Atomistry » Nickel » PDB 4z8g-5bnc » 5b7z
Atomistry »
  Nickel »
    PDB 4z8g-5bnc »
      5b7z »

Nickel in PDB 5b7z: Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+

Protein crystallography data

The structure of Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+, PDB code: 5b7z was solved by T.P.Cao, S.M.Shin, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.51 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.225, 55.220, 58.693, 107.16, 102.23, 92.35
R / Rfree (%) 17.2 / 19.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+ (pdb code 5b7z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+, PDB code: 5b7z:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5b7z

Go back to Nickel Binding Sites List in 5b7z
Nickel binding site 1 out of 2 in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni305

b:10.8
occ:1.00
ND1 A:HIS208 2.0 8.7 1.0
OD2 A:ASP182 2.0 11.4 1.0
OE2 A:GLU149 2.0 9.2 1.0
OE2 A:GLU243 2.1 11.0 1.0
O A:HOH429 2.3 15.4 1.0
CE1 A:HIS208 2.9 11.4 1.0
CD A:GLU149 3.0 9.5 1.0
CG A:HIS208 3.0 9.9 1.0
CD A:GLU243 3.0 13.4 1.0
CG A:ASP182 3.1 9.4 1.0
OE1 A:GLU149 3.3 10.5 1.0
OE1 A:GLU243 3.3 14.7 1.0
CB A:HIS208 3.4 10.4 1.0
CB A:ASP182 3.5 9.4 1.0
O A:HOH568 3.9 13.6 1.0
NH2 A:ARG214 4.0 13.5 1.0
NE2 A:HIS208 4.1 10.4 1.0
CD2 A:HIS208 4.1 9.9 1.0
OD1 A:ASP182 4.2 9.9 1.0
O A:HOH554 4.2 12.5 1.0
CD2 A:HIS185 4.3 8.9 1.0
CG A:GLU149 4.3 7.9 1.0
CG A:GLU243 4.4 12.6 1.0
NE2 A:HIS185 4.6 10.6 1.0
CB A:GLU243 4.7 9.7 1.0
CA A:ASP182 4.8 9.4 1.0
O A:HOH658 4.9 30.4 1.0
CA A:HIS208 4.9 9.6 1.0

Nickel binding site 2 out of 2 in 5b7z

Go back to Nickel Binding Sites List in 5b7z
Nickel binding site 2 out of 2 in the Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Hyperthermophilic Thermotoga Maritima L-Ketose-3- Epimerase with NI2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:12.3
occ:1.00
OD2 B:ASP182 2.0 11.8 1.0
OE2 B:GLU149 2.0 11.4 1.0
ND1 B:HIS208 2.0 10.6 1.0
OE2 B:GLU243 2.1 13.2 1.0
O B:HOH418 2.3 16.4 1.0
CD B:GLU149 3.0 11.1 1.0
CD B:GLU243 3.0 14.2 1.0
CE1 B:HIS208 3.0 12.7 1.0
CG B:HIS208 3.0 9.7 1.0
CG B:ASP182 3.1 10.9 1.0
OE1 B:GLU149 3.3 10.7 1.0
OE1 B:GLU243 3.3 14.7 1.0
CB B:HIS208 3.4 10.7 1.0
CB B:ASP182 3.5 9.6 1.0
O B:HOH536 3.9 14.2 1.0
NH2 B:ARG214 4.0 14.0 1.0
NE2 B:HIS208 4.1 11.7 1.0
CD2 B:HIS208 4.2 11.7 1.0
OD1 B:ASP182 4.2 11.3 1.0
O B:HOH561 4.2 14.0 1.0
CG B:GLU149 4.3 9.1 1.0
CD2 B:HIS185 4.3 10.3 1.0
CG B:GLU243 4.3 12.4 1.0
NE2 B:HIS185 4.5 10.6 1.0
CB B:GLU243 4.6 12.1 1.0
CA B:ASP182 4.8 10.3 1.0
CA B:HIS208 4.9 11.7 1.0

Reference:

S.M.Shin, T.P.Cao, J.M.Choi, S.B.Kim, S.J.Lee, S.H.Lee, D.W.Lee. TM0416, A Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5AND C6EPIMERIZATION Reactions Appl. Environ. Microbiol. V. 83 2017.
ISSN: ESSN 1098-5336
PubMed: 28258150
DOI: 10.1128/AEM.03291-16
Page generated: Thu Oct 10 06:14:57 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy