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Magnesium in PDB 1vfz: Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4

Protein crystallography data

The structure of Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4, PDB code: 1vfz was solved by R.Nitta, M.Kikkawa, Y.Okada, N.Hirokawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.36 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.471, 51.805, 156.992, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.9

Other elements in 1vfz:

The structure of Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4 also contains other interesting chemical elements:

Vanadium (V) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4 (pdb code 1vfz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4, PDB code: 1vfz:

Magnesium binding site 1 out of 1 in 1vfz

Go back to Magnesium Binding Sites List in 1vfz
Magnesium binding site 1 out of 1 in the Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the KIF1A Motor Domain Complexed with Adp-Mg-VO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:26.5
occ:1.00
O A:HOH595 2.2 33.5 1.0
O A:HOH596 2.2 17.3 1.0
OG A:SER104 2.2 18.8 1.0
O A:HOH594 2.2 26.9 1.0
O A:HOH502 2.3 20.9 1.0
O3B A:ADP500 2.4 19.0 1.0
CB A:SER104 3.1 8.5 1.0
PB A:ADP500 3.3 16.8 1.0
O3A A:ADP500 3.4 28.0 1.0
O1B A:ADP500 3.5 21.2 1.0
OD2 A:ASP248 3.8 19.8 1.0
N A:SER104 3.9 12.0 1.0
CA A:SER104 4.1 14.9 1.0
O A:HOH619 4.1 42.1 1.0
O2A A:ADP500 4.3 27.9 1.0
O A:SER214 4.3 21.0 1.0
OD1 A:ASP248 4.3 16.2 1.0
O A:HOH506 4.3 12.5 1.0
O1A A:ADP500 4.3 29.9 1.0
O A:HOH597 4.3 28.7 1.0
NH2 A:ARG203 4.4 26.6 1.0
CG A:ASP248 4.5 15.7 1.0
PA A:ADP500 4.6 25.4 1.0
O2B A:ADP500 4.7 32.3 1.0
O A:HOH505 4.8 17.6 1.0
NZ A:LYS103 5.0 11.8 1.0

Reference:

R.Nitta, M.Kikkawa, Y.Okada, N.Hirokawa. KIF1A Alternately Uses Two Loops to Bind Microtubules Science V. 305 678 2004.
ISSN: ISSN 0036-8075
PubMed: 15286375
DOI: 10.1126/SCIENCE.1096621
Page generated: Mon Dec 14 06:54:27 2020

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