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Magnesium in PDB 5zbs: Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant

Protein crystallography data

The structure of Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant, PDB code: 5zbs was solved by J.Q.Ren, S.Wang, W.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.44 / 2.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 107.311, 107.311, 91.599, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant (pdb code 5zbs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant, PDB code: 5zbs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5zbs

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Magnesium binding site 1 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant


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 Kinesin-3 KIF13B Motor Y73C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:38.9
occ:1.00
 O1G B:ANP402 2.0 23.4 0.5
O1B B:ANP402 2.1 31.0 1.0
O B:HOH526 2.1 32.1 1.0
O B:HOH582 2.3 42.9 1.0
OG B:SER110 2.3 36.1 1.0
O B:HOH506 2.4 29.9 1.0
CB B:SER110 3.1 33.1 1.0
PG B:ANP402 3.2 34.0 0.5
PB B:ANP402 3.3 35.0 1.0
N3B B:ANP402 3.6 37.0 1.0
N B:SER110 3.8 27.4 1.0
O B:HOH622 3.9 49.4 1.0
O2G B:ANP402 4.0 27.3 0.5
OD1 B:ASP253 4.0 41.5 1.0
CA B:SER110 4.0 33.0 1.0
O2A B:ANP402 4.1 37.2 1.0
O2B B:ANP402 4.3 30.9 1.0
OD2 B:ASP253 4.3 44.0 1.0
O3G B:ANP402 4.4 44.0 0.5
O3A B:ANP402 4.4 38.7 1.0
O1A B:ANP402 4.6 46.3 1.0
PA B:ANP402 4.7 37.1 1.0
CG B:ASP253 4.7 40.0 1.0
CB B:LYS109 4.8 35.0 1.0
C B:LYS109 4.9 37.5 1.0

Magnesium binding site 2 out of 5 in 5zbs

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Magnesium binding site 2 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:40.8
occ:1.00
 O1G A:ANP401 1.8 31.8 0.5
O A:HOH510 2.1 31.8 1.0
O A:HOH507 2.2 30.0 1.0
O A:HOH546 2.2 43.4 1.0
OG A:SER110 2.3 37.3 1.0
O1B A:ANP401 2.3 28.6 1.0
CB A:SER110 3.1 27.6 1.0
PG A:ANP401 3.2 39.4 0.5
PB A:ANP401 3.5 27.7 1.0
N3B A:ANP401 3.7 31.5 1.0
OD2 A:ASP253 4.0 37.3 1.0
O2A A:ANP401 4.0 38.4 1.0
N A:SER110 4.0 23.6 1.0
O A:HOH597 4.0 48.0 1.0
O2G A:ANP401 4.1 59.9 0.5
CA A:SER110 4.1 28.7 1.0
O3G A:ANP401 4.2 31.9 0.5
O A:HOH572 4.2 69.7 1.0
OD1 A:ASP253 4.5 40.2 1.0
O3A A:ANP401 4.5 27.8 1.0
PA A:ANP401 4.6 38.0 1.0
O2B A:ANP401 4.7 31.2 1.0
CG A:ASP253 4.7 39.2 1.0
O1A A:ANP401 4.7 30.7 1.0
NH1 A:ARG208 4.9 68.2 1.0

Magnesium binding site 3 out of 5 in 5zbs

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Magnesium binding site 3 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:42.3
occ:1.00
 O A:HOH571 2.8 25.2 1.0
O A:GLN76 3.0 29.0 1.0
C A:GLY121 3.3 31.3 1.0
CD A:ARG125 3.3 30.6 1.0
N A:LEU122 3.3 26.4 1.0
NE A:ARG125 3.4 37.4 1.0
CA A:GLY121 3.6 29.4 1.0
O A:GLY121 3.6 32.7 1.0
CA A:LEU122 3.7 31.1 1.0
CB A:PHE80 3.8 34.0 1.0
N A:PHE80 3.8 31.8 1.0
C A:GLN76 3.8 29.5 1.0
CG A:LEU122 3.9 38.4 1.0
CD2 A:LEU122 4.0 32.1 1.0
CA A:GLN76 4.1 21.5 1.0
CA A:PHE80 4.2 40.3 1.0
CB A:GLN76 4.2 29.2 1.0
O A:PRO120 4.2 30.5 1.0
CB A:VAL79 4.3 32.6 1.0
CB A:LEU122 4.4 32.9 1.0
CZ A:ARG125 4.4 36.0 1.0
CG1 A:VAL79 4.4 31.0 1.0
OE1 A:GLN76 4.5 31.6 1.0
CG A:ARG125 4.6 29.3 1.0
C A:VAL79 4.6 35.7 1.0
CD A:GLN76 4.7 27.8 1.0
N A:GLY121 4.7 31.7 1.0
O A:THR112 4.7 29.8 1.0
CD1 A:PHE80 4.7 36.4 1.0
CG A:PHE80 4.7 36.8 1.0
C A:PRO120 4.9 32.4 1.0
CA A:VAL79 5.0 36.9 1.0
N A:ASP77 5.0 29.5 1.0
C A:LEU122 5.0 35.0 1.0

