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Nickel in PDB 4ybn: Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis

Protein crystallography data

The structure of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis, PDB code: 4ybn was solved by F.H.Ahmed, P.D.Carr, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.73 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.722, 59.876, 89.658, 90.00, 93.83, 90.00
R / Rfree (%) 17.4 / 22.3

Other elements in 4ybn:

The structure of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis (pdb code 4ybn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis, PDB code: 4ybn:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4ybn

Go back to Nickel Binding Sites List in 4ybn
Nickel binding site 1 out of 2 in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:26.4
occ:0.20
OD2 A:ASP125 1.9 42.4 1.0
O2 A:SO4302 2.6 64.7 1.0
CG A:ASP125 2.9 37.1 1.0
CB A:ASP125 3.4 27.6 1.0
O A:ARG121 3.7 25.0 1.0
S A:SO4302 3.8 66.7 1.0
CA A:GLY122 3.8 21.6 1.0
OD1 A:ASP125 3.8 39.8 1.0
O3 A:SO4302 4.0 74.0 1.0
C A:ARG121 4.1 24.9 1.0
CG A:ARG121 4.1 27.0 1.0
N A:GLY122 4.2 21.9 1.0
O4 A:SO4302 4.4 65.6 1.0
O A:HOH426 4.5 25.2 1.0
CD A:ARG121 4.6 31.7 1.0
O A:GLY122 4.7 25.5 1.0
C A:GLY122 4.7 24.5 1.0
CA A:ASP125 4.8 27.4 1.0
O1 A:SO4302 5.0 65.5 1.0
CB A:ARG121 5.0 26.1 1.0

Nickel binding site 2 out of 2 in 4ybn

Go back to Nickel Binding Sites List in 4ybn
Nickel binding site 2 out of 2 in the Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Fad and Heme Binding Protein MSMEG_4975 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni303

b:37.2
occ:0.25
OD2 B:ASP125 2.2 39.6 1.0
O3 B:SO4304 3.0 65.5 1.0
CG B:ASP125 3.2 39.2 1.0
O1 B:SO4304 3.3 64.7 1.0
S B:SO4304 3.4 56.3 1.0
O2 B:SO4304 3.5 72.0 1.0
CB B:ASP125 3.6 30.8 1.0
O B:ARG121 3.7 25.3 1.0
CA B:GLY122 3.8 24.2 1.0
CG B:ARG121 4.0 30.4 1.0
C B:ARG121 4.1 23.2 1.0
N B:GLY122 4.2 21.0 1.0
OD1 B:ASP125 4.3 42.7 1.0
CD B:ARG121 4.6 32.4 1.0
O B:GLY122 4.8 25.9 1.0
C B:GLY122 4.8 24.2 1.0
O B:HOH469 4.8 30.6 1.0
O4 B:SO4304 4.9 61.1 1.0
CB B:ARG121 4.9 26.4 1.0

Reference:

F.H.Ahmed, P.D.Carr, B.M.Lee, L.Afriat-Jurnou, A.E.Mohamed, N.S.Hong, J.Flanagan, M.C.Taylor, C.Greening, C.J.Jackson. Sequence-Structure-Function Classification of A Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. J.Mol.Biol. V. 427 3554 2015.
ISSN: ESSN 1089-8638
PubMed: 26434506
DOI: 10.1016/J.JMB.2015.09.021
Page generated: Wed Dec 16 01:38:15 2020

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