6 15.5 1.0
O A:HOH376 3.7 33.1 1.0
CB A:ALA138 4.3 17.9 1.0
CA A:ALA138 4.3 9.9 1.0
N A:ALA138 4.3 12.4 1.0
O A:HOH377 4.4 32.4 1.0
OE1 A:GLN143 4.4 11.6 1.0
CG A:GLU137 4.5 18.8 1.0
N A:VAL139 4.6 13.0 1.0
NE2 A:GLN143 4.7 13.0 1.0
CA A:VAL139 4.8 9.2 1.0
OE2 A:GLU137 4.8 23.1 1.0

Reference:

K.D.Yamada, N.Kunishima, Y.Matsuura, K.Nakai, H.Naitow, Y.Fukasawa, K.Tomii. Designing Better Diffracting Crystals of Biotin Carboxyl Carrier Protein From Pyrococcus Horikoshii By A Mutation Based on the Crystal-Packing Propensity of Amino Acids. Acta Crystallogr D Struct V. 73 757 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28876239
DOI: 10.1107/S2059798317010932
Page generated: Tue Dec 15 11:02:03 2020

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