Magnesium binding site 4 out of 5 in 5zbs

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Magnesium binding site 4 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:44.8
occ:1.00
 O1G C:ANP401 1.8 39.0 0.5
O C:HOH506 2.0 37.7 1.0
O C:HOH520 2.0 38.0 1.0
OG C:SER110 2.0 44.7 1.0
O1B C:ANP401 2.3 31.9 1.0
CB C:SER110 3.2 36.4 1.0
PG C:ANP401 3.3 39.9 0.5
PB C:ANP401 3.7 39.6 1.0
N3B C:ANP401 3.9 41.7 1.0
O3G C:ANP401 4.1 54.6 0.5
OD1 C:ASP253 4.1 51.2 1.0
N C:SER110 4.1 32.2 1.0
O2A C:ANP401 4.1 41.6 1.0
CA C:SER110 4.2 34.0 1.0
O2G C:ANP401 4.3 26.8 0.5
OD2 C:ASP253 4.4 48.1 1.0
O3A C:ANP401 4.6 37.2 1.0
CG C:ASP253 4.7 48.3 1.0
O C:HOH509 4.7 63.0 1.0
O2B C:ANP401 4.7 32.9 1.0
PA C:ANP401 4.8 36.7 1.0
O1A C:ANP401 5.0 39.1 1.0

Magnesium binding site 5 out of 5 in 5zbs

Go back to Magnesium Binding Sites List in 5zbs
Magnesium binding site 5 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Kinesin-3 KIF13B Motor Y73C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:81.4
occ:1.00
 O C:ILE276 2.8 58.6 1.0
N C:ASN155 2.8 54.1 1.0
O C:ARG221 3.1 54.5 1.0
O C:HOH555 3.2 54.5 1.0
CA C:TYR154 3.6 53.6 1.0
O C:HOH543 3.6 50.4 1.0
C C:TYR154 3.6 53.6 1.0
CA C:ASN155 3.7 53.8 1.0
C C:ILE276 3.9 61.5 1.0
O C:ILE153 4.1 45.2 1.0
CD1 C:TYR154 4.2 70.2 1.0
C C:ARG221 4.2 60.7 1.0
N C:GLU156 4.4 61.4 1.0
N C:TYR154 4.4 46.9 1.0
CA C:ILE276 4.4 62.3 1.0
NE2 C:HIS223 4.4 45.2 1.0
CD2 C:HIS223 4.4 47.1 1.0
C C:ILE153 4.5 42.5 1.0
CG C:TYR154 4.6 68.2 1.0
C C:ASN155 4.6 60.9 1.0
CB C:TYR154 4.7 60.3 1.0
CA C:SER222 4.7 53.1 1.0
CG2 C:ILE276 4.8 70.5 1.0
CD1 C:ILE276 4.8 66.9 1.0
CE1 C:TYR154 4.8 69.8 1.0
O C:TYR154 4.8 54.0 1.0
O C:ASN275 4.8 63.0 1.0
CB C:ASN155 4.9 61.7 1.0
N C:SER222 4.9 54.1 1.0
N C:ASN277 5.0 61.2 1.0

Reference:

J.Ren, Y.Zhang, S.Wang, L.Huo, J.Lou, W.Feng. Structural Delineation of the Neck Linker of Kinesin-3 For Processive Movement. J. Mol. Biol. V. 430 2030 2018.
ISSN: ESSN 1089-8638
PubMed: 29752968
DOI: 10.1016/J.JMB.2018.05.010
Page generated: Mon Sep 30 11:48:28 2024

